From mad at biol.unlp.edu.ar Fri Feb 8 03:58:19 2002 From: mad at biol.unlp.edu.ar (Martin Sarachu ) Date: Fri, 08 Feb 2002 11:58:19 +0300 Subject: problems building EMNU Message-ID: <3C63932B.40BE5C1A@biol.unlp.edu.ar> Hi, I get this when building EMNU Undefined first referenced symbol in file initscr32 emnu.o (symbol belongs to implicit dependency /usr/lib/libcurses.so.1) box32 emnu.o (symbol belongs to implicit dependency /usr/lib/libcurses.so.1) w32attron emnu.o (symbol belongs to implicit dependency /usr/lib/libcurses.so.1) w32attroff emnu.o (symbol belongs to implicit dependency /usr/lib/libcurses.so.1) getcurx emnu.o (symbol belongs to implicit dependency /usr/lib/libcurses.so.1) getcury emnu.o (symbol belongs to implicit dependency /usr/lib/libcurses.so.1) acs32map emnu.o (symbol belongs to implicit dependency /usr/lib/libcurses.so.1) getbegx emnu.o (symbol belongs to implicit dependency /usr/lib/libcurses.so.1) getbegy emnu.o (symbol belongs to implicit dependency /usr/lib/libcurses.so.1) ld: fatal: Symbol referencing errors. No output written to .libs/emnu ncurses v5.2 are installed and EMBOSS programs compiled ok. any idea? Thanks, -- Martin Sarachu ICQ: 123797358 EMBnet Argentina: http://www.ar.embnet.org From cquijano at iib.uam.es Tue Feb 12 09:26:02 2002 From: cquijano at iib.uam.es (Carlos Quijano) Date: Tue, 12 Feb 2002 15:26:02 +0100 Subject: [EMBOSS] Segmentation fault RH5.2 + EMBOSS2.0.1 Message-ID: <3C6925FA.7010508@iib.uam.es> I have installed Emboss 2.0.1 with a PentiumIII, kernel 2.2.7 after installing, wossname -auto, and some others apps works well but showing "Segmentation fault" as last message. Does somebody out there fixed it or seen it before me? Tanks you all. From ableasby at hgmp.mrc.ac.uk Tue Feb 12 09:55:45 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 12 Feb 2002 14:55:45 GMT Subject: [EMBOSS] Segmentation fault RH5.2 + EMBOSS2.0.1 Message-ID: <200202121455.OAA09657@bromine.hgmp.mrc.ac.uk> File handling was changed a while ago (as I remember) and I can believe that combination of EMBOSS and operating system would fail. You're best upgrading to EMBOSS 2.2.0 and RH7.2. Cheers Alan From peter.rice at uk.lionbioscience.com Tue Feb 12 11:59:10 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 12 Feb 2002 16:59:10 +0000 Subject: Blast format change at NCBI Message-ID: <3C6949DE.A50485B2@uk.lionbioscience.com> NCBI's FTP server will be releasing BLAST formatted databases in a new format (version 4) from February 19th. This format is not supported by EMBOSS dbiblast indexing (or by NCBI's blastall before the current version 2.2.2) See ftp://ftp.ncbi.nih.gov/blast/db/NewFormattedDatabases/README If you have the fasta format files, you should be able to use dbifasta to index the same entries. The blast 2.2.2 release notes say "Fastacmd will dump out an entire BLAST database in FASTA format if the new -D option is used", but I have not tried this yet to see how well it fits with EMBOSS. Has anyone else looked into this yet? -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From mathog at mendel.bio.caltech.edu Tue Feb 12 12:42:30 2002 From: mathog at mendel.bio.caltech.edu (David Mathog) Date: Tue, 12 Feb 2002 09:42:30 -0800 Subject: Blast format change at NCBI Message-ID: > NCBI's FTP server will be releasing BLAST formatted databases in a new > format (version 4) from February 19th. > > This format is not supported by EMBOSS dbiblast indexing (or by NCBI's > blastall before the current version 2.2.2) > > See ftp://ftp.ncbi.nih.gov/blast/db/NewFormattedDatabases/README > > If you have the fasta format files, you should be able to use dbifasta to > index the same entries. > > The blast 2.2.2 release notes say "Fastacmd will dump out an entire BLAST > database in FASTA format if the new -D option is used", but I have not > tried this yet to see how well it fits with EMBOSS. > > Has anyone else looked into this yet? Sorry, no. I imagine that it will break GCG's BLAST implementation as well though. I have used fastacmd (which is undocumented, of course) in the past with success but obviously not with -D. Usage was: fastacmd -d nt -s "" This snippet of code (from an older NCBI version) is the only documentation I've found for the fastacmd command line options: static Args myargs [NUMARG] = { { "Database", NULL, NULL, NULL, TRUE, 'd', ARG_STRING, 0.0, 0, NULL}, { "Search string: GIs, accessions and locuses may be used delimited\n" " by comma or space)", NULL, NULL, NULL, TRUE, 's', ARG_STRING, 0.0, 0, NULL}, { "Input file wilth GIs/accessions/locuses for batch retrieval", NULL, NULL, NULL, TRUE, 'i', ARG_STRING, 0.0, 0, NULL}, { "Retrieve duplicated accessions", "F", NULL, NULL, TRUE, 'a', ARG_BOOLEAN, 0.0, 0, NULL}, { "Line length for sequence", "80", NULL, NULL, TRUE, 'l', ARG_INT, 0.0, 0, NULL} } A more pressing problem for us regarding BLAST is that nr (entire) and nt_lcl (fragments of 1/9th nt) both just grew beyond the point where the data can fit along with blast and linux in the 512 Mb on each of our 9 DS10 nodes. Consequently local BLAST runs on these databases now crawl since all data must be read from disk for each run. The NCBI must have something like 10Gb in their main server these days to keep both nr and nt (and whatever else) in memory. I'd _kill_ for MPI or PVM BLAST, but it seems like the NCBI is not going to see the need to write that until they reach the memory limit on their huge server. I'd add it myself but a horrible experience tracking down the gi list memory leak bug in one version of BLAST taught me once and for all that their code structure is so complex that the task would be extraordinarily difficult. Others must have come to the same conclusion since nobody else has done it either. Regards, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From jrvalverde at cnb.uam.es Wed Feb 13 05:59:01 2002 From: jrvalverde at cnb.uam.es (jrvalverde at cnb.uam.es) Date: Wed, 13 Feb 2002 11:59:01 +0100 (MET) Subject: Blast format change at NCBI In-Reply-To: Message-ID: <200202131059.g1DAx2W696962@embnet.cnb.uam.es> "David Mathog" wrote: > nr and nt (and whatever else) in memory. I'd _kill_ for MPI or PVM > BLAST, but it seems > like the NCBI is not going to see the need to write that until they > reach the memory limit > on their huge server. I'd add it myself but a horrible experience You don't want that. It would crawl even more having to access data over the net. What you want is to create partial databases that fit in memory, and a script that sends the same query against each of the database sections, collects the results and colates them, selecting the highest scores. I don't have such a script (having only one machine to run things), but understand that others have done it already. j From duhaimj at ircm.qc.ca Wed Feb 13 10:09:05 2002 From: duhaimj at ircm.qc.ca (Johanne Duhaime) Date: Wed, 13 Feb 2002 10:09:05 -0500 Subject: Problem with png driver for emboss Message-ID: <3C6A8191.F991A2D8@ircm.qc.ca> Hi I have problem installing the PNG stuff in order to use graphics in EMBOSS. I have tried to build gd on solaris 2.6 and could not succeed. There is a message about : gdImageCreateFromPng. Would you mind to help? I had spent several hours on compiling Png stuff. I would appreciate very much your help. Following is the error message, the include and library and finally the makefile. Thank in advance. mercure{root}48: make gcc -I. -I/usr/include/freetype2 -I/usr/include/X11 -I/usr/X11R6/include/X11 -I/usr/local/include -I/opt/sasircm/drivers/drivers/include pngtogd.o -o pngtogd -L. -L/usr/local/lib -L/usr/lib/X11 -L/usr/X11R6/lib -L/opt/sasircm/drivers/drivers/lib -L/usr/ucblib -lgd -lpng -lz -lm Undefined first referenced symbol in file gdImageCreateFromPng pngtogd.o ld: fatal: Symbol referencing errors. No output written to pngtogd *** Error code 1 make: Fatal error: Command failed for target `pngtogd' Librairies and include: total 466 drwxrwxrwx 2 sasircm sequence 512 Feb 8 15:10 ./ drwxrwxrwx 4 sasircm sequence 512 Feb 8 14:54 ../ -rw-r--r-- 1 sasircm sequence 133396 Feb 11 16:32 png.h -rw-r--r-- 1 sasircm sequence 39838 Feb 11 16:32 pngconf.h -rw-r--r-- 1 sasircm sequence 7810 Feb 8 14:54 zconf.h -rw-r--r-- 1 sasircm sequence 40898 Feb 8 14:54 zlib.h mercure{root}50: l /opt/sasircm/drivers/drivers/lib total 1058 drwxrwxrwx 2 sasircm sequence 512 Feb 11 16:32 ./ drwxrwxrwx 4 sasircm sequence 512 Feb 8 14:54 ../ -rw-rw-rw- 1 sasircm sequence 205316 Feb 11 16:32 libpng.a lrwxrwxrwx 1 root other 11 Feb 11 16:32 libpng.so -> libpng.so.3* lrwxrwxrwx 1 root other 17 Feb 11 16:32 libpng.so.3 -> libpng.so.3.1.2.1* -rwxr-xr-x 1 sasircm sequence 229816 Feb 11 16:32 libpng.so.3.1.2.1* -rwxr-xr-x 1 sasircm sequence 70488 Feb 8 14:54 libz.a* mercure{root}51: Makefile mercure{root}59: more Makefile #Depending on your system, you will need to modify this makefile. #If you do not have gcc, change the setting for COMPILER, but you must #use an ANSI standard C compiler (NOT the old SunOS 4.1.3 cc #compiler; get gcc if you are still using it). COMPILER=gcc #If the ar command fails on your system, consult the ar manpage #for your system. AR=ar #If you don't have FreeType, libjpeg and/or Xpm installed, including the #header files, uncomment this (default). You really must install #libpng and zlib to get anywhere if you wish to create PNG images. #Mis la ligne suivante en commentaire #CFLAGS=-O -DHAVE_LIBPNG -DHAVE_LIBJPEG #If you do have FreeType, libjpeg and/or Xpm fully installed, uncomment a #variation of this and comment out the line above. See also LIBS below. #CFLAGS=-O -DHAVE_LIBXPM -DHAVE_LIBPNG -DHAVE_LIBJPEG \ # -DHAVE_LIBFREETYPE -DHAVE_LIBTTF #To use the old FreeType 1.x library, add this additional #define #to the line above #-DHAVE_LIBTTF #If you don't have FreeType Xpm fully installed, uncomment this #(default). #PLEASE NOTE: YOU MAY HAVE TO JUGGLE THE ORDER OF THE LIBRARIES. #Some systems are very picky about link order. They don't all agree #on the right order, either. LIBS=-lgd -lpng -lz -lm #If you do have FreeType, JPEG and/or Xpm fully installed, uncomment a #variation of this and comment out the line above. Note that #Xpm requires X11. See also CFLAGS above. #LIBS=-lgd -lpng -lz -ljpeg -lfreetype -lm -lttf #Note: for Freetype 1.x, use DHAVE_LIBTTF and -lttf instead. #Typical install locations for freetype, zlib, xpm, libjpeg and libpng header #files. If yours are somewhere else, change this. -I. is important to #ensure that the version of gd you are installing is used, and not an #older release in your directory tree somewhere. INCLUDEDIRS=-I. -I/usr/include/freetype2 -I/usr/include/X11 -I/usr/X11R6/include/X11 -I/usr/local/include -I/opt/sasircm/drivers/dri vers/include #Typical install locations for freetype, zlib, xpm and libpng libraries. #If yours are somewhere else, other than a standard location #such as /lib or /usr/lib, then change this. Be sure to keep #-L. as this allows the gd library itself to be found. #Put -L. first so that old versions of the gd library elsewhere #on your system can't cause conflicts while building a new one. #This line shouldn't hurt if you don't actually have some of the #optional libraries and directories. #LIBDIRS=-L. -L/usr/local/lib -L/usr/lib/X11 -L/usr/X11R6/lib -L/opt/sasircm/drivers/drivers/lib -L/opt/sasircm/drivers/libpng LIBDIRS=-L. -L/usr/local/lib -L/usr/lib/X11 -L/usr/X11R6/lib -L/opt/sasircm/drivers/drivers/lib -L/usr/ucblib #Location where libgd.a should be installed by "make install". #INSTALL_LIB=/usr/local/lib INSTALL_LIB=/opt/sasircm/drivers/drivers/lib #Location where .h files should be installed by "make install". #INSTALL_INCLUDE=/usr/local/include INSTALL_INCLUDE=/opt/sasircm/drivers/drivers/include #Location where useful non-test programs should be installed by "make install". #INSTALL_BIN=/usr/local/bin INSTALL_BIN=/opt/sasircm/drivers/drivers/bin # # # Changes should not be required below here. # # VERSION=1.8.4 CC=$(COMPILER) $(INCLUDEDIRS) LINK=$(CC) $(LIBDIRS) $(LIBS) PROGRAMS=$(BIN_PROGRAMS) $(TEST_PROGRAMS) BIN_PROGRAMS=pngtogd pngtogd2 gdtopng gd2topng gd2copypal gdparttopng webpng TEST_PROGRAMS=gdtest gddemo gd2time gdtestft gdtestttf all: libgd.a $(PROGRAMS) install: libgd.a $(BIN_PROGRAMS) sh ./install-item 644 libgd.a $(INSTALL_LIB)/libgd.a sh ./install-item 755 pngtogd $(INSTALL_BIN)/pngtogd sh ./install-item 755 pngtogd2 $(INSTALL_BIN)/pngtogd2 sh ./install-item 755 gdtopng $(INSTALL_BIN)/gdtopng sh ./install-item 755 gd2topng $(INSTALL_BIN)/gd2topng sh ./install-item 755 gd2copypal $(INSTALL_BIN)/gd2copypal sh ./install-item 755 gdparttopng $(INSTALL_BIN)/gdparttopng sh ./install-item 755 webpng $(INSTALL_BIN)/webpng sh ./install-item 755 bdftogd $(INSTALL_BIN)/bdftogd sh ./install-item 644 gd.h $(INSTALL_INCLUDE)/gd.h sh ./install-item 644 gdcache.h $(INSTALL_INCLUDE)/gdcache.h sh ./install-item 644 gd_io.h $(INSTALL_INCLUDE)/gd_io.h sh ./install-item 644 gdfontg.h $(INSTALL_INCLUDE)/gdfontg.h sh ./install-item 644 gdfontl.h $(INSTALL_INCLUDE)/gdfontl.h sh ./install-item 644 gdfontmb.h $(INSTALL_INCLUDE)/gdfontmb.h sh ./install-item 644 gdfonts.h $(INSTALL_INCLUDE)/gdfonts.h sh ./install-item 644 gdfontt.h $(INSTALL_INCLUDE)/gdfontt.h gddemo: gddemo.o libgd.a $(CC) gddemo.o -o gddemo $(LIBDIRS) $(LIBS) pngtogd: pngtogd.o libgd.a $(CC) pngtogd.o -o pngtogd $(LIBDIRS) $(LIBS) webpng: webpng.o libgd.a $(CC) webpng.o -o webpng $(LIBDIRS) $(LIBS) pngtogd2: pngtogd2.o libgd.a $(CC) pngtogd2.o -o pngtogd2 $(LIBDIRS) $(LIBS) gdtopng: gdtopng.o libgd.a $(CC) gdtopng.o -o gdtopng $(LIBDIRS) $(LIBS) gd2topng: gd2topng.o libgd.a $(CC) gd2topng.o -o gd2topng $(LIBDIRS) $(LIBS) gd2copypal: gd2copypal.o libgd.a $(CC) gd2copypal.o -o gd2copypal $(LIBDIRS) $(LIBS) gdparttopng: gdparttopng.o libgd.a $(CC) gdparttopng.o -o gdparttopng $(LIBDIRS) $(LIBS) gdtest: gdtest.o libgd.a $(CC) gdtest.o -o gdtest $(LIBDIRS) $(LIBS) gd2time: gd2time.o libgd.a $(CC) gd2time.o -o gd2time $(LIBDIRS) $(LIBS) gdtestft: gdtestft.o libgd.a $(CC) --verbose gdtestft.o -o gdtestft $(LIBDIRS) $(LIBS) gdtestttf: gdtestttf.o libgd.a $(CC) --verbose gdtestttf.o -o gdtestttf $(LIBDIRS) $(LIBS) libgd.a: gd.o gd_gd.o gd_gd2.o gd_io.o gd_io_dp.o gd_io_file.o gd_ss.o \ gd_io_ss.o gd_png.o gdxpm.o gdfontt.o gdfonts.o gdfontmb.o gdfontl.o \ gdfontg.o gdtables.o gdft.o gdttf.o gdcache.o gdkanji.o wbmp.o \ gd_wbmp.o gdhelpers.o gd.h gdfontt.h gdfonts.h gdfontmb.h gdfontl.h \ gdfontg.h gdhelpers.h rm -f libgd.a $(AR) rc libgd.a gd.o gd_gd.o gd_gd2.o gd_io.o gd_io_dp.o \ gd_io_file.o gd_ss.o gd_io_ss.o gd_png.o gdxpm.o \ gdfontt.o gdfonts.o gdfontmb.o gdfontl.o gdfontg.o \ gdtables.o gdft.o gdttf.o gdcache.o gdkanji.o wbmp.o \ gd_wbmp.o gdhelpers.o -ranlib libgd.a #libgd.a: gd.o gd_gd.o gd_gd2.o gd_io.o gd_io_dp.o gd_io_file.o gd_ss.o \ # gd_io_ss.o gd_png.o gd_jpeg.o gdxpm.o gdfontt.o gdfonts.o gdfontmb.o gdfontl.o \ # gdfontg.o gdtables.o gdft.o gdttf.o gdcache.o gdkanji.o wbmp.o \ # gd_wbmp.o gdhelpers.o gd.h gdfontt.h gdfonts.h gdfontmb.h gdfontl.h \ # gdfontg.h gdhelpers.h # rm -f libgd.a # $(AR) rc libgd.a gd.o gd_gd.o gd_gd2.o gd_io.o gd_io_dp.o \ # gd_io_file.o gd_ss.o gd_io_ss.o gd_png.o gd_jpeg.o gdxpm.o \ # gdfontt.o gdfonts.o gdfontmb.o gdfontl.o gdfontg.o \ # gdtables.o gdft.o gdttf.o gdcache.o gdkanji.o wbmp.o \ # gd_wbmp.o gdhelpers.o # -ranlib libgd.a clean: rm -f *.o *.a ${PROGRAMS} test/gdtest.jpg test/gdtest.wbmp -- Johanne Duhaime IRCM 110 Ave des Pins O Montreal, Quebec 987-5556 (tel) 987-5644 (fax) Johanne_Duhaime at ircm.qc.ca http://www.ircm.qc.ca From dmartin at bioinformatics.msiwtb.dundee.ac.uk Wed Feb 13 10:28:04 2002 From: dmartin at bioinformatics.msiwtb.dundee.ac.uk (David Martin) Date: Wed, 13 Feb 2002 15:28:04 +0000 (GMT) Subject: Problem with png driver for emboss In-Reply-To: <3C6A8191.F991A2D8@ircm.qc.ca> Message-ID: On Wed, 13 Feb 2002, Johanne Duhaime wrote: > Hi > > I have problem installing the PNG stuff in order to use graphics in > EMBOSS. > > I have tried to build gd on solaris 2.6 and could not succeed. There is > a message about : gdImageCreateFromPng. > Would you mind to help? I had spent several hours on compiling Png > stuff. I would appreciate very much your help. Last time I did anything on Solaris was at ISMB2001, and it worked flawlessly installing the packages from the solaris freeware site. You may need the libPNG and libz installed before compiling GD. ..d > > Following is the error message, the include and library and finally the > makefile. Thank in advance. > > mercure{root}48: make > gcc -I. -I/usr/include/freetype2 -I/usr/include/X11 > -I/usr/X11R6/include/X11 -I/usr/local/include > -I/opt/sasircm/drivers/drivers/include pngtogd.o -o pngtogd -L. > -L/usr/local/lib -L/usr/lib/X11 -L/usr/X11R6/lib > -L/opt/sasircm/drivers/drivers/lib -L/usr/ucblib -lgd -lpng -lz -lm > Undefined first referenced > symbol in file > gdImageCreateFromPng pngtogd.o > ld: fatal: Symbol referencing errors. No output written to pngtogd > *** Error code 1 > make: Fatal error: Command failed for target `pngtogd' > > > > > > Librairies and include: > total 466 > drwxrwxrwx 2 sasircm sequence 512 Feb 8 15:10 ./ > drwxrwxrwx 4 sasircm sequence 512 Feb 8 14:54 ../ > -rw-r--r-- 1 sasircm sequence 133396 Feb 11 16:32 png.h > -rw-r--r-- 1 sasircm sequence 39838 Feb 11 16:32 pngconf.h > -rw-r--r-- 1 sasircm sequence 7810 Feb 8 14:54 zconf.h > -rw-r--r-- 1 sasircm sequence 40898 Feb 8 14:54 zlib.h > mercure{root}50: l /opt/sasircm/drivers/drivers/lib > total 1058 > drwxrwxrwx 2 sasircm sequence 512 Feb 11 16:32 ./ > drwxrwxrwx 4 sasircm sequence 512 Feb 8 14:54 ../ > -rw-rw-rw- 1 sasircm sequence 205316 Feb 11 16:32 libpng.a > lrwxrwxrwx 1 root other 11 Feb 11 16:32 libpng.so -> > libpng.so.3* > lrwxrwxrwx 1 root other 17 Feb 11 16:32 libpng.so.3 -> > libpng.so.3.1.2.1* > -rwxr-xr-x 1 sasircm sequence 229816 Feb 11 16:32 libpng.so.3.1.2.1* > > -rwxr-xr-x 1 sasircm sequence 70488 Feb 8 14:54 libz.a* > mercure{root}51: > > > Makefile > > mercure{root}59: more Makefile > #Depending on your system, you will need to modify this makefile. > > #If you do not have gcc, change the setting for COMPILER, but you must > #use an ANSI standard C compiler (NOT the old SunOS 4.1.3 cc > #compiler; get gcc if you are still using it). > COMPILER=gcc > > #If the ar command fails on your system, consult the ar manpage > #for your system. > AR=ar > > #If you don't have FreeType, libjpeg and/or Xpm installed, including the > > #header files, uncomment this (default). You really must install > #libpng and zlib to get anywhere if you wish to create PNG images. > #Mis la ligne suivante en commentaire > #CFLAGS=-O -DHAVE_LIBPNG -DHAVE_LIBJPEG > > #If you do have FreeType, libjpeg and/or Xpm fully installed, uncomment > a > #variation of this and comment out the line above. See also LIBS below. > #CFLAGS=-O -DHAVE_LIBXPM -DHAVE_LIBPNG -DHAVE_LIBJPEG \ > # -DHAVE_LIBFREETYPE -DHAVE_LIBTTF > > #To use the old FreeType 1.x library, add this additional #define > #to the line above > #-DHAVE_LIBTTF > > #If you don't have FreeType Xpm fully installed, uncomment this > #(default). > > #PLEASE NOTE: YOU MAY HAVE TO JUGGLE THE ORDER OF THE LIBRARIES. > #Some systems are very picky about link order. They don't all agree > #on the right order, either. > > LIBS=-lgd -lpng -lz -lm > > #If you do have FreeType, JPEG and/or Xpm fully installed, uncomment a > #variation of this and comment out the line above. Note that > #Xpm requires X11. See also CFLAGS above. > > #LIBS=-lgd -lpng -lz -ljpeg -lfreetype -lm -lttf > > #Note: for Freetype 1.x, use DHAVE_LIBTTF and -lttf instead. > > #Typical install locations for freetype, zlib, xpm, libjpeg and libpng > header > #files. If yours are somewhere else, change this. -I. is important to > #ensure that the version of gd you are installing is used, and not an > #older release in your directory tree somewhere. > > INCLUDEDIRS=-I. -I/usr/include/freetype2 -I/usr/include/X11 > -I/usr/X11R6/include/X11 -I/usr/local/include -I/opt/sasircm/drivers/dri > > vers/include > > #Typical install locations for freetype, zlib, xpm and libpng libraries. > > #If yours are somewhere else, other than a standard location > #such as /lib or /usr/lib, then change this. Be sure to keep > #-L. as this allows the gd library itself to be found. > #Put -L. first so that old versions of the gd library elsewhere > #on your system can't cause conflicts while building a new one. > #This line shouldn't hurt if you don't actually have some of the > #optional libraries and directories. > > #LIBDIRS=-L. -L/usr/local/lib -L/usr/lib/X11 -L/usr/X11R6/lib > -L/opt/sasircm/drivers/drivers/lib -L/opt/sasircm/drivers/libpng > LIBDIRS=-L. -L/usr/local/lib -L/usr/lib/X11 -L/usr/X11R6/lib > -L/opt/sasircm/drivers/drivers/lib -L/usr/ucblib > #Location where libgd.a should be installed by "make install". > #INSTALL_LIB=/usr/local/lib > INSTALL_LIB=/opt/sasircm/drivers/drivers/lib > > #Location where .h files should be installed by "make install". > #INSTALL_INCLUDE=/usr/local/include > INSTALL_INCLUDE=/opt/sasircm/drivers/drivers/include > > #Location where useful non-test programs should be installed by "make > install". > #INSTALL_BIN=/usr/local/bin > INSTALL_BIN=/opt/sasircm/drivers/drivers/bin > > # > # > # Changes should not be required below here. > # > # > > VERSION=1.8.4 > > CC=$(COMPILER) $(INCLUDEDIRS) > LINK=$(CC) $(LIBDIRS) $(LIBS) > > PROGRAMS=$(BIN_PROGRAMS) $(TEST_PROGRAMS) > > BIN_PROGRAMS=pngtogd pngtogd2 gdtopng gd2topng gd2copypal gdparttopng > webpng > TEST_PROGRAMS=gdtest gddemo gd2time gdtestft gdtestttf > > all: libgd.a $(PROGRAMS) > > install: libgd.a $(BIN_PROGRAMS) > sh ./install-item 644 libgd.a $(INSTALL_LIB)/libgd.a > sh ./install-item 755 pngtogd $(INSTALL_BIN)/pngtogd > sh ./install-item 755 pngtogd2 $(INSTALL_BIN)/pngtogd2 > sh ./install-item 755 gdtopng $(INSTALL_BIN)/gdtopng > sh ./install-item 755 gd2topng $(INSTALL_BIN)/gd2topng > sh ./install-item 755 gd2copypal $(INSTALL_BIN)/gd2copypal > sh ./install-item 755 gdparttopng $(INSTALL_BIN)/gdparttopng > sh ./install-item 755 webpng $(INSTALL_BIN)/webpng > sh ./install-item 755 bdftogd $(INSTALL_BIN)/bdftogd > sh ./install-item 644 gd.h $(INSTALL_INCLUDE)/gd.h > sh ./install-item 644 gdcache.h $(INSTALL_INCLUDE)/gdcache.h > sh ./install-item 644 gd_io.h $(INSTALL_INCLUDE)/gd_io.h > sh ./install-item 644 gdfontg.h $(INSTALL_INCLUDE)/gdfontg.h > sh ./install-item 644 gdfontl.h $(INSTALL_INCLUDE)/gdfontl.h > sh ./install-item 644 gdfontmb.h $(INSTALL_INCLUDE)/gdfontmb.h > sh ./install-item 644 gdfonts.h $(INSTALL_INCLUDE)/gdfonts.h > sh ./install-item 644 gdfontt.h $(INSTALL_INCLUDE)/gdfontt.h > > gddemo: gddemo.o libgd.a > $(CC) gddemo.o -o gddemo $(LIBDIRS) $(LIBS) > > pngtogd: pngtogd.o libgd.a > $(CC) pngtogd.o -o pngtogd $(LIBDIRS) $(LIBS) > > webpng: webpng.o libgd.a > $(CC) webpng.o -o webpng $(LIBDIRS) $(LIBS) > > pngtogd2: pngtogd2.o libgd.a > $(CC) pngtogd2.o -o pngtogd2 $(LIBDIRS) $(LIBS) > > gdtopng: gdtopng.o libgd.a > $(CC) gdtopng.o -o gdtopng $(LIBDIRS) $(LIBS) > > gd2topng: gd2topng.o libgd.a > $(CC) gd2topng.o -o gd2topng $(LIBDIRS) $(LIBS) > > gd2copypal: gd2copypal.o libgd.a > $(CC) gd2copypal.o -o gd2copypal $(LIBDIRS) $(LIBS) > > gdparttopng: gdparttopng.o libgd.a > $(CC) gdparttopng.o -o gdparttopng $(LIBDIRS) $(LIBS) > > gdtest: gdtest.o libgd.a > $(CC) gdtest.o -o gdtest $(LIBDIRS) $(LIBS) > > gd2time: gd2time.o libgd.a > $(CC) gd2time.o -o gd2time $(LIBDIRS) $(LIBS) > > gdtestft: gdtestft.o libgd.a > $(CC) --verbose gdtestft.o -o gdtestft $(LIBDIRS) $(LIBS) > gdtestttf: gdtestttf.o libgd.a > $(CC) --verbose gdtestttf.o -o gdtestttf $(LIBDIRS) $(LIBS) > > libgd.a: gd.o gd_gd.o gd_gd2.o gd_io.o gd_io_dp.o gd_io_file.o gd_ss.o \ > > gd_io_ss.o gd_png.o gdxpm.o gdfontt.o gdfonts.o gdfontmb.o > gdfontl.o \ > gdfontg.o gdtables.o gdft.o gdttf.o gdcache.o gdkanji.o wbmp.o \ > > gd_wbmp.o gdhelpers.o gd.h gdfontt.h gdfonts.h gdfontmb.h > gdfontl.h \ > gdfontg.h gdhelpers.h > rm -f libgd.a > $(AR) rc libgd.a gd.o gd_gd.o gd_gd2.o gd_io.o gd_io_dp.o \ > gd_io_file.o gd_ss.o gd_io_ss.o gd_png.o gdxpm.o \ > gdfontt.o gdfonts.o gdfontmb.o gdfontl.o gdfontg.o \ > gdtables.o gdft.o gdttf.o gdcache.o gdkanji.o wbmp.o \ > gd_wbmp.o gdhelpers.o > -ranlib libgd.a > > #libgd.a: gd.o gd_gd.o gd_gd2.o gd_io.o gd_io_dp.o gd_io_file.o gd_ss.o > \ > # gd_io_ss.o gd_png.o gd_jpeg.o gdxpm.o gdfontt.o gdfonts.o > gdfontmb.o gdfontl.o \ > # gdfontg.o gdtables.o gdft.o gdttf.o gdcache.o gdkanji.o wbmp.o \ > > # gd_wbmp.o gdhelpers.o gd.h gdfontt.h gdfonts.h gdfontmb.h > gdfontl.h \ > # gdfontg.h gdhelpers.h > # rm -f libgd.a > # $(AR) rc libgd.a gd.o gd_gd.o gd_gd2.o gd_io.o gd_io_dp.o \ > # gd_io_file.o gd_ss.o gd_io_ss.o gd_png.o gd_jpeg.o > gdxpm.o \ > # gdfontt.o gdfonts.o gdfontmb.o gdfontl.o gdfontg.o \ > # gdtables.o gdft.o gdttf.o gdcache.o gdkanji.o wbmp.o \ > # gd_wbmp.o gdhelpers.o > # -ranlib libgd.a > clean: > rm -f *.o *.a ${PROGRAMS} test/gdtest.jpg test/gdtest.wbmp > > > > > -- > Johanne Duhaime > IRCM > 110 Ave des Pins O > Montreal, Quebec > 987-5556 (tel) 987-5644 (fax) > Johanne_Duhaime at ircm.qc.ca > http://www.ircm.qc.ca > > ---------------------------------- David Martin PhD Bioinformatics Scientific Officer Wellcome Trust Biocentre, Dundee ---------------------------------- From David.Bauer at SCHERING.DE Wed Feb 13 12:02:50 2002 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Wed, 13 Feb 2002 18:02:50 +0100 Subject: Antwort: Problem with png driver for emboss Message-ID: Hi, I just had a similar problem with having the png and gd libs in a non standard location on a Solaris system. Did you try to give configure the png lib location? I think in your case this should be: --with-pngdriver=/opt/sasircm/drivers/drivers Also if you look at the output from configure do you see any problem messages about the gdImageCreateFromPng? I hope this helps, David. From jgomez at rz.uni-potsdam.de Thu Feb 14 08:02:09 2002 From: jgomez at rz.uni-potsdam.de (Judit Lucia Gomez) Date: Thu, 14 Feb 2002 14:02:09 +0100 Subject: Databases Message-ID: <3C6BB551.4070107@rz.uni-potsdam.de> I installed EMBOSS on my computer, and when I typed _%showdb_ no one db was displayed, I would like to know if I must install also the databases, or if is any chance to run EMBOSS programs making a link with the databases. Regards Judith Gomez ========================== Judith Lucia Gomez Doktorandin Universit?t Potsdam Institut f?r Biochemie und Biologie AG M?ller-R?ber Arbeitsgruppe Molekularbiologie Karl-liebknecht-Str. 24/25 Haus 20, 1.O4 14476 Golm Germany From David.Bauer at SCHERING.DE Thu Feb 14 08:57:23 2002 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Thu, 14 Feb 2002 14:57:23 +0100 Subject: Antwort: Databases Message-ID: Hi Judit, you need the databases if you want to get sequences directly from there. In /usr/local/share/EMBOSS you find a emboss.default.template. This must be copied to emboss.default and include definitions for databases you have installed locally. There is a nice administration guide from David Martin at http://www.uk.embnet.org/Software/EMBOSS/Doc/Admin_guide/admin.pdf which has an extensive chapter on how to handle databases with emboss. David. |--------+---------------------------> | | Judit Lucia Gomez| | | | | | Gesendet von: | | | owner-emboss at hgmp| | | .mrc.ac.uk | | | | | | | | | 14.02.02 14:02 | | | | |--------+---------------------------> >-----------------------------------------------------------------------| | | | | | | |An: emboss at embnet.org | |Kopie: | |Thema: Databases | >-----------------------------------------------------------------------| I installed EMBOSS on my computer, and when I typed _%showdb_ no one db was displayed, I would like to know if I must install also the databases, or if is any chance to run EMBOSS programs making a link with the databases. Regards Judith Gomez ========================== Judith Lucia Gomez Doktorandin Universit?t Potsdam Institut f?r Biochemie und Biologie AG M?ller-R?ber Arbeitsgruppe Molekularbiologie Karl-liebknecht-Str. 24/25 Haus 20, 1.O4 14476 Golm Germany From mad at biol.unlp.edu.ar Thu Feb 14 08:22:53 2002 From: mad at biol.unlp.edu.ar (Martin Sarachu) Date: Thu, 14 Feb 2002 16:22:53 +0300 Subject: png trouble Message-ID: <3C6BBA2D.EBA334EB@biol.unlp.edu.ar> Hi, I'm using libpng 1.2.0 which was installed as a package from sunfreeware, EMBOSS-2.2.0 on a Sun/Solaris 8 EMBOSS compiled fine but when I exec an application and choose png as the output I get libpng warning: Application was compiled with png.h from libpng-1.0.6 libpng warning: Application is running with png.c from libpng-1.2.0 gd-png: fatal libpng error: Incompatible libpng version in application and library Segmentation Fault (core dumped) Thanks, martin. -- Martin Sarachu ICQ: 123797358 EMBnet Argentina: http://www.ar.embnet.org From ableasby at hgmp.mrc.ac.uk Thu Feb 14 14:49:43 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Thu, 14 Feb 2002 19:49:43 GMT Subject: png trouble Message-ID: <200202141949.TAA17294@bromine.hgmp.mrc.ac.uk> If you have libpng, libz or libgd in /usr/lib then EMBOSS will use it (them) and use only use the --with-pngdriver=dir specification to find any remaining libraries. You can either make sure that any such libraries in /usr/lib are up-to-date or temporarily rename them and use --with-pngdriver=dir to point to an appropriate location where you've compiled them. Similar considerations apply to /usr/local/lib in the case of png support (not quite the same but similar). HTH Alan From mad at biol.unlp.edu.ar Thu Feb 14 10:05:51 2002 From: mad at biol.unlp.edu.ar (Martin Sarachu) Date: Thu, 14 Feb 2002 18:05:51 +0300 Subject: png trouble References: <200202141949.TAA17294@bromine.hgmp.mrc.ac.uk> Message-ID: <3C6BD24F.F548AECD@biol.unlp.edu.ar> Only libz was in both /usr/lib and /usr/local/lib, I've renamed it and now configure does not find libpng, libz and libgd altough they are installed under /usr/local and work fine and I specify --with-pngdriver=/usr/local this is the output > checking if png driver is wanted... yes > checking for inflateEnd in -lz... no > checking for png_destroy_read_struct in -lpng... no > checking for gdImageCreateFromPng in -lgd... no > checking for inflateEnd in -lz... no > checking for inflateEnd in -lz... no > No png driver will be made due to librarys missing/old. martin. ableasby at hgmp.mrc.ac.uk wrote: > > If you have libpng, libz or libgd in /usr/lib then EMBOSS will > use it (them) and use only use the --with-pngdriver=dir > specification to find any remaining libraries. You can either > make sure that any such libraries in /usr/lib are up-to-date > or temporarily rename them and use --with-pngdriver=dir > to point to an appropriate location where you've compiled > them. > > Similar considerations apply to /usr/local/lib in the case of > png support (not quite the same but similar). > > HTH > Alan -- Martin Sarachu ICQ: 123797358 EMBnet Argentina: http://www.ar.embnet.org From GUIDO.STEINER at Roche.COM Fri Feb 15 03:04:54 2002 From: GUIDO.STEINER at Roche.COM (Steiner, Guido {PRBT~Basel}) Date: Fri, 15 Feb 2002 09:04:54 +0100 Subject: png trouble Message-ID: <49D79AF0A39CD511AAFE0002A55CC07A0393706A@rbamsem2.bas.roche.com> After having installed EMBOSS 2.2.0 with png support on SGI IRIX 6.5 (finally with success :) I may add another thing to watch out in case some SGI users face the same problems than I did. If you have the graphics libraries (like libgd) installed in a directory other than /usr/freeware/lib64 (or /usr/freeware/lib32), don't forget to modify the hardcoded library path in the EMBOSS configure file (line 4624, see SGI porting notes at http://www.sgi.com/solutions/sciences/chembio/resources/emboss/porting_notes.html ) accordingly and _remove_ the reference to /usr/freeware if you don't need any library from there, otherwise all EMBOSS applications produce runtime linking errors, no matter what you've specified in the --with-pngdriver option. This cost me some hours to find out, as I was no longer aware of the patching I did in the first place and presumed the error would be in a completely different place. Guido Steiner From GUIDO.STEINER at Roche.COM Fri Feb 15 03:13:32 2002 From: GUIDO.STEINER at Roche.COM (Steiner, Guido {PRBT~Basel}) Date: Fri, 15 Feb 2002 09:13:32 +0100 Subject: EMBOSS produces an error when doing wildcard searches Message-ID: <49D79AF0A39CD511AAFE0002A55CC07A0393706B@rbamsem2.bas.roche.com> Dear all, has anybody else experienced problems when iterating over a database with a wildcard search? For example, when I state infoseq embl:\* , everything works as expected, but when I say infoseq embl:p\* , after a while the output stops and the following error message is displayed: EMBOSS An error in ajseqdb.c at line 2550: Cannot open sequence file 'em_in2_000.seq' Of course this file exists and is not corrupted. Since other commands like seqret show the same behaviour, the problem really seems to be in the ajax library. Setup: EMBOSS 2.2.0 (64 bit build) on IRIX 6.5 from uname -a: IRIX64 rbaw20 6.5 10100655 IP27 from hinv: ... 16 400 MHZ IP27 Processors CPU: MIPS R12000 Processor Chip Revision: 3.5 FPU: MIPS R12010 Floating Point Chip Revision: 3.5 Main memory size: 4096 Mbytes ... Thanks for any help. Guido Steiner From GUIDO.STEINER at Roche.COM Fri Feb 15 03:50:24 2002 From: GUIDO.STEINER at Roche.COM (Steiner, Guido {PRBT~Basel}) Date: Fri, 15 Feb 2002 09:50:24 +0100 Subject: Linking issue (TOPO-0.1) Message-ID: <49D79AF0A39CD511AAFE0002A55CC07A0393706C@rbamsem2.bas.roche.com> If I'm allowed to post once more (I promise this will be the last problem submitted today :-).... When trying to compile Topo 0.1 (of the EMBASSY package) with png support enabled, I get a linking error as follows: ld64: ERROR 33: Unresolved text symbol "floor" -- 1st referenced by /soft/bi/pdsoft64/lib/libgd.a(gd.o). Use linker option -v to see when and which objects, archives and dsos are loaded. ld64: ERROR 33: Unresolved text symbol "pow" -- 1st referenced by ./ldtmpa1gUXE/libpng.a(pngrtran.o).o. Use linker option -v to see when and which objects, archives and dsos are loaded. ld64: INFO 152: Output file removed because of error. This seems to be due to the fact that the math libraries are linked in the wrong order. The following is done: cc -O -L/soft/bi/pdsoft64/lib -o topo topo.o ../../../ajax/libajaxg.la ../../../ajax/libajax.la ../../../plplot/libplplot.la -lX11 -lsocket -lm -lgd -lpng -lz And what should be actually done (IMHO): cc -O -L/soft/bi/pdsoft64/lib -o topo topo.o ../../../ajax/libajaxg.la ../../../ajax/libajax.la ../../../plplot/libplplot.la -lX11 -lsocket -lgd -lpng -lz -lm The configure script, however, proofed resistant to my efforts in altering the linking order. I just don't see how the LIBS variable is put together. Ideas anyone? :) Guido Steiner From ableasby at hgmp.mrc.ac.uk Fri Feb 15 04:39:04 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Fri, 15 Feb 2002 09:39:04 GMT Subject: Linking issue (TOPO-0.1) Message-ID: <200202150939.JAA20172@bromine.hgmp.mrc.ac.uk> I've put a replacement ftp://ftp.uk.embnet.org/pub/EMBOSS/TOPO-0.1.tar.gz on the server. This ought to clear your problem. If it doesn't then let me know directly. Cheers Alan From H.Davidson at ed.ac.uk Fri Feb 15 07:47:17 2002 From: H.Davidson at ed.ac.uk (Heather Davidson) Date: Fri, 15 Feb 2002 12:47:17 +0000 Subject: restrict and supermatcher Message-ID: <3C6D0355.1ABF1D5F@ed.ac.uk> I would like to know how to use supermatcher. I have used matcher with no problems. I want to compare one long sequence against a lot of other smaller sequences. In GCG one made a file of filenames of the smaller sequences and the comparison was done all at once. I do not know how to do this on supermatcher and the help does not help. Also I have used restrict but the output is not what I want. Basically I want an output like mapsort in GCG and I have asked support at HGMP and they cannot help either. I want the enzymes listed alphabetically ( which I know it does fine except it does a long line instead of across the paper) and with the site location but then with the size of fragments produced from that digest listed underneath I have only used emboss twice and each time I cannot get what I used to be able to get effortlessly from GCG Thanks Heather -- Heather Davidson Lab Manager | Email: Mailto:H.Davidson at ed.ac.uk Medical Genetics Section | WWW: http://www.ed.ac.uk Department of Medical Sciences | Fax: +44 (0)131 651 1059 The University of Edinburgh | Phone: +44 (0)131 651 1042 Molecular Medicine Centre Western General Hospital Crewe Road Edinburgh EH4 2XU From peter.rice at uk.lionbioscience.com Fri Feb 15 08:02:38 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Fri, 15 Feb 2002 13:02:38 +0000 Subject: restrict and supermatcher References: <3C6D0355.1ABF1D5F@ed.ac.uk> Message-ID: <3C6D06EE.5B785692@uk.lionbioscience.com> Heather Davidson wrote: > > I would like to know how to use supermatcher. I have used matcher with > no problems. I want to compare one long sequence against a lot of other > smaller sequences. In GCG one made a file of filenames of the smaller > sequences and the comparison was done all at once. I do not know how to > do this on supermatcher and the help does not help. The file of filenames is a VMS concept ... used by GCG and by EMBOSS. Put the filenames into a list, and use @filename on the command line. There are some known problems (for example if a file does not exist, or with complicated USAs or nested files of filenames) but as a simple list it should be fine. > Also I have used restrict but the output is not what I want. Basically I > want an output like mapsort in GCG and I have asked support at HGMP and > they cannot help either. I want the enzymes listed alphabetically ( > which I know it does fine except it does a long line instead of across > the paper) and with the site location but then with the size of > fragments produced from that digest listed underneath Interesting .... Restrict now produces a feature report, with a qualifier 'enzyme'. (Try 'restrict -rf embl' to see what is really happening inside). What you really are asking is to sort the report output by a named column/qualifier. This is quite easy to implement ... a sort by one or more qualifiers (internal or printed names) and then by start/end position. Once implemented, this would apply to all EMBOSS programs that have the new 'report' output .... this will grow to include all programs that generate sequence annotation. For restrict, it would be a command line option: % restrict -rsort enzyme (as they are in the feature table, you could also sort by 5prime instead of the start of the site match) Report qualifiers never have spaces, so a list of names with spaces would be fine. ACD sees the full list of report columns/qualifiers, so EMBOSS can give an error message at the start of the program. > I have only used emboss twice and each time I cannot get what I used to > be able to get effortlessly from GCG Ah, you should perhaps not expect to get what GCG gives you!!! Remember, with EMBOSS you can effortlessly get things that GCG cannot do ... ... and that includes some requests for new features :-) regards, Peter Rice -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From mathog at mendel.bio.caltech.edu Fri Feb 15 11:53:44 2002 From: mathog at mendel.bio.caltech.edu (David Mathog) Date: Fri, 15 Feb 2002 08:53:44 -0800 Subject: EMBOSS produces an error when doing wildcard searches Message-ID: > > Dear all, > > has anybody else experienced problems when iterating over a database with a wildcard search? > For example, when I state > infoseq embl:\* , > everything works as expected, but when I say > infoseq embl:p\* , > after a while the output stops and the following error message is displayed: It doesn't work here either. EMBOSS-2.2.0 on Solaris 5.8 on a Sparc. We keep our Genbank database in GCG format. It was indexed with: dbigcg -dbname genbank \ -directory $WORKDIR \ -indexdirectory $EMBOSSINDEXDIR \ -release "$THERELEASE" \ -date "$THEMONTH/$THEDAY/$THE2YEAR" \ -idformat GENBANK \ -filename "*.seq" When this is run: % infoseq genbank:\* -outfile=/tmp/testwild.txt it stops (no error messages) after 32993 lines with the last entry at: AC003118 which is just slightly into gb_htg. More interestingly: wc /export/home/gcg/data/gcggenbank/*seqcat 32940 417123 3441822 /export/home/gcg/data/gcggenbank/gb_ba.seqcat 93349 1323961 11229588 /export/home/gcg/data/gcggenbank/gb_htg.seqcat 108723 1578814 13275437 /export/home/gcg/data/gcggenbank/gb_in.seqcat 32993 - 32940 = 53. Looks like the indexing lookup functions do not transition properly from one file to another. Or it could be a signed short is used somewhere it shouldn't since 32993 isn't that much more than 32768. Or maybe it's a memory leak? Run it again and watch the process... Doesn't look like it, it grew slowly to (top output): 22941 root 1 0 10 9552K 5968K run 2:14 98.31% infoseq and stabilized there. So not a memory leak. Let the run complete and see if it fails at the same place... Yes, it did. Is it just infoseek or other programs as well? Try fuzznuc with: % fuzznuc -sequence=genbank:\* '-pattern=' -outf=fuzznucout.txt -mismatch=0 That works. Let's see where it stops... Looks bad folks, the output file has 32992 lines this time and the last line is, you guessed it: AC003118 94882 G Definitely a bug in the low level wildcard retrieval routines somewhere. Alan, please move this one way up the priority list - it probably means all wildcarded database operations are broken. The worst part is that here these are failing as if they were completing normally - there are no error messages to tip off the user that things have gone wrong. Regards, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From melsonr at earthlink.net Fri Feb 15 15:27:46 2002 From: melsonr at earthlink.net (Bob Melson) Date: Fri, 15 Feb 2002 13:27:46 -0700 Subject: Installation woes Message-ID: <3C6D6F42.1020900@earthlink.net> I've been trying to configure, compile and install v2.2.0 on a NetBSD system for the last couple of days with less than satisfactory results. The basic problem appears to be that the created Makefile doesn't link in the X11 libraries, no matter how they're specified in the configure session. I've included the flags "--x-libraries=/usr/X11R6/lib" and "--x-includes=/usr/X11R6/include" (no success); I've accepted default values by _not_ including the flags, I've specified "--with-x", I've ignored it. I've even gone so far as to hand edit the Makefile after configure, all to no avail. Each time I try to run, e.g. wossname, I get the error message "Shared object "libX11.so.6" not found" and if I run "ldd wossname", I get the following message: /usr/pkg/emboss/bin/wossname: -lnucleus.1 => /usr/pkg/emboss/lib/libnucleus.so.1 -lajaxg.1 => /usr/pkg/emboss/lib/libajaxg.so.1 -lajax.1 => /usr/pkg/emboss/lib/libajax.so.1 -lplplot.5 => /usr/pkg/emboss/lib/libplplot.so.5 -lX11.6 => not found -lm.0 => /usr/lib/libm387.so.0 -lm.0 => /usr/lib/libm.so.0 -lc.12 => /usr/lib/libc.so.1"fix" this problem? As you can see, all libraries _except_ the libX11 library are linked in at compile time. It goes without saying that I'm about at my wits end. Anybody have any ideas what I might do to "fix" this problem? ADVA{thanks}NCE, Bob Melson Dept. of Biology NM State University Las Cruces, NM, USA From ableasby at hgmp.mrc.ac.uk Sat Feb 16 18:02:46 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Sat, 16 Feb 2002 23:02:46 GMT Subject: Installation woes Message-ID: <200202162302.XAA01961@bromine.hgmp.mrc.ac.uk> Bob, The problem is the way your system is configured rather than an EMBOSS one. You've got two choices: 1) setenv LD_LIBRARY_PATH /usr/X11R6/lib or 2) Add the following on a line of its own at the end of /etc/ld.so.conf /usr/X11R6/lib Then type 'ldconfig' I'm assuming you have a fairly standard NetBSD 1.52-ish system. There may be even more choices but, being from a SYSV background, I'll leave someone else to mention them. Option 2 is probably the best. HTH Alan From gilbertd at bio.indiana.edu Sat Feb 16 21:23:32 2002 From: gilbertd at bio.indiana.edu (Don Gilbert) Date: Sat, 16 Feb 2002 21:23:32 -0500 (EST) Subject: macosx install note Message-ID: <200202170223.VAA25966@cricket.bio.indiana.edu> Dear emboss folks, |i saw you acknowledged in the emboss admin file for having worked out |the modifications required for installing it on mac os x (page 10 of |the guide at http://www.hgmp.mrc.ac.uk/Software/EMBOSS/admin.html). The current release of emboss (2.2.0 or later) doesn't need those instructions for compiling on macosx; newer configuration software handles macosx without any edits to files. You can also find a compiled version of emboss for macosx at ftp://iubio.bio.indiana.edu/biogrid/bioapps/bin/ as emboss-2.2.0-powerpc-apple-darwin5.1-gcc.tar.gz Unpack this from a terminal window to some folder of your choice with gnutar -zxf emboss-2.2.0-powerpc-apple-darwin5.1-gcc.tar.gz or double-clicking the .tar.gz file from macosx finder should unpack via unstuffit. then from terminal window, source the emboss/setenv file for emboss environment settings, and test, as with wossname -- Don Gilbert -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd at bio.indiana.edu From charles at moulinette.dyndns.org Fri Feb 22 04:51:31 2002 From: charles at moulinette.dyndns.org (Charles Plessy) Date: Fri, 22 Feb 2002 10:51:31 +0100 Subject: searching local databases Message-ID: <20020222095131.GA26315@moulinette.dyndns.org> Hello, In GCG, i used to make a local blast database from a few hundred of sequences coming from a screen (for example), in order to be able to use gcg's databese searching tools on it. With emboss, i have built a local index of fasta files and modified my ~/.embossrc so that i can access them with the db:ID syntax. I am now stuck. Could anyone point me to ressources explaining how I can install fasta or blast on my linux, and how to instruct those guys to use my homemade emboss fasta database?? Thank you, Charles From dmartin at bioinformatics.msiwtb.dundee.ac.uk Fri Feb 22 06:07:35 2002 From: dmartin at bioinformatics.msiwtb.dundee.ac.uk (David Martin) Date: Fri, 22 Feb 2002 11:07:35 +0000 (GMT) Subject: searching local databases In-Reply-To: <20020222095131.GA26315@moulinette.dyndns.org> Message-ID: On Fri, 22 Feb 2002, Charles Plessy wrote: > Hello, > > In GCG, i used to make a local blast database from a few hundred of > sequences coming from a screen (for example), in order to be able to > use gcg's databese searching tools on it. > > With emboss, i have built a local index of fasta files and modified my > ~/.embossrc so that i can access them with the db:ID syntax. > > I am now stuck. Could anyone point me to ressources explaining how I > can install fasta or blast on my linux, and how to instruct those guys > to use my homemade emboss fasta database?? I have a tutorial to do just this.. There are a few slightly misleading bits in it (section ordering mostly) but otherwise it is fine. It doesn't cover installing BLAST, use the readme from NCBI for that. those who are interested can email me for a copy (pdf). It requires NCBI Blast and EMBOSS with the Swissprot database installed. ..d > > Thank you, > > Charles > ---------------------------------- David Martin PhD Bioinformatics Scientific Officer Wellcome Trust Biocentre, Dundee ---------------------------------- From dmartin at bioinformatics.msiwtb.dundee.ac.uk Fri Feb 22 08:39:55 2002 From: dmartin at bioinformatics.msiwtb.dundee.ac.uk (David Martin) Date: Fri, 22 Feb 2002 13:39:55 +0000 (GMT) Subject: BLAST tutorial. Message-ID: I have been snowed under with requests. I have sent a copy of the Blast tutorial and an advanced Unix tutorial (more of a what it can do than a true tutorial) to Gary and asked him to make them available via the EMBOSS ftp site. He will confirm this with a URL in due course. The advanced unix tutorial uses analysis of PDB files as a scenario but can be applied to anything appropriate. Unfortunately the PDF I sent out initially to some of you is not complete. Gary has the complete one. ..d ---------------------------------- David Martin PhD Bioinformatics Scientific Officer Wellcome Trust Biocentre, Dundee ---------------------------------- From gwilliam at hgmp.mrc.ac.uk Fri Feb 22 08:56:01 2002 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Fri, 22 Feb 2002 13:56:01 +0000 Subject: BLAST tutorial. References: Message-ID: <3C764DF1.D4D99F5B@hgmp.mrc.ac.uk> The Blast setup tutorial and the advanced UNIX guide are now available at: ftp://ftp.uk.embnet.org/pub/EMBOSS/tutorials/ in the files: adv_unix_tut.pdf blasttut.pdf Gary David Martin wrote: > > I have been snowed under with requests. I have sent a copy of the Blast > tutorial and an advanced Unix tutorial (more of a what it can do than a > true tutorial) to Gary and asked him to make them available via the EMBOSS > ftp site. He will confirm this with a URL in due course. > > The advanced unix tutorial uses analysis of PDB files as a scenario but > can be applied to anything appropriate. > > Unfortunately the PDF I sent out initially to some of you is not complete. > Gary has the complete one. > > ..d > > ---------------------------------- > David Martin PhD > Bioinformatics Scientific Officer > Wellcome Trust Biocentre, Dundee > ---------------------------------- -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From peter.rice at uk.lionbioscience.com Fri Feb 22 14:28:33 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Fri, 22 Feb 2002 19:28:33 +0000 Subject: EMBOSS produces an error when doing wildcard searches References: Message-ID: <3C769BE1.76952726@uk.lionbioscience.com> Hi David, Got the files thanks. No time to test them, but ... The first entry after AC003118 is the first split entry (in 8 parts). I think shorts are innocent. Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From charles at moulinette.dyndns.org Sat Feb 23 11:26:57 2002 From: charles at moulinette.dyndns.org (Charles Plessy) Date: Sat, 23 Feb 2002 17:26:57 +0100 Subject: searching local databases In-Reply-To: References: <20020222095131.GA26315@moulinette.dyndns.org> Message-ID: <20020223162657.GA5129@gizmotronics.dyndns.org> > > I am now stuck. Could anyone point me to resources explaining how I > > can install fasta or blast on my linux, and how to instruct those guys > > to use my homemade emboss fasta database?? > > I have a tutorial to do just this.. There are a few slightly misleading > bits in it (section ordering mostly) but otherwise it is fine. First, thank you for your helpful tutorials. I succeeded in creating a blast DB, and indexing it. I modified my .embossrc in order to access it with seqret. However, I'm only able to access blast databases in the ncbi format ; how can I avoid reformatting the headers to something like >lcl|accession ? What are the other accepted formats? Charles From David.Bauer at SCHERING.DE Tue Feb 26 05:28:21 2002 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Tue, 26 Feb 2002 11:28:21 +0100 Subject: seqret via url with spaces Message-ID: Hi, to retrieve sequences from a local server I need to specify the folowing url: ...../www_find.cgi?-e+'{GENESEQ}:[([AccNumber%20EQ%20text:%s;])]' If I do this in emboss.default, than ajstr complains with: Uncaught exception: Allocation bad byte count, raised at ajstr.c:368 So what is the right way to code the spaces? Thanks, David. P.S. I have not written the www_find.cgi...... From peter.rice at uk.lionbioscience.com Tue Feb 26 06:04:46 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 26 Feb 2002 11:04:46 +0000 Subject: seqret via url with spaces References: Message-ID: <3C7B6BCE.1CF2FF26@uk.lionbioscience.com> David.Bauer at SCHERING.DE wrote: > ...../www_find.cgi?-e+'{GENESEQ}:[([AccNumber%20EQ%20text:%s;])]' > If I do this in emboss.default, than ajstr complains with: > Uncaught exception: Allocation bad byte count, raised at ajstr.c:368 > > So what is the right way to code the spaces? This is an ANSI C format to print the %s string. You need %%20 for the other % signs. These convert to single '%' for the URL that is used. -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From David.Bauer at SCHERING.DE Tue Feb 26 07:25:18 2002 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Tue, 26 Feb 2002 13:25:18 +0100 Subject: Antwort: Re: seqret via url with spaces Message-ID: Thanks, it works but I had to do another change. The opening [({ are fine but the closing ])} get an aditional space inbetween them before they are passed to the web server (as I can see in the .dbg file). I had to code them as %%5D etc. David. Peter Rice Gesendet von: An: David.Bauer at SCHERING.DE owner-emboss at hgmp.mrc.ac Kopie: emboss at embnet.org .uk Thema: Re: seqret via url with spaces 26.02.02 12:04 David.Bauer at SCHERING.DE wrote: > ...../www_find.cgi?-e+'{GENESEQ}:[([AccNumber%20EQ%20text:%s;])]' > If I do this in emboss.default, than ajstr complains with: > Uncaught exception: Allocation bad byte count, raised at ajstr.c:368 > > So what is the right way to code the spaces? This is an ANSI C format to print the %s string. You need %%20 for the other % signs. These convert to single '%' for the URL that is used. -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From peter.rice at uk.lionbioscience.com Tue Feb 26 07:41:12 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 26 Feb 2002 12:41:12 +0000 Subject: Antwort: Re: seqret via url with spaces References: Message-ID: <3C7B8268.757309E6@uk.lionbioscience.com> David.Bauer at SCHERING.DE wrote: > it works but I had to do another change. > > The opening [({ are fine but the closing ])} get an aditional space > inbetween them before they are passed to the web server > (as I can see in the .dbg file). > I had to code them as %%5D etc. > David.Bauer at SCHERING.DE wrote: > > ...../www_find.cgi?-e+'{GENESEQ}:[([AccNumber%20EQ%20text:%s;])]' The cause is the use of '' inside a "" string. Fixed in the next release. Your change will still work. Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From charles at moulinette.dyndns.org Wed Feb 27 01:31:46 2002 From: charles at moulinette.dyndns.org (Charles Plessy) Date: Wed, 27 Feb 2002 07:31:46 +0100 Subject: blast frontend? Message-ID: <20020227063146.GA838@gizmotronics.dyndns.org> Hello, Is there somewhere in emboss a blast frontend that would allow to call (t)blastn,p,x with USA as input parameter, and/or being asked questions interactively ? Charles From peter.rice at uk.lionbioscience.com Wed Feb 27 04:54:47 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 27 Feb 2002 09:54:47 +0000 Subject: blast frontend? References: <20020227063146.GA838@gizmotronics.dyndns.org> Message-ID: <3C7CACE7.F9236750@uk.lionbioscience.com> Charles Plessy wrote: > > Is there somewhere in emboss a blast frontend that would allow to call > (t)blastn,p,x with USA as input parameter, and/or being asked > questions interactively ? Not yet ... but I did make plans some time back to integrate 3rd party applications under an ACD interface. We have this with emma (clustalw) and eprimer3 (primer3) but they gather up the oprions and make an internal system call. The idea was to run something like 'acdc' (nothing more than an embInit call) that simply runs through the ACD interface and then starts up a program. For blast this means renaming command line options, and it stalled a little on how to specify the new command line ... but really that just needs a simple specification and a simple parser. This application even had a name: emboss (so you could run 'emboss blastp' for example). If there is interest, we could revive this. Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From gbottu at ben.vub.ac.be Wed Feb 27 08:18:20 2002 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Wed, 27 Feb 2002 14:18:20 +0100 (CET) Subject: blast frontend? Message-ID: <200202271318.OAA0001538214@ben.vub.ac.be> from : BEN Peter Rice wrote: > Not yet ... but I did make plans some time back to integrate 3rd party > applications under an ACD interface. We have this with emma (clustalw) and > eprimer3 (primer3) but they gather up the oprions and make an internal > system call. The idea was to run something like 'acdc' (nothing more than > an embInit call) that simply runs through the ACD interface and then starts > up a program. For blast this means renaming command line options, and it > stalled a little on how to specify the new command line ... but really that > just needs a simple specification and a simple parser. This application > even had a name: emboss (so you could run 'emboss blastp' for example). An easy way to integrate applications under EMBOSS is certainly welcome. Parsing the ACD file and writing a command line is however not enough. It should be possible to take sequences and other data in EMBOSS style and pass them over in the appropriate format to the application. Guy Bottu From peter.rice at uk.lionbioscience.com Wed Feb 27 08:48:11 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 27 Feb 2002 13:48:11 +0000 Subject: blast frontend? References: <200202271318.OAA0001538214@ben.vub.ac.be> Message-ID: <3C7CE39B.B8E5D8C5@uk.lionbioscience.com> Guy Bottu wrote: > An easy way to integrate applications under EMBOSS is certainly welcome. > Parsing the ACD file and writing a command line is however not enough. > It should be possible to take sequences and other data in EMBOSS > style and pass them over in the appropriate format to the application. This is where things get just a little complicated. We need to convert, for example, the input sequence into a format blast can use. Fortunately a simple conversion to FASTA format will work for most applications (either directly, or by piping in the output of seqret ... though if it is from stdin a little care may be needed). A list of possible third party applications would be helpful. blast and fasta as starters I assume. -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From David.Bauer at SCHERING.DE Thu Feb 28 01:56:11 2002 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Thu, 28 Feb 2002 07:56:11 +0100 Subject: transeq frame list Message-ID: Hi, transeq -help says that -frame should be a list. But if I specify -frame=1,2,3 it crashes with segmentation fault and no visible error in the debug file. The last message there is that it correctly recognised the frame list. It seems frame can only be a character. In fact it is OK because there is the F as alias for 1,2,3 but -help should give the correct type. Ciao, David. From peter.rice at uk.lionbioscience.com Thu Feb 28 05:13:21 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Thu, 28 Feb 2002 10:13:21 +0000 Subject: transeq frame list References: Message-ID: <3C7E02C1.FEDBF198@uk.lionbioscience.com> David.Bauer at SCHERING.DE wrote: > > transeq -help says that -frame should be a list. > But if I specify -frame=1,2,3 it crashes with segmentation fault > and no visible error in the debug file. > The last message there is that it correctly recognised the frame list. > It seems frame can only be a character. > In fact it is OK because there is the F as alias for 1,2,3 > but -help should give the correct type. Ah, small problem with the English language. In EMBOSS, a 'list' is a list of values with short names. 'Select' is a list of values with no short name but with generated numbers (so far only embossdata uses this type). 'Lists' can take a 'list of values' (1,2,3) if they allow more than one value to be set. Transeq only allows a maximum of 1. Frame can be 1, 2, 3, -1, -2, -3, F, R, "Forward" or "Reverse". (Long names are given for "F" and "R". The long form for "1" is "1"). The simple solution is: 1. Fix the segmentation fault (strangely, it is in a debug messsage call in processing the list value - the array element passed in the call does not exist :-) 2. Change the help message for lists and selects to explain "Choose 1 from a list of values" or "Choose up to 4 from a list of values". 3. Look again at long names. The long name for "F" is really "Forward three frames" but if you put this on the command line, the spaces maked it 3 items "Forward", "Three" and "Frames". As lists and selects normally allow only 1 value, this can change to force 3 values to use the comma, something like -frame=1,2,3 and to not allow -frame="1 2 3". Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From gwilliam at hgmp.mrc.ac.uk Thu Feb 28 05:19:55 2002 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 28 Feb 2002 10:19:55 +0000 Subject: transeq frame list References: <3C7E02C1.FEDBF198@uk.lionbioscience.com> Message-ID: <3C7E044B.BC3B1765@hgmp.mrc.ac.uk> Peter Rice wrote: > > David.Bauer at SCHERING.DE wrote: > > > > transeq -help says that -frame should be a list. > > But if I specify -frame=1,2,3 it crashes with segmentation fault > > and no visible error in the debug file. > > The last message there is that it correctly recognised the frame list. > > It seems frame can only be a character. > > In fact it is OK because there is the F as alias for 1,2,3 > > but -help should give the correct type. > > Ah, small problem with the English language. David has also suggested a change of the name of ACD type 'list' to be 'menu'. This would break lots of parsers, but perhaps we could keep the ACD type 'list' in the .acd files, but the name 'list' could be changed to be 'menu' when displaying -help? -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From gwilliam at hgmp.mrc.ac.uk Thu Feb 28 05:53:53 2002 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 28 Feb 2002 10:53:53 +0000 Subject: transeq frame list References: Message-ID: <3C7E0C41.8721CD1@hgmp.mrc.ac.uk> David.Bauer at SCHERING.DE wrote: > > Hi, > > transeq -help says that -frame should be a list. > But if I specify -frame=1,2,3 it crashes with segmentation fault and no visible > error in the debug file. > The last message there is that it correctly recognised the frame list. > It seems frame can only be a character. > In fact it is OK because there is the F as alias for 1,2,3 but -help should give > the correct type. > > Ciao, David. I have changed transeq's '-frame' qualifier so that it can take one or more frame values, as: -frame=1,2,3 The transeq.c and transeq.acd files are available from: ftp://ftp.uk.embnet.org/pub/EMBOSS/patchfiles/ Gary -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From peter.rice at uk.lionbioscience.com Thu Feb 28 07:21:16 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Thu, 28 Feb 2002 12:21:16 +0000 Subject: transeq frame list References: <3C7E0C41.8721CD1@hgmp.mrc.ac.uk> Message-ID: <3C7E20BC.1033DDA1@uk.lionbioscience.com> "Gary Williams, Tel 01223 494522" wrote: > > David.Bauer at SCHERING.DE wrote: > > > > transeq -help says that -frame should be a list. > > But if I specify -frame=1,2,3 it crashes with segmentation fault > > and no visible error in the debug file. > > The last message there is that it correctly recognised the frame list. > > It seems frame can only be a character. > > In fact it is OK because there is the F as alias for 1,2,3 > > but -help should give the correct type. > > I have changed transeq's '-frame' qualifier so that it can take one or > more frame values: OK. I tested it. -frame=1,2,3 gives the same results as -frame=f > David has also suggested a change of the name of ACD type 'list' > to be 'menu'. > > This would break lots of parsers, but perhaps we could keep the > ACD type 'list' in the .acd files, but the name 'list' could be > changed to be 'menu' when displaying -help? Done. Lists will say 'menu list' in messages, and 'menu' in the help output. Selects will say 'selection list'. Also, the error message for a bad list or select option will include the valid options (for lists this is the short code). For example: % transeq tembl:paamir -frame=4 Translate nucleic acid sequences Error: '4' is not a valid menu option Accepted short codes are: 1,2,3,F,-1,-2,-3,R,6 Error: Bad menu option '4' The list and select options must be in a comma-separated list (-frame=1,2,3). White space was allowed up to now (-frame="1 2 3"), but I think is rarely used (it is easy to turn on again). Now you can use: % transeq -frame="Forward three frames" ... which is the long name for 'F' in the ACD file. Users never see these unless they are prompted for a required/optional value, as for example in msbar which has 3 prompted lists (menus). The list/menu and message changes are all in ajax/ajacd.c ... which can be added to the patchfiles although I suspect we are close to a new release anyway. Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From mad at biol.unlp.edu.ar Thu Feb 28 03:37:02 2002 From: mad at biol.unlp.edu.ar (Martin Sarachu) Date: Thu, 28 Feb 2002 11:37:02 +0300 Subject: Jemboss Message-ID: <3C7DEC2E.54789265@biol.unlp.edu.ar> I'm using EMBOSS-2.2.0 on Sparc/Solaris 8, with j2sdk1.4.0 besides the built-in java that came with solaris. When trying to compile Jemboss I do %/usr/j2sdk1.4.0/bin/javac org/emboss/jemboss/server/JembossServer.java I get >org/emboss/jemboss/server/JembossServer.java:499: cannot resolve symbol >symbol : class JembossThread >location: class org.emboss.jemboss.server.JembossServer > JembossThread jt = new JembossThread(rea.getProcess(),project); > ^ >org/emboss/jemboss/server/JembossServer.java:499: cannot resolve symbol >symbol : class JembossThread >location: class org.emboss.jemboss.server.JembossServer > JembossThread jt = new JembossThread(rea.getProcess(),project); > ^ >2 errors EMBOSS was configured --with-java=/usr/j2sdk1.4.0/include --with-javaos=/usr/j2sdk1.4.0/include/solaris, it compiled fine and runs ok. I didn't remove the java packages that came with solaris, I don't know if this can be a problem. martin -- Martin Sarachu ICQ: 123797358 EMBnet Argentina: http://www.ar.embnet.org From mad at biol.unlp.edu.ar Fri Feb 8 08:58:19 2002 From: mad at biol.unlp.edu.ar (Martin Sarachu ) Date: Fri, 08 Feb 2002 11:58:19 +0300 Subject: problems building EMNU Message-ID: <3C63932B.40BE5C1A@biol.unlp.edu.ar> Hi, I get this when building EMNU Undefined first referenced symbol in file initscr32 emnu.o (symbol belongs to implicit dependency /usr/lib/libcurses.so.1) box32 emnu.o (symbol belongs to implicit dependency /usr/lib/libcurses.so.1) w32attron emnu.o (symbol belongs to implicit dependency /usr/lib/libcurses.so.1) w32attroff emnu.o (symbol belongs to implicit dependency /usr/lib/libcurses.so.1) getcurx emnu.o (symbol belongs to implicit dependency /usr/lib/libcurses.so.1) getcury emnu.o (symbol belongs to implicit dependency /usr/lib/libcurses.so.1) acs32map emnu.o (symbol belongs to implicit dependency /usr/lib/libcurses.so.1) getbegx emnu.o (symbol belongs to implicit dependency /usr/lib/libcurses.so.1) getbegy emnu.o (symbol belongs to implicit dependency /usr/lib/libcurses.so.1) ld: fatal: Symbol referencing errors. No output written to .libs/emnu ncurses v5.2 are installed and EMBOSS programs compiled ok. any idea? Thanks, -- Martin Sarachu ICQ: 123797358 EMBnet Argentina: http://www.ar.embnet.org From cquijano at iib.uam.es Tue Feb 12 14:26:02 2002 From: cquijano at iib.uam.es (Carlos Quijano) Date: Tue, 12 Feb 2002 15:26:02 +0100 Subject: [EMBOSS] Segmentation fault RH5.2 + EMBOSS2.0.1 Message-ID: <3C6925FA.7010508@iib.uam.es> I have installed Emboss 2.0.1 with a PentiumIII, kernel 2.2.7 after installing, wossname -auto, and some others apps works well but showing "Segmentation fault" as last message. Does somebody out there fixed it or seen it before me? Tanks you all. From ableasby at hgmp.mrc.ac.uk Tue Feb 12 14:55:45 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 12 Feb 2002 14:55:45 GMT Subject: [EMBOSS] Segmentation fault RH5.2 + EMBOSS2.0.1 Message-ID: <200202121455.OAA09657@bromine.hgmp.mrc.ac.uk> File handling was changed a while ago (as I remember) and I can believe that combination of EMBOSS and operating system would fail. You're best upgrading to EMBOSS 2.2.0 and RH7.2. Cheers Alan From peter.rice at uk.lionbioscience.com Tue Feb 12 16:59:10 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 12 Feb 2002 16:59:10 +0000 Subject: Blast format change at NCBI Message-ID: <3C6949DE.A50485B2@uk.lionbioscience.com> NCBI's FTP server will be releasing BLAST formatted databases in a new format (version 4) from February 19th. This format is not supported by EMBOSS dbiblast indexing (or by NCBI's blastall before the current version 2.2.2) See ftp://ftp.ncbi.nih.gov/blast/db/NewFormattedDatabases/README If you have the fasta format files, you should be able to use dbifasta to index the same entries. The blast 2.2.2 release notes say "Fastacmd will dump out an entire BLAST database in FASTA format if the new -D option is used", but I have not tried this yet to see how well it fits with EMBOSS. Has anyone else looked into this yet? -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From mathog at mendel.bio.caltech.edu Tue Feb 12 17:42:30 2002 From: mathog at mendel.bio.caltech.edu (David Mathog) Date: Tue, 12 Feb 2002 09:42:30 -0800 Subject: Blast format change at NCBI Message-ID: > NCBI's FTP server will be releasing BLAST formatted databases in a new > format (version 4) from February 19th. > > This format is not supported by EMBOSS dbiblast indexing (or by NCBI's > blastall before the current version 2.2.2) > > See ftp://ftp.ncbi.nih.gov/blast/db/NewFormattedDatabases/README > > If you have the fasta format files, you should be able to use dbifasta to > index the same entries. > > The blast 2.2.2 release notes say "Fastacmd will dump out an entire BLAST > database in FASTA format if the new -D option is used", but I have not > tried this yet to see how well it fits with EMBOSS. > > Has anyone else looked into this yet? Sorry, no. I imagine that it will break GCG's BLAST implementation as well though. I have used fastacmd (which is undocumented, of course) in the past with success but obviously not with -D. Usage was: fastacmd -d nt -s "" This snippet of code (from an older NCBI version) is the only documentation I've found for the fastacmd command line options: static Args myargs [NUMARG] = { { "Database", NULL, NULL, NULL, TRUE, 'd', ARG_STRING, 0.0, 0, NULL}, { "Search string: GIs, accessions and locuses may be used delimited\n" " by comma or space)", NULL, NULL, NULL, TRUE, 's', ARG_STRING, 0.0, 0, NULL}, { "Input file wilth GIs/accessions/locuses for batch retrieval", NULL, NULL, NULL, TRUE, 'i', ARG_STRING, 0.0, 0, NULL}, { "Retrieve duplicated accessions", "F", NULL, NULL, TRUE, 'a', ARG_BOOLEAN, 0.0, 0, NULL}, { "Line length for sequence", "80", NULL, NULL, TRUE, 'l', ARG_INT, 0.0, 0, NULL} } A more pressing problem for us regarding BLAST is that nr (entire) and nt_lcl (fragments of 1/9th nt) both just grew beyond the point where the data can fit along with blast and linux in the 512 Mb on each of our 9 DS10 nodes. Consequently local BLAST runs on these databases now crawl since all data must be read from disk for each run. The NCBI must have something like 10Gb in their main server these days to keep both nr and nt (and whatever else) in memory. I'd _kill_ for MPI or PVM BLAST, but it seems like the NCBI is not going to see the need to write that until they reach the memory limit on their huge server. I'd add it myself but a horrible experience tracking down the gi list memory leak bug in one version of BLAST taught me once and for all that their code structure is so complex that the task would be extraordinarily difficult. Others must have come to the same conclusion since nobody else has done it either. Regards, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From jrvalverde at cnb.uam.es Wed Feb 13 10:59:01 2002 From: jrvalverde at cnb.uam.es (jrvalverde at cnb.uam.es) Date: Wed, 13 Feb 2002 11:59:01 +0100 (MET) Subject: Blast format change at NCBI In-Reply-To: Message-ID: <200202131059.g1DAx2W696962@embnet.cnb.uam.es> "David Mathog" wrote: > nr and nt (and whatever else) in memory. I'd _kill_ for MPI or PVM > BLAST, but it seems > like the NCBI is not going to see the need to write that until they > reach the memory limit > on their huge server. I'd add it myself but a horrible experience You don't want that. It would crawl even more having to access data over the net. What you want is to create partial databases that fit in memory, and a script that sends the same query against each of the database sections, collects the results and colates them, selecting the highest scores. I don't have such a script (having only one machine to run things), but understand that others have done it already. j From duhaimj at ircm.qc.ca Wed Feb 13 15:09:05 2002 From: duhaimj at ircm.qc.ca (Johanne Duhaime) Date: Wed, 13 Feb 2002 10:09:05 -0500 Subject: Problem with png driver for emboss Message-ID: <3C6A8191.F991A2D8@ircm.qc.ca> Hi I have problem installing the PNG stuff in order to use graphics in EMBOSS. I have tried to build gd on solaris 2.6 and could not succeed. There is a message about : gdImageCreateFromPng. Would you mind to help? I had spent several hours on compiling Png stuff. I would appreciate very much your help. Following is the error message, the include and library and finally the makefile. Thank in advance. mercure{root}48: make gcc -I. -I/usr/include/freetype2 -I/usr/include/X11 -I/usr/X11R6/include/X11 -I/usr/local/include -I/opt/sasircm/drivers/drivers/include pngtogd.o -o pngtogd -L. -L/usr/local/lib -L/usr/lib/X11 -L/usr/X11R6/lib -L/opt/sasircm/drivers/drivers/lib -L/usr/ucblib -lgd -lpng -lz -lm Undefined first referenced symbol in file gdImageCreateFromPng pngtogd.o ld: fatal: Symbol referencing errors. No output written to pngtogd *** Error code 1 make: Fatal error: Command failed for target `pngtogd' Librairies and include: total 466 drwxrwxrwx 2 sasircm sequence 512 Feb 8 15:10 ./ drwxrwxrwx 4 sasircm sequence 512 Feb 8 14:54 ../ -rw-r--r-- 1 sasircm sequence 133396 Feb 11 16:32 png.h -rw-r--r-- 1 sasircm sequence 39838 Feb 11 16:32 pngconf.h -rw-r--r-- 1 sasircm sequence 7810 Feb 8 14:54 zconf.h -rw-r--r-- 1 sasircm sequence 40898 Feb 8 14:54 zlib.h mercure{root}50: l /opt/sasircm/drivers/drivers/lib total 1058 drwxrwxrwx 2 sasircm sequence 512 Feb 11 16:32 ./ drwxrwxrwx 4 sasircm sequence 512 Feb 8 14:54 ../ -rw-rw-rw- 1 sasircm sequence 205316 Feb 11 16:32 libpng.a lrwxrwxrwx 1 root other 11 Feb 11 16:32 libpng.so -> libpng.so.3* lrwxrwxrwx 1 root other 17 Feb 11 16:32 libpng.so.3 -> libpng.so.3.1.2.1* -rwxr-xr-x 1 sasircm sequence 229816 Feb 11 16:32 libpng.so.3.1.2.1* -rwxr-xr-x 1 sasircm sequence 70488 Feb 8 14:54 libz.a* mercure{root}51: Makefile mercure{root}59: more Makefile #Depending on your system, you will need to modify this makefile. #If you do not have gcc, change the setting for COMPILER, but you must #use an ANSI standard C compiler (NOT the old SunOS 4.1.3 cc #compiler; get gcc if you are still using it). COMPILER=gcc #If the ar command fails on your system, consult the ar manpage #for your system. AR=ar #If you don't have FreeType, libjpeg and/or Xpm installed, including the #header files, uncomment this (default). You really must install #libpng and zlib to get anywhere if you wish to create PNG images. #Mis la ligne suivante en commentaire #CFLAGS=-O -DHAVE_LIBPNG -DHAVE_LIBJPEG #If you do have FreeType, libjpeg and/or Xpm fully installed, uncomment a #variation of this and comment out the line above. See also LIBS below. #CFLAGS=-O -DHAVE_LIBXPM -DHAVE_LIBPNG -DHAVE_LIBJPEG \ # -DHAVE_LIBFREETYPE -DHAVE_LIBTTF #To use the old FreeType 1.x library, add this additional #define #to the line above #-DHAVE_LIBTTF #If you don't have FreeType Xpm fully installed, uncomment this #(default). #PLEASE NOTE: YOU MAY HAVE TO JUGGLE THE ORDER OF THE LIBRARIES. #Some systems are very picky about link order. They don't all agree #on the right order, either. LIBS=-lgd -lpng -lz -lm #If you do have FreeType, JPEG and/or Xpm fully installed, uncomment a #variation of this and comment out the line above. Note that #Xpm requires X11. See also CFLAGS above. #LIBS=-lgd -lpng -lz -ljpeg -lfreetype -lm -lttf #Note: for Freetype 1.x, use DHAVE_LIBTTF and -lttf instead. #Typical install locations for freetype, zlib, xpm, libjpeg and libpng header #files. If yours are somewhere else, change this. -I. is important to #ensure that the version of gd you are installing is used, and not an #older release in your directory tree somewhere. INCLUDEDIRS=-I. -I/usr/include/freetype2 -I/usr/include/X11 -I/usr/X11R6/include/X11 -I/usr/local/include -I/opt/sasircm/drivers/dri vers/include #Typical install locations for freetype, zlib, xpm and libpng libraries. #If yours are somewhere else, other than a standard location #such as /lib or /usr/lib, then change this. Be sure to keep #-L. as this allows the gd library itself to be found. #Put -L. first so that old versions of the gd library elsewhere #on your system can't cause conflicts while building a new one. #This line shouldn't hurt if you don't actually have some of the #optional libraries and directories. #LIBDIRS=-L. -L/usr/local/lib -L/usr/lib/X11 -L/usr/X11R6/lib -L/opt/sasircm/drivers/drivers/lib -L/opt/sasircm/drivers/libpng LIBDIRS=-L. -L/usr/local/lib -L/usr/lib/X11 -L/usr/X11R6/lib -L/opt/sasircm/drivers/drivers/lib -L/usr/ucblib #Location where libgd.a should be installed by "make install". #INSTALL_LIB=/usr/local/lib INSTALL_LIB=/opt/sasircm/drivers/drivers/lib #Location where .h files should be installed by "make install". #INSTALL_INCLUDE=/usr/local/include INSTALL_INCLUDE=/opt/sasircm/drivers/drivers/include #Location where useful non-test programs should be installed by "make install". #INSTALL_BIN=/usr/local/bin INSTALL_BIN=/opt/sasircm/drivers/drivers/bin # # # Changes should not be required below here. # # VERSION=1.8.4 CC=$(COMPILER) $(INCLUDEDIRS) LINK=$(CC) $(LIBDIRS) $(LIBS) PROGRAMS=$(BIN_PROGRAMS) $(TEST_PROGRAMS) BIN_PROGRAMS=pngtogd pngtogd2 gdtopng gd2topng gd2copypal gdparttopng webpng TEST_PROGRAMS=gdtest gddemo gd2time gdtestft gdtestttf all: libgd.a $(PROGRAMS) install: libgd.a $(BIN_PROGRAMS) sh ./install-item 644 libgd.a $(INSTALL_LIB)/libgd.a sh ./install-item 755 pngtogd $(INSTALL_BIN)/pngtogd sh ./install-item 755 pngtogd2 $(INSTALL_BIN)/pngtogd2 sh ./install-item 755 gdtopng $(INSTALL_BIN)/gdtopng sh ./install-item 755 gd2topng $(INSTALL_BIN)/gd2topng sh ./install-item 755 gd2copypal $(INSTALL_BIN)/gd2copypal sh ./install-item 755 gdparttopng $(INSTALL_BIN)/gdparttopng sh ./install-item 755 webpng $(INSTALL_BIN)/webpng sh ./install-item 755 bdftogd $(INSTALL_BIN)/bdftogd sh ./install-item 644 gd.h $(INSTALL_INCLUDE)/gd.h sh ./install-item 644 gdcache.h $(INSTALL_INCLUDE)/gdcache.h sh ./install-item 644 gd_io.h $(INSTALL_INCLUDE)/gd_io.h sh ./install-item 644 gdfontg.h $(INSTALL_INCLUDE)/gdfontg.h sh ./install-item 644 gdfontl.h $(INSTALL_INCLUDE)/gdfontl.h sh ./install-item 644 gdfontmb.h $(INSTALL_INCLUDE)/gdfontmb.h sh ./install-item 644 gdfonts.h $(INSTALL_INCLUDE)/gdfonts.h sh ./install-item 644 gdfontt.h $(INSTALL_INCLUDE)/gdfontt.h gddemo: gddemo.o libgd.a $(CC) gddemo.o -o gddemo $(LIBDIRS) $(LIBS) pngtogd: pngtogd.o libgd.a $(CC) pngtogd.o -o pngtogd $(LIBDIRS) $(LIBS) webpng: webpng.o libgd.a $(CC) webpng.o -o webpng $(LIBDIRS) $(LIBS) pngtogd2: pngtogd2.o libgd.a $(CC) pngtogd2.o -o pngtogd2 $(LIBDIRS) $(LIBS) gdtopng: gdtopng.o libgd.a $(CC) gdtopng.o -o gdtopng $(LIBDIRS) $(LIBS) gd2topng: gd2topng.o libgd.a $(CC) gd2topng.o -o gd2topng $(LIBDIRS) $(LIBS) gd2copypal: gd2copypal.o libgd.a $(CC) gd2copypal.o -o gd2copypal $(LIBDIRS) $(LIBS) gdparttopng: gdparttopng.o libgd.a $(CC) gdparttopng.o -o gdparttopng $(LIBDIRS) $(LIBS) gdtest: gdtest.o libgd.a $(CC) gdtest.o -o gdtest $(LIBDIRS) $(LIBS) gd2time: gd2time.o libgd.a $(CC) gd2time.o -o gd2time $(LIBDIRS) $(LIBS) gdtestft: gdtestft.o libgd.a $(CC) --verbose gdtestft.o -o gdtestft $(LIBDIRS) $(LIBS) gdtestttf: gdtestttf.o libgd.a $(CC) --verbose gdtestttf.o -o gdtestttf $(LIBDIRS) $(LIBS) libgd.a: gd.o gd_gd.o gd_gd2.o gd_io.o gd_io_dp.o gd_io_file.o gd_ss.o \ gd_io_ss.o gd_png.o gdxpm.o gdfontt.o gdfonts.o gdfontmb.o gdfontl.o \ gdfontg.o gdtables.o gdft.o gdttf.o gdcache.o gdkanji.o wbmp.o \ gd_wbmp.o gdhelpers.o gd.h gdfontt.h gdfonts.h gdfontmb.h gdfontl.h \ gdfontg.h gdhelpers.h rm -f libgd.a $(AR) rc libgd.a gd.o gd_gd.o gd_gd2.o gd_io.o gd_io_dp.o \ gd_io_file.o gd_ss.o gd_io_ss.o gd_png.o gdxpm.o \ gdfontt.o gdfonts.o gdfontmb.o gdfontl.o gdfontg.o \ gdtables.o gdft.o gdttf.o gdcache.o gdkanji.o wbmp.o \ gd_wbmp.o gdhelpers.o -ranlib libgd.a #libgd.a: gd.o gd_gd.o gd_gd2.o gd_io.o gd_io_dp.o gd_io_file.o gd_ss.o \ # gd_io_ss.o gd_png.o gd_jpeg.o gdxpm.o gdfontt.o gdfonts.o gdfontmb.o gdfontl.o \ # gdfontg.o gdtables.o gdft.o gdttf.o gdcache.o gdkanji.o wbmp.o \ # gd_wbmp.o gdhelpers.o gd.h gdfontt.h gdfonts.h gdfontmb.h gdfontl.h \ # gdfontg.h gdhelpers.h # rm -f libgd.a # $(AR) rc libgd.a gd.o gd_gd.o gd_gd2.o gd_io.o gd_io_dp.o \ # gd_io_file.o gd_ss.o gd_io_ss.o gd_png.o gd_jpeg.o gdxpm.o \ # gdfontt.o gdfonts.o gdfontmb.o gdfontl.o gdfontg.o \ # gdtables.o gdft.o gdttf.o gdcache.o gdkanji.o wbmp.o \ # gd_wbmp.o gdhelpers.o # -ranlib libgd.a clean: rm -f *.o *.a ${PROGRAMS} test/gdtest.jpg test/gdtest.wbmp -- Johanne Duhaime IRCM 110 Ave des Pins O Montreal, Quebec 987-5556 (tel) 987-5644 (fax) Johanne_Duhaime at ircm.qc.ca http://www.ircm.qc.ca From dmartin at bioinformatics.msiwtb.dundee.ac.uk Wed Feb 13 15:28:04 2002 From: dmartin at bioinformatics.msiwtb.dundee.ac.uk (David Martin) Date: Wed, 13 Feb 2002 15:28:04 +0000 (GMT) Subject: Problem with png driver for emboss In-Reply-To: <3C6A8191.F991A2D8@ircm.qc.ca> Message-ID: On Wed, 13 Feb 2002, Johanne Duhaime wrote: > Hi > > I have problem installing the PNG stuff in order to use graphics in > EMBOSS. > > I have tried to build gd on solaris 2.6 and could not succeed. There is > a message about : gdImageCreateFromPng. > Would you mind to help? I had spent several hours on compiling Png > stuff. I would appreciate very much your help. Last time I did anything on Solaris was at ISMB2001, and it worked flawlessly installing the packages from the solaris freeware site. You may need the libPNG and libz installed before compiling GD. ..d > > Following is the error message, the include and library and finally the > makefile. Thank in advance. > > mercure{root}48: make > gcc -I. -I/usr/include/freetype2 -I/usr/include/X11 > -I/usr/X11R6/include/X11 -I/usr/local/include > -I/opt/sasircm/drivers/drivers/include pngtogd.o -o pngtogd -L. > -L/usr/local/lib -L/usr/lib/X11 -L/usr/X11R6/lib > -L/opt/sasircm/drivers/drivers/lib -L/usr/ucblib -lgd -lpng -lz -lm > Undefined first referenced > symbol in file > gdImageCreateFromPng pngtogd.o > ld: fatal: Symbol referencing errors. No output written to pngtogd > *** Error code 1 > make: Fatal error: Command failed for target `pngtogd' > > > > > > Librairies and include: > total 466 > drwxrwxrwx 2 sasircm sequence 512 Feb 8 15:10 ./ > drwxrwxrwx 4 sasircm sequence 512 Feb 8 14:54 ../ > -rw-r--r-- 1 sasircm sequence 133396 Feb 11 16:32 png.h > -rw-r--r-- 1 sasircm sequence 39838 Feb 11 16:32 pngconf.h > -rw-r--r-- 1 sasircm sequence 7810 Feb 8 14:54 zconf.h > -rw-r--r-- 1 sasircm sequence 40898 Feb 8 14:54 zlib.h > mercure{root}50: l /opt/sasircm/drivers/drivers/lib > total 1058 > drwxrwxrwx 2 sasircm sequence 512 Feb 11 16:32 ./ > drwxrwxrwx 4 sasircm sequence 512 Feb 8 14:54 ../ > -rw-rw-rw- 1 sasircm sequence 205316 Feb 11 16:32 libpng.a > lrwxrwxrwx 1 root other 11 Feb 11 16:32 libpng.so -> > libpng.so.3* > lrwxrwxrwx 1 root other 17 Feb 11 16:32 libpng.so.3 -> > libpng.so.3.1.2.1* > -rwxr-xr-x 1 sasircm sequence 229816 Feb 11 16:32 libpng.so.3.1.2.1* > > -rwxr-xr-x 1 sasircm sequence 70488 Feb 8 14:54 libz.a* > mercure{root}51: > > > Makefile > > mercure{root}59: more Makefile > #Depending on your system, you will need to modify this makefile. > > #If you do not have gcc, change the setting for COMPILER, but you must > #use an ANSI standard C compiler (NOT the old SunOS 4.1.3 cc > #compiler; get gcc if you are still using it). > COMPILER=gcc > > #If the ar command fails on your system, consult the ar manpage > #for your system. > AR=ar > > #If you don't have FreeType, libjpeg and/or Xpm installed, including the > > #header files, uncomment this (default). You really must install > #libpng and zlib to get anywhere if you wish to create PNG images. > #Mis la ligne suivante en commentaire > #CFLAGS=-O -DHAVE_LIBPNG -DHAVE_LIBJPEG > > #If you do have FreeType, libjpeg and/or Xpm fully installed, uncomment > a > #variation of this and comment out the line above. See also LIBS below. > #CFLAGS=-O -DHAVE_LIBXPM -DHAVE_LIBPNG -DHAVE_LIBJPEG \ > # -DHAVE_LIBFREETYPE -DHAVE_LIBTTF > > #To use the old FreeType 1.x library, add this additional #define > #to the line above > #-DHAVE_LIBTTF > > #If you don't have FreeType Xpm fully installed, uncomment this > #(default). > > #PLEASE NOTE: YOU MAY HAVE TO JUGGLE THE ORDER OF THE LIBRARIES. > #Some systems are very picky about link order. They don't all agree > #on the right order, either. > > LIBS=-lgd -lpng -lz -lm > > #If you do have FreeType, JPEG and/or Xpm fully installed, uncomment a > #variation of this and comment out the line above. Note that > #Xpm requires X11. See also CFLAGS above. > > #LIBS=-lgd -lpng -lz -ljpeg -lfreetype -lm -lttf > > #Note: for Freetype 1.x, use DHAVE_LIBTTF and -lttf instead. > > #Typical install locations for freetype, zlib, xpm, libjpeg and libpng > header > #files. If yours are somewhere else, change this. -I. is important to > #ensure that the version of gd you are installing is used, and not an > #older release in your directory tree somewhere. > > INCLUDEDIRS=-I. -I/usr/include/freetype2 -I/usr/include/X11 > -I/usr/X11R6/include/X11 -I/usr/local/include -I/opt/sasircm/drivers/dri > > vers/include > > #Typical install locations for freetype, zlib, xpm and libpng libraries. > > #If yours are somewhere else, other than a standard location > #such as /lib or /usr/lib, then change this. Be sure to keep > #-L. as this allows the gd library itself to be found. > #Put -L. first so that old versions of the gd library elsewhere > #on your system can't cause conflicts while building a new one. > #This line shouldn't hurt if you don't actually have some of the > #optional libraries and directories. > > #LIBDIRS=-L. -L/usr/local/lib -L/usr/lib/X11 -L/usr/X11R6/lib > -L/opt/sasircm/drivers/drivers/lib -L/opt/sasircm/drivers/libpng > LIBDIRS=-L. -L/usr/local/lib -L/usr/lib/X11 -L/usr/X11R6/lib > -L/opt/sasircm/drivers/drivers/lib -L/usr/ucblib > #Location where libgd.a should be installed by "make install". > #INSTALL_LIB=/usr/local/lib > INSTALL_LIB=/opt/sasircm/drivers/drivers/lib > > #Location where .h files should be installed by "make install". > #INSTALL_INCLUDE=/usr/local/include > INSTALL_INCLUDE=/opt/sasircm/drivers/drivers/include > > #Location where useful non-test programs should be installed by "make > install". > #INSTALL_BIN=/usr/local/bin > INSTALL_BIN=/opt/sasircm/drivers/drivers/bin > > # > # > # Changes should not be required below here. > # > # > > VERSION=1.8.4 > > CC=$(COMPILER) $(INCLUDEDIRS) > LINK=$(CC) $(LIBDIRS) $(LIBS) > > PROGRAMS=$(BIN_PROGRAMS) $(TEST_PROGRAMS) > > BIN_PROGRAMS=pngtogd pngtogd2 gdtopng gd2topng gd2copypal gdparttopng > webpng > TEST_PROGRAMS=gdtest gddemo gd2time gdtestft gdtestttf > > all: libgd.a $(PROGRAMS) > > install: libgd.a $(BIN_PROGRAMS) > sh ./install-item 644 libgd.a $(INSTALL_LIB)/libgd.a > sh ./install-item 755 pngtogd $(INSTALL_BIN)/pngtogd > sh ./install-item 755 pngtogd2 $(INSTALL_BIN)/pngtogd2 > sh ./install-item 755 gdtopng $(INSTALL_BIN)/gdtopng > sh ./install-item 755 gd2topng $(INSTALL_BIN)/gd2topng > sh ./install-item 755 gd2copypal $(INSTALL_BIN)/gd2copypal > sh ./install-item 755 gdparttopng $(INSTALL_BIN)/gdparttopng > sh ./install-item 755 webpng $(INSTALL_BIN)/webpng > sh ./install-item 755 bdftogd $(INSTALL_BIN)/bdftogd > sh ./install-item 644 gd.h $(INSTALL_INCLUDE)/gd.h > sh ./install-item 644 gdcache.h $(INSTALL_INCLUDE)/gdcache.h > sh ./install-item 644 gd_io.h $(INSTALL_INCLUDE)/gd_io.h > sh ./install-item 644 gdfontg.h $(INSTALL_INCLUDE)/gdfontg.h > sh ./install-item 644 gdfontl.h $(INSTALL_INCLUDE)/gdfontl.h > sh ./install-item 644 gdfontmb.h $(INSTALL_INCLUDE)/gdfontmb.h > sh ./install-item 644 gdfonts.h $(INSTALL_INCLUDE)/gdfonts.h > sh ./install-item 644 gdfontt.h $(INSTALL_INCLUDE)/gdfontt.h > > gddemo: gddemo.o libgd.a > $(CC) gddemo.o -o gddemo $(LIBDIRS) $(LIBS) > > pngtogd: pngtogd.o libgd.a > $(CC) pngtogd.o -o pngtogd $(LIBDIRS) $(LIBS) > > webpng: webpng.o libgd.a > $(CC) webpng.o -o webpng $(LIBDIRS) $(LIBS) > > pngtogd2: pngtogd2.o libgd.a > $(CC) pngtogd2.o -o pngtogd2 $(LIBDIRS) $(LIBS) > > gdtopng: gdtopng.o libgd.a > $(CC) gdtopng.o -o gdtopng $(LIBDIRS) $(LIBS) > > gd2topng: gd2topng.o libgd.a > $(CC) gd2topng.o -o gd2topng $(LIBDIRS) $(LIBS) > > gd2copypal: gd2copypal.o libgd.a > $(CC) gd2copypal.o -o gd2copypal $(LIBDIRS) $(LIBS) > > gdparttopng: gdparttopng.o libgd.a > $(CC) gdparttopng.o -o gdparttopng $(LIBDIRS) $(LIBS) > > gdtest: gdtest.o libgd.a > $(CC) gdtest.o -o gdtest $(LIBDIRS) $(LIBS) > > gd2time: gd2time.o libgd.a > $(CC) gd2time.o -o gd2time $(LIBDIRS) $(LIBS) > > gdtestft: gdtestft.o libgd.a > $(CC) --verbose gdtestft.o -o gdtestft $(LIBDIRS) $(LIBS) > gdtestttf: gdtestttf.o libgd.a > $(CC) --verbose gdtestttf.o -o gdtestttf $(LIBDIRS) $(LIBS) > > libgd.a: gd.o gd_gd.o gd_gd2.o gd_io.o gd_io_dp.o gd_io_file.o gd_ss.o \ > > gd_io_ss.o gd_png.o gdxpm.o gdfontt.o gdfonts.o gdfontmb.o > gdfontl.o \ > gdfontg.o gdtables.o gdft.o gdttf.o gdcache.o gdkanji.o wbmp.o \ > > gd_wbmp.o gdhelpers.o gd.h gdfontt.h gdfonts.h gdfontmb.h > gdfontl.h \ > gdfontg.h gdhelpers.h > rm -f libgd.a > $(AR) rc libgd.a gd.o gd_gd.o gd_gd2.o gd_io.o gd_io_dp.o \ > gd_io_file.o gd_ss.o gd_io_ss.o gd_png.o gdxpm.o \ > gdfontt.o gdfonts.o gdfontmb.o gdfontl.o gdfontg.o \ > gdtables.o gdft.o gdttf.o gdcache.o gdkanji.o wbmp.o \ > gd_wbmp.o gdhelpers.o > -ranlib libgd.a > > #libgd.a: gd.o gd_gd.o gd_gd2.o gd_io.o gd_io_dp.o gd_io_file.o gd_ss.o > \ > # gd_io_ss.o gd_png.o gd_jpeg.o gdxpm.o gdfontt.o gdfonts.o > gdfontmb.o gdfontl.o \ > # gdfontg.o gdtables.o gdft.o gdttf.o gdcache.o gdkanji.o wbmp.o \ > > # gd_wbmp.o gdhelpers.o gd.h gdfontt.h gdfonts.h gdfontmb.h > gdfontl.h \ > # gdfontg.h gdhelpers.h > # rm -f libgd.a > # $(AR) rc libgd.a gd.o gd_gd.o gd_gd2.o gd_io.o gd_io_dp.o \ > # gd_io_file.o gd_ss.o gd_io_ss.o gd_png.o gd_jpeg.o > gdxpm.o \ > # gdfontt.o gdfonts.o gdfontmb.o gdfontl.o gdfontg.o \ > # gdtables.o gdft.o gdttf.o gdcache.o gdkanji.o wbmp.o \ > # gd_wbmp.o gdhelpers.o > # -ranlib libgd.a > clean: > rm -f *.o *.a ${PROGRAMS} test/gdtest.jpg test/gdtest.wbmp > > > > > -- > Johanne Duhaime > IRCM > 110 Ave des Pins O > Montreal, Quebec > 987-5556 (tel) 987-5644 (fax) > Johanne_Duhaime at ircm.qc.ca > http://www.ircm.qc.ca > > ---------------------------------- David Martin PhD Bioinformatics Scientific Officer Wellcome Trust Biocentre, Dundee ---------------------------------- From David.Bauer at SCHERING.DE Wed Feb 13 17:02:50 2002 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Wed, 13 Feb 2002 18:02:50 +0100 Subject: Antwort: Problem with png driver for emboss Message-ID: Hi, I just had a similar problem with having the png and gd libs in a non standard location on a Solaris system. Did you try to give configure the png lib location? I think in your case this should be: --with-pngdriver=/opt/sasircm/drivers/drivers Also if you look at the output from configure do you see any problem messages about the gdImageCreateFromPng? I hope this helps, David. From jgomez at rz.uni-potsdam.de Thu Feb 14 13:02:09 2002 From: jgomez at rz.uni-potsdam.de (Judit Lucia Gomez) Date: Thu, 14 Feb 2002 14:02:09 +0100 Subject: Databases Message-ID: <3C6BB551.4070107@rz.uni-potsdam.de> I installed EMBOSS on my computer, and when I typed _%showdb_ no one db was displayed, I would like to know if I must install also the databases, or if is any chance to run EMBOSS programs making a link with the databases. Regards Judith Gomez ========================== Judith Lucia Gomez Doktorandin Universit?t Potsdam Institut f?r Biochemie und Biologie AG M?ller-R?ber Arbeitsgruppe Molekularbiologie Karl-liebknecht-Str. 24/25 Haus 20, 1.O4 14476 Golm Germany From David.Bauer at SCHERING.DE Thu Feb 14 13:57:23 2002 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Thu, 14 Feb 2002 14:57:23 +0100 Subject: Antwort: Databases Message-ID: Hi Judit, you need the databases if you want to get sequences directly from there. In /usr/local/share/EMBOSS you find a emboss.default.template. This must be copied to emboss.default and include definitions for databases you have installed locally. There is a nice administration guide from David Martin at http://www.uk.embnet.org/Software/EMBOSS/Doc/Admin_guide/admin.pdf which has an extensive chapter on how to handle databases with emboss. David. |--------+---------------------------> | | Judit Lucia Gomez| | | | | | Gesendet von: | | | owner-emboss at hgmp| | | .mrc.ac.uk | | | | | | | | | 14.02.02 14:02 | | | | |--------+---------------------------> >-----------------------------------------------------------------------| | | | | | | |An: emboss at embnet.org | |Kopie: | |Thema: Databases | >-----------------------------------------------------------------------| I installed EMBOSS on my computer, and when I typed _%showdb_ no one db was displayed, I would like to know if I must install also the databases, or if is any chance to run EMBOSS programs making a link with the databases. Regards Judith Gomez ========================== Judith Lucia Gomez Doktorandin Universit?t Potsdam Institut f?r Biochemie und Biologie AG M?ller-R?ber Arbeitsgruppe Molekularbiologie Karl-liebknecht-Str. 24/25 Haus 20, 1.O4 14476 Golm Germany From mad at biol.unlp.edu.ar Thu Feb 14 13:22:53 2002 From: mad at biol.unlp.edu.ar (Martin Sarachu) Date: Thu, 14 Feb 2002 16:22:53 +0300 Subject: png trouble Message-ID: <3C6BBA2D.EBA334EB@biol.unlp.edu.ar> Hi, I'm using libpng 1.2.0 which was installed as a package from sunfreeware, EMBOSS-2.2.0 on a Sun/Solaris 8 EMBOSS compiled fine but when I exec an application and choose png as the output I get libpng warning: Application was compiled with png.h from libpng-1.0.6 libpng warning: Application is running with png.c from libpng-1.2.0 gd-png: fatal libpng error: Incompatible libpng version in application and library Segmentation Fault (core dumped) Thanks, martin. -- Martin Sarachu ICQ: 123797358 EMBnet Argentina: http://www.ar.embnet.org From ableasby at hgmp.mrc.ac.uk Thu Feb 14 19:49:43 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Thu, 14 Feb 2002 19:49:43 GMT Subject: png trouble Message-ID: <200202141949.TAA17294@bromine.hgmp.mrc.ac.uk> If you have libpng, libz or libgd in /usr/lib then EMBOSS will use it (them) and use only use the --with-pngdriver=dir specification to find any remaining libraries. You can either make sure that any such libraries in /usr/lib are up-to-date or temporarily rename them and use --with-pngdriver=dir to point to an appropriate location where you've compiled them. Similar considerations apply to /usr/local/lib in the case of png support (not quite the same but similar). HTH Alan From mad at biol.unlp.edu.ar Thu Feb 14 15:05:51 2002 From: mad at biol.unlp.edu.ar (Martin Sarachu) Date: Thu, 14 Feb 2002 18:05:51 +0300 Subject: png trouble References: <200202141949.TAA17294@bromine.hgmp.mrc.ac.uk> Message-ID: <3C6BD24F.F548AECD@biol.unlp.edu.ar> Only libz was in both /usr/lib and /usr/local/lib, I've renamed it and now configure does not find libpng, libz and libgd altough they are installed under /usr/local and work fine and I specify --with-pngdriver=/usr/local this is the output > checking if png driver is wanted... yes > checking for inflateEnd in -lz... no > checking for png_destroy_read_struct in -lpng... no > checking for gdImageCreateFromPng in -lgd... no > checking for inflateEnd in -lz... no > checking for inflateEnd in -lz... no > No png driver will be made due to librarys missing/old. martin. ableasby at hgmp.mrc.ac.uk wrote: > > If you have libpng, libz or libgd in /usr/lib then EMBOSS will > use it (them) and use only use the --with-pngdriver=dir > specification to find any remaining libraries. You can either > make sure that any such libraries in /usr/lib are up-to-date > or temporarily rename them and use --with-pngdriver=dir > to point to an appropriate location where you've compiled > them. > > Similar considerations apply to /usr/local/lib in the case of > png support (not quite the same but similar). > > HTH > Alan -- Martin Sarachu ICQ: 123797358 EMBnet Argentina: http://www.ar.embnet.org From GUIDO.STEINER at Roche.COM Fri Feb 15 08:04:54 2002 From: GUIDO.STEINER at Roche.COM (Steiner, Guido {PRBT~Basel}) Date: Fri, 15 Feb 2002 09:04:54 +0100 Subject: png trouble Message-ID: <49D79AF0A39CD511AAFE0002A55CC07A0393706A@rbamsem2.bas.roche.com> After having installed EMBOSS 2.2.0 with png support on SGI IRIX 6.5 (finally with success :) I may add another thing to watch out in case some SGI users face the same problems than I did. If you have the graphics libraries (like libgd) installed in a directory other than /usr/freeware/lib64 (or /usr/freeware/lib32), don't forget to modify the hardcoded library path in the EMBOSS configure file (line 4624, see SGI porting notes at http://www.sgi.com/solutions/sciences/chembio/resources/emboss/porting_notes.html ) accordingly and _remove_ the reference to /usr/freeware if you don't need any library from there, otherwise all EMBOSS applications produce runtime linking errors, no matter what you've specified in the --with-pngdriver option. This cost me some hours to find out, as I was no longer aware of the patching I did in the first place and presumed the error would be in a completely different place. Guido Steiner From GUIDO.STEINER at Roche.COM Fri Feb 15 08:13:32 2002 From: GUIDO.STEINER at Roche.COM (Steiner, Guido {PRBT~Basel}) Date: Fri, 15 Feb 2002 09:13:32 +0100 Subject: EMBOSS produces an error when doing wildcard searches Message-ID: <49D79AF0A39CD511AAFE0002A55CC07A0393706B@rbamsem2.bas.roche.com> Dear all, has anybody else experienced problems when iterating over a database with a wildcard search? For example, when I state infoseq embl:\* , everything works as expected, but when I say infoseq embl:p\* , after a while the output stops and the following error message is displayed: EMBOSS An error in ajseqdb.c at line 2550: Cannot open sequence file 'em_in2_000.seq' Of course this file exists and is not corrupted. Since other commands like seqret show the same behaviour, the problem really seems to be in the ajax library. Setup: EMBOSS 2.2.0 (64 bit build) on IRIX 6.5 from uname -a: IRIX64 rbaw20 6.5 10100655 IP27 from hinv: ... 16 400 MHZ IP27 Processors CPU: MIPS R12000 Processor Chip Revision: 3.5 FPU: MIPS R12010 Floating Point Chip Revision: 3.5 Main memory size: 4096 Mbytes ... Thanks for any help. Guido Steiner From GUIDO.STEINER at Roche.COM Fri Feb 15 08:50:24 2002 From: GUIDO.STEINER at Roche.COM (Steiner, Guido {PRBT~Basel}) Date: Fri, 15 Feb 2002 09:50:24 +0100 Subject: Linking issue (TOPO-0.1) Message-ID: <49D79AF0A39CD511AAFE0002A55CC07A0393706C@rbamsem2.bas.roche.com> If I'm allowed to post once more (I promise this will be the last problem submitted today :-).... When trying to compile Topo 0.1 (of the EMBASSY package) with png support enabled, I get a linking error as follows: ld64: ERROR 33: Unresolved text symbol "floor" -- 1st referenced by /soft/bi/pdsoft64/lib/libgd.a(gd.o). Use linker option -v to see when and which objects, archives and dsos are loaded. ld64: ERROR 33: Unresolved text symbol "pow" -- 1st referenced by ./ldtmpa1gUXE/libpng.a(pngrtran.o).o. Use linker option -v to see when and which objects, archives and dsos are loaded. ld64: INFO 152: Output file removed because of error. This seems to be due to the fact that the math libraries are linked in the wrong order. The following is done: cc -O -L/soft/bi/pdsoft64/lib -o topo topo.o ../../../ajax/libajaxg.la ../../../ajax/libajax.la ../../../plplot/libplplot.la -lX11 -lsocket -lm -lgd -lpng -lz And what should be actually done (IMHO): cc -O -L/soft/bi/pdsoft64/lib -o topo topo.o ../../../ajax/libajaxg.la ../../../ajax/libajax.la ../../../plplot/libplplot.la -lX11 -lsocket -lgd -lpng -lz -lm The configure script, however, proofed resistant to my efforts in altering the linking order. I just don't see how the LIBS variable is put together. Ideas anyone? :) Guido Steiner From ableasby at hgmp.mrc.ac.uk Fri Feb 15 09:39:04 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Fri, 15 Feb 2002 09:39:04 GMT Subject: Linking issue (TOPO-0.1) Message-ID: <200202150939.JAA20172@bromine.hgmp.mrc.ac.uk> I've put a replacement ftp://ftp.uk.embnet.org/pub/EMBOSS/TOPO-0.1.tar.gz on the server. This ought to clear your problem. If it doesn't then let me know directly. Cheers Alan From H.Davidson at ed.ac.uk Fri Feb 15 12:47:17 2002 From: H.Davidson at ed.ac.uk (Heather Davidson) Date: Fri, 15 Feb 2002 12:47:17 +0000 Subject: restrict and supermatcher Message-ID: <3C6D0355.1ABF1D5F@ed.ac.uk> I would like to know how to use supermatcher. I have used matcher with no problems. I want to compare one long sequence against a lot of other smaller sequences. In GCG one made a file of filenames of the smaller sequences and the comparison was done all at once. I do not know how to do this on supermatcher and the help does not help. Also I have used restrict but the output is not what I want. Basically I want an output like mapsort in GCG and I have asked support at HGMP and they cannot help either. I want the enzymes listed alphabetically ( which I know it does fine except it does a long line instead of across the paper) and with the site location but then with the size of fragments produced from that digest listed underneath I have only used emboss twice and each time I cannot get what I used to be able to get effortlessly from GCG Thanks Heather -- Heather Davidson Lab Manager | Email: Mailto:H.Davidson at ed.ac.uk Medical Genetics Section | WWW: http://www.ed.ac.uk Department of Medical Sciences | Fax: +44 (0)131 651 1059 The University of Edinburgh | Phone: +44 (0)131 651 1042 Molecular Medicine Centre Western General Hospital Crewe Road Edinburgh EH4 2XU From peter.rice at uk.lionbioscience.com Fri Feb 15 13:02:38 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Fri, 15 Feb 2002 13:02:38 +0000 Subject: restrict and supermatcher References: <3C6D0355.1ABF1D5F@ed.ac.uk> Message-ID: <3C6D06EE.5B785692@uk.lionbioscience.com> Heather Davidson wrote: > > I would like to know how to use supermatcher. I have used matcher with > no problems. I want to compare one long sequence against a lot of other > smaller sequences. In GCG one made a file of filenames of the smaller > sequences and the comparison was done all at once. I do not know how to > do this on supermatcher and the help does not help. The file of filenames is a VMS concept ... used by GCG and by EMBOSS. Put the filenames into a list, and use @filename on the command line. There are some known problems (for example if a file does not exist, or with complicated USAs or nested files of filenames) but as a simple list it should be fine. > Also I have used restrict but the output is not what I want. Basically I > want an output like mapsort in GCG and I have asked support at HGMP and > they cannot help either. I want the enzymes listed alphabetically ( > which I know it does fine except it does a long line instead of across > the paper) and with the site location but then with the size of > fragments produced from that digest listed underneath Interesting .... Restrict now produces a feature report, with a qualifier 'enzyme'. (Try 'restrict -rf embl' to see what is really happening inside). What you really are asking is to sort the report output by a named column/qualifier. This is quite easy to implement ... a sort by one or more qualifiers (internal or printed names) and then by start/end position. Once implemented, this would apply to all EMBOSS programs that have the new 'report' output .... this will grow to include all programs that generate sequence annotation. For restrict, it would be a command line option: % restrict -rsort enzyme (as they are in the feature table, you could also sort by 5prime instead of the start of the site match) Report qualifiers never have spaces, so a list of names with spaces would be fine. ACD sees the full list of report columns/qualifiers, so EMBOSS can give an error message at the start of the program. > I have only used emboss twice and each time I cannot get what I used to > be able to get effortlessly from GCG Ah, you should perhaps not expect to get what GCG gives you!!! Remember, with EMBOSS you can effortlessly get things that GCG cannot do ... ... and that includes some requests for new features :-) regards, Peter Rice -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From mathog at mendel.bio.caltech.edu Fri Feb 15 16:53:44 2002 From: mathog at mendel.bio.caltech.edu (David Mathog) Date: Fri, 15 Feb 2002 08:53:44 -0800 Subject: EMBOSS produces an error when doing wildcard searches Message-ID: > > Dear all, > > has anybody else experienced problems when iterating over a database with a wildcard search? > For example, when I state > infoseq embl:\* , > everything works as expected, but when I say > infoseq embl:p\* , > after a while the output stops and the following error message is displayed: It doesn't work here either. EMBOSS-2.2.0 on Solaris 5.8 on a Sparc. We keep our Genbank database in GCG format. It was indexed with: dbigcg -dbname genbank \ -directory $WORKDIR \ -indexdirectory $EMBOSSINDEXDIR \ -release "$THERELEASE" \ -date "$THEMONTH/$THEDAY/$THE2YEAR" \ -idformat GENBANK \ -filename "*.seq" When this is run: % infoseq genbank:\* -outfile=/tmp/testwild.txt it stops (no error messages) after 32993 lines with the last entry at: AC003118 which is just slightly into gb_htg. More interestingly: wc /export/home/gcg/data/gcggenbank/*seqcat 32940 417123 3441822 /export/home/gcg/data/gcggenbank/gb_ba.seqcat 93349 1323961 11229588 /export/home/gcg/data/gcggenbank/gb_htg.seqcat 108723 1578814 13275437 /export/home/gcg/data/gcggenbank/gb_in.seqcat 32993 - 32940 = 53. Looks like the indexing lookup functions do not transition properly from one file to another. Or it could be a signed short is used somewhere it shouldn't since 32993 isn't that much more than 32768. Or maybe it's a memory leak? Run it again and watch the process... Doesn't look like it, it grew slowly to (top output): 22941 root 1 0 10 9552K 5968K run 2:14 98.31% infoseq and stabilized there. So not a memory leak. Let the run complete and see if it fails at the same place... Yes, it did. Is it just infoseek or other programs as well? Try fuzznuc with: % fuzznuc -sequence=genbank:\* '-pattern=' -outf=fuzznucout.txt -mismatch=0 That works. Let's see where it stops... Looks bad folks, the output file has 32992 lines this time and the last line is, you guessed it: AC003118 94882 G Definitely a bug in the low level wildcard retrieval routines somewhere. Alan, please move this one way up the priority list - it probably means all wildcarded database operations are broken. The worst part is that here these are failing as if they were completing normally - there are no error messages to tip off the user that things have gone wrong. Regards, David Mathog mathog at caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech From melsonr at earthlink.net Fri Feb 15 20:27:46 2002 From: melsonr at earthlink.net (Bob Melson) Date: Fri, 15 Feb 2002 13:27:46 -0700 Subject: Installation woes Message-ID: <3C6D6F42.1020900@earthlink.net> I've been trying to configure, compile and install v2.2.0 on a NetBSD system for the last couple of days with less than satisfactory results. The basic problem appears to be that the created Makefile doesn't link in the X11 libraries, no matter how they're specified in the configure session. I've included the flags "--x-libraries=/usr/X11R6/lib" and "--x-includes=/usr/X11R6/include" (no success); I've accepted default values by _not_ including the flags, I've specified "--with-x", I've ignored it. I've even gone so far as to hand edit the Makefile after configure, all to no avail. Each time I try to run, e.g. wossname, I get the error message "Shared object "libX11.so.6" not found" and if I run "ldd wossname", I get the following message: /usr/pkg/emboss/bin/wossname: -lnucleus.1 => /usr/pkg/emboss/lib/libnucleus.so.1 -lajaxg.1 => /usr/pkg/emboss/lib/libajaxg.so.1 -lajax.1 => /usr/pkg/emboss/lib/libajax.so.1 -lplplot.5 => /usr/pkg/emboss/lib/libplplot.so.5 -lX11.6 => not found -lm.0 => /usr/lib/libm387.so.0 -lm.0 => /usr/lib/libm.so.0 -lc.12 => /usr/lib/libc.so.1"fix" this problem? As you can see, all libraries _except_ the libX11 library are linked in at compile time. It goes without saying that I'm about at my wits end. Anybody have any ideas what I might do to "fix" this problem? ADVA{thanks}NCE, Bob Melson Dept. of Biology NM State University Las Cruces, NM, USA From ableasby at hgmp.mrc.ac.uk Sat Feb 16 23:02:46 2002 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Sat, 16 Feb 2002 23:02:46 GMT Subject: Installation woes Message-ID: <200202162302.XAA01961@bromine.hgmp.mrc.ac.uk> Bob, The problem is the way your system is configured rather than an EMBOSS one. You've got two choices: 1) setenv LD_LIBRARY_PATH /usr/X11R6/lib or 2) Add the following on a line of its own at the end of /etc/ld.so.conf /usr/X11R6/lib Then type 'ldconfig' I'm assuming you have a fairly standard NetBSD 1.52-ish system. There may be even more choices but, being from a SYSV background, I'll leave someone else to mention them. Option 2 is probably the best. HTH Alan From gilbertd at bio.indiana.edu Sun Feb 17 02:23:32 2002 From: gilbertd at bio.indiana.edu (Don Gilbert) Date: Sat, 16 Feb 2002 21:23:32 -0500 (EST) Subject: macosx install note Message-ID: <200202170223.VAA25966@cricket.bio.indiana.edu> Dear emboss folks, |i saw you acknowledged in the emboss admin file for having worked out |the modifications required for installing it on mac os x (page 10 of |the guide at http://www.hgmp.mrc.ac.uk/Software/EMBOSS/admin.html). The current release of emboss (2.2.0 or later) doesn't need those instructions for compiling on macosx; newer configuration software handles macosx without any edits to files. You can also find a compiled version of emboss for macosx at ftp://iubio.bio.indiana.edu/biogrid/bioapps/bin/ as emboss-2.2.0-powerpc-apple-darwin5.1-gcc.tar.gz Unpack this from a terminal window to some folder of your choice with gnutar -zxf emboss-2.2.0-powerpc-apple-darwin5.1-gcc.tar.gz or double-clicking the .tar.gz file from macosx finder should unpack via unstuffit. then from terminal window, source the emboss/setenv file for emboss environment settings, and test, as with wossname -- Don Gilbert -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd at bio.indiana.edu From charles at moulinette.dyndns.org Fri Feb 22 09:51:31 2002 From: charles at moulinette.dyndns.org (Charles Plessy) Date: Fri, 22 Feb 2002 10:51:31 +0100 Subject: searching local databases Message-ID: <20020222095131.GA26315@moulinette.dyndns.org> Hello, In GCG, i used to make a local blast database from a few hundred of sequences coming from a screen (for example), in order to be able to use gcg's databese searching tools on it. With emboss, i have built a local index of fasta files and modified my ~/.embossrc so that i can access them with the db:ID syntax. I am now stuck. Could anyone point me to ressources explaining how I can install fasta or blast on my linux, and how to instruct those guys to use my homemade emboss fasta database?? Thank you, Charles From dmartin at bioinformatics.msiwtb.dundee.ac.uk Fri Feb 22 11:07:35 2002 From: dmartin at bioinformatics.msiwtb.dundee.ac.uk (David Martin) Date: Fri, 22 Feb 2002 11:07:35 +0000 (GMT) Subject: searching local databases In-Reply-To: <20020222095131.GA26315@moulinette.dyndns.org> Message-ID: On Fri, 22 Feb 2002, Charles Plessy wrote: > Hello, > > In GCG, i used to make a local blast database from a few hundred of > sequences coming from a screen (for example), in order to be able to > use gcg's databese searching tools on it. > > With emboss, i have built a local index of fasta files and modified my > ~/.embossrc so that i can access them with the db:ID syntax. > > I am now stuck. Could anyone point me to ressources explaining how I > can install fasta or blast on my linux, and how to instruct those guys > to use my homemade emboss fasta database?? I have a tutorial to do just this.. There are a few slightly misleading bits in it (section ordering mostly) but otherwise it is fine. It doesn't cover installing BLAST, use the readme from NCBI for that. those who are interested can email me for a copy (pdf). It requires NCBI Blast and EMBOSS with the Swissprot database installed. ..d > > Thank you, > > Charles > ---------------------------------- David Martin PhD Bioinformatics Scientific Officer Wellcome Trust Biocentre, Dundee ---------------------------------- From dmartin at bioinformatics.msiwtb.dundee.ac.uk Fri Feb 22 13:39:55 2002 From: dmartin at bioinformatics.msiwtb.dundee.ac.uk (David Martin) Date: Fri, 22 Feb 2002 13:39:55 +0000 (GMT) Subject: BLAST tutorial. Message-ID: I have been snowed under with requests. I have sent a copy of the Blast tutorial and an advanced Unix tutorial (more of a what it can do than a true tutorial) to Gary and asked him to make them available via the EMBOSS ftp site. He will confirm this with a URL in due course. The advanced unix tutorial uses analysis of PDB files as a scenario but can be applied to anything appropriate. Unfortunately the PDF I sent out initially to some of you is not complete. Gary has the complete one. ..d ---------------------------------- David Martin PhD Bioinformatics Scientific Officer Wellcome Trust Biocentre, Dundee ---------------------------------- From gwilliam at hgmp.mrc.ac.uk Fri Feb 22 13:56:01 2002 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Fri, 22 Feb 2002 13:56:01 +0000 Subject: BLAST tutorial. References: Message-ID: <3C764DF1.D4D99F5B@hgmp.mrc.ac.uk> The Blast setup tutorial and the advanced UNIX guide are now available at: ftp://ftp.uk.embnet.org/pub/EMBOSS/tutorials/ in the files: adv_unix_tut.pdf blasttut.pdf Gary David Martin wrote: > > I have been snowed under with requests. I have sent a copy of the Blast > tutorial and an advanced Unix tutorial (more of a what it can do than a > true tutorial) to Gary and asked him to make them available via the EMBOSS > ftp site. He will confirm this with a URL in due course. > > The advanced unix tutorial uses analysis of PDB files as a scenario but > can be applied to anything appropriate. > > Unfortunately the PDF I sent out initially to some of you is not complete. > Gary has the complete one. > > ..d > > ---------------------------------- > David Martin PhD > Bioinformatics Scientific Officer > Wellcome Trust Biocentre, Dundee > ---------------------------------- -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From peter.rice at uk.lionbioscience.com Fri Feb 22 19:28:33 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Fri, 22 Feb 2002 19:28:33 +0000 Subject: EMBOSS produces an error when doing wildcard searches References: Message-ID: <3C769BE1.76952726@uk.lionbioscience.com> Hi David, Got the files thanks. No time to test them, but ... The first entry after AC003118 is the first split entry (in 8 parts). I think shorts are innocent. Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From charles at moulinette.dyndns.org Sat Feb 23 16:26:57 2002 From: charles at moulinette.dyndns.org (Charles Plessy) Date: Sat, 23 Feb 2002 17:26:57 +0100 Subject: searching local databases In-Reply-To: References: <20020222095131.GA26315@moulinette.dyndns.org> Message-ID: <20020223162657.GA5129@gizmotronics.dyndns.org> > > I am now stuck. Could anyone point me to resources explaining how I > > can install fasta or blast on my linux, and how to instruct those guys > > to use my homemade emboss fasta database?? > > I have a tutorial to do just this.. There are a few slightly misleading > bits in it (section ordering mostly) but otherwise it is fine. First, thank you for your helpful tutorials. I succeeded in creating a blast DB, and indexing it. I modified my .embossrc in order to access it with seqret. However, I'm only able to access blast databases in the ncbi format ; how can I avoid reformatting the headers to something like >lcl|accession ? What are the other accepted formats? Charles From David.Bauer at SCHERING.DE Tue Feb 26 10:28:21 2002 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Tue, 26 Feb 2002 11:28:21 +0100 Subject: seqret via url with spaces Message-ID: Hi, to retrieve sequences from a local server I need to specify the folowing url: ...../www_find.cgi?-e+'{GENESEQ}:[([AccNumber%20EQ%20text:%s;])]' If I do this in emboss.default, than ajstr complains with: Uncaught exception: Allocation bad byte count, raised at ajstr.c:368 So what is the right way to code the spaces? Thanks, David. P.S. I have not written the www_find.cgi...... From peter.rice at uk.lionbioscience.com Tue Feb 26 11:04:46 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 26 Feb 2002 11:04:46 +0000 Subject: seqret via url with spaces References: Message-ID: <3C7B6BCE.1CF2FF26@uk.lionbioscience.com> David.Bauer at SCHERING.DE wrote: > ...../www_find.cgi?-e+'{GENESEQ}:[([AccNumber%20EQ%20text:%s;])]' > If I do this in emboss.default, than ajstr complains with: > Uncaught exception: Allocation bad byte count, raised at ajstr.c:368 > > So what is the right way to code the spaces? This is an ANSI C format to print the %s string. You need %%20 for the other % signs. These convert to single '%' for the URL that is used. -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From David.Bauer at SCHERING.DE Tue Feb 26 12:25:18 2002 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Tue, 26 Feb 2002 13:25:18 +0100 Subject: Antwort: Re: seqret via url with spaces Message-ID: Thanks, it works but I had to do another change. The opening [({ are fine but the closing ])} get an aditional space inbetween them before they are passed to the web server (as I can see in the .dbg file). I had to code them as %%5D etc. David. Peter Rice Gesendet von: An: David.Bauer at SCHERING.DE owner-emboss at hgmp.mrc.ac Kopie: emboss at embnet.org .uk Thema: Re: seqret via url with spaces 26.02.02 12:04 David.Bauer at SCHERING.DE wrote: > ...../www_find.cgi?-e+'{GENESEQ}:[([AccNumber%20EQ%20text:%s;])]' > If I do this in emboss.default, than ajstr complains with: > Uncaught exception: Allocation bad byte count, raised at ajstr.c:368 > > So what is the right way to code the spaces? This is an ANSI C format to print the %s string. You need %%20 for the other % signs. These convert to single '%' for the URL that is used. -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From peter.rice at uk.lionbioscience.com Tue Feb 26 12:41:12 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Tue, 26 Feb 2002 12:41:12 +0000 Subject: Antwort: Re: seqret via url with spaces References: Message-ID: <3C7B8268.757309E6@uk.lionbioscience.com> David.Bauer at SCHERING.DE wrote: > it works but I had to do another change. > > The opening [({ are fine but the closing ])} get an aditional space > inbetween them before they are passed to the web server > (as I can see in the .dbg file). > I had to code them as %%5D etc. > David.Bauer at SCHERING.DE wrote: > > ...../www_find.cgi?-e+'{GENESEQ}:[([AccNumber%20EQ%20text:%s;])]' The cause is the use of '' inside a "" string. Fixed in the next release. Your change will still work. Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From charles at moulinette.dyndns.org Wed Feb 27 06:31:46 2002 From: charles at moulinette.dyndns.org (Charles Plessy) Date: Wed, 27 Feb 2002 07:31:46 +0100 Subject: blast frontend? Message-ID: <20020227063146.GA838@gizmotronics.dyndns.org> Hello, Is there somewhere in emboss a blast frontend that would allow to call (t)blastn,p,x with USA as input parameter, and/or being asked questions interactively ? Charles From peter.rice at uk.lionbioscience.com Wed Feb 27 09:54:47 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 27 Feb 2002 09:54:47 +0000 Subject: blast frontend? References: <20020227063146.GA838@gizmotronics.dyndns.org> Message-ID: <3C7CACE7.F9236750@uk.lionbioscience.com> Charles Plessy wrote: > > Is there somewhere in emboss a blast frontend that would allow to call > (t)blastn,p,x with USA as input parameter, and/or being asked > questions interactively ? Not yet ... but I did make plans some time back to integrate 3rd party applications under an ACD interface. We have this with emma (clustalw) and eprimer3 (primer3) but they gather up the oprions and make an internal system call. The idea was to run something like 'acdc' (nothing more than an embInit call) that simply runs through the ACD interface and then starts up a program. For blast this means renaming command line options, and it stalled a little on how to specify the new command line ... but really that just needs a simple specification and a simple parser. This application even had a name: emboss (so you could run 'emboss blastp' for example). If there is interest, we could revive this. Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From gbottu at ben.vub.ac.be Wed Feb 27 13:18:20 2002 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Wed, 27 Feb 2002 14:18:20 +0100 (CET) Subject: blast frontend? Message-ID: <200202271318.OAA0001538214@ben.vub.ac.be> from : BEN Peter Rice wrote: > Not yet ... but I did make plans some time back to integrate 3rd party > applications under an ACD interface. We have this with emma (clustalw) and > eprimer3 (primer3) but they gather up the oprions and make an internal > system call. The idea was to run something like 'acdc' (nothing more than > an embInit call) that simply runs through the ACD interface and then starts > up a program. For blast this means renaming command line options, and it > stalled a little on how to specify the new command line ... but really that > just needs a simple specification and a simple parser. This application > even had a name: emboss (so you could run 'emboss blastp' for example). An easy way to integrate applications under EMBOSS is certainly welcome. Parsing the ACD file and writing a command line is however not enough. It should be possible to take sequences and other data in EMBOSS style and pass them over in the appropriate format to the application. Guy Bottu From peter.rice at uk.lionbioscience.com Wed Feb 27 13:48:11 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Wed, 27 Feb 2002 13:48:11 +0000 Subject: blast frontend? References: <200202271318.OAA0001538214@ben.vub.ac.be> Message-ID: <3C7CE39B.B8E5D8C5@uk.lionbioscience.com> Guy Bottu wrote: > An easy way to integrate applications under EMBOSS is certainly welcome. > Parsing the ACD file and writing a command line is however not enough. > It should be possible to take sequences and other data in EMBOSS > style and pass them over in the appropriate format to the application. This is where things get just a little complicated. We need to convert, for example, the input sequence into a format blast can use. Fortunately a simple conversion to FASTA format will work for most applications (either directly, or by piping in the output of seqret ... though if it is from stdin a little care may be needed). A list of possible third party applications would be helpful. blast and fasta as starters I assume. -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From David.Bauer at SCHERING.DE Thu Feb 28 06:56:11 2002 From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE) Date: Thu, 28 Feb 2002 07:56:11 +0100 Subject: transeq frame list Message-ID: Hi, transeq -help says that -frame should be a list. But if I specify -frame=1,2,3 it crashes with segmentation fault and no visible error in the debug file. The last message there is that it correctly recognised the frame list. It seems frame can only be a character. In fact it is OK because there is the F as alias for 1,2,3 but -help should give the correct type. Ciao, David. From peter.rice at uk.lionbioscience.com Thu Feb 28 10:13:21 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Thu, 28 Feb 2002 10:13:21 +0000 Subject: transeq frame list References: Message-ID: <3C7E02C1.FEDBF198@uk.lionbioscience.com> David.Bauer at SCHERING.DE wrote: > > transeq -help says that -frame should be a list. > But if I specify -frame=1,2,3 it crashes with segmentation fault > and no visible error in the debug file. > The last message there is that it correctly recognised the frame list. > It seems frame can only be a character. > In fact it is OK because there is the F as alias for 1,2,3 > but -help should give the correct type. Ah, small problem with the English language. In EMBOSS, a 'list' is a list of values with short names. 'Select' is a list of values with no short name but with generated numbers (so far only embossdata uses this type). 'Lists' can take a 'list of values' (1,2,3) if they allow more than one value to be set. Transeq only allows a maximum of 1. Frame can be 1, 2, 3, -1, -2, -3, F, R, "Forward" or "Reverse". (Long names are given for "F" and "R". The long form for "1" is "1"). The simple solution is: 1. Fix the segmentation fault (strangely, it is in a debug messsage call in processing the list value - the array element passed in the call does not exist :-) 2. Change the help message for lists and selects to explain "Choose 1 from a list of values" or "Choose up to 4 from a list of values". 3. Look again at long names. The long name for "F" is really "Forward three frames" but if you put this on the command line, the spaces maked it 3 items "Forward", "Three" and "Frames". As lists and selects normally allow only 1 value, this can change to force 3 values to use the comma, something like -frame=1,2,3 and to not allow -frame="1 2 3". Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From gwilliam at hgmp.mrc.ac.uk Thu Feb 28 10:19:55 2002 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 28 Feb 2002 10:19:55 +0000 Subject: transeq frame list References: <3C7E02C1.FEDBF198@uk.lionbioscience.com> Message-ID: <3C7E044B.BC3B1765@hgmp.mrc.ac.uk> Peter Rice wrote: > > David.Bauer at SCHERING.DE wrote: > > > > transeq -help says that -frame should be a list. > > But if I specify -frame=1,2,3 it crashes with segmentation fault > > and no visible error in the debug file. > > The last message there is that it correctly recognised the frame list. > > It seems frame can only be a character. > > In fact it is OK because there is the F as alias for 1,2,3 > > but -help should give the correct type. > > Ah, small problem with the English language. David has also suggested a change of the name of ACD type 'list' to be 'menu'. This would break lots of parsers, but perhaps we could keep the ACD type 'list' in the .acd files, but the name 'list' could be changed to be 'menu' when displaying -help? -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From gwilliam at hgmp.mrc.ac.uk Thu Feb 28 10:53:53 2002 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 28 Feb 2002 10:53:53 +0000 Subject: transeq frame list References: Message-ID: <3C7E0C41.8721CD1@hgmp.mrc.ac.uk> David.Bauer at SCHERING.DE wrote: > > Hi, > > transeq -help says that -frame should be a list. > But if I specify -frame=1,2,3 it crashes with segmentation fault and no visible > error in the debug file. > The last message there is that it correctly recognised the frame list. > It seems frame can only be a character. > In fact it is OK because there is the F as alias for 1,2,3 but -help should give > the correct type. > > Ciao, David. I have changed transeq's '-frame' qualifier so that it can take one or more frame values, as: -frame=1,2,3 The transeq.c and transeq.acd files are available from: ftp://ftp.uk.embnet.org/pub/EMBOSS/patchfiles/ Gary -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From peter.rice at uk.lionbioscience.com Thu Feb 28 12:21:16 2002 From: peter.rice at uk.lionbioscience.com (Peter Rice) Date: Thu, 28 Feb 2002 12:21:16 +0000 Subject: transeq frame list References: <3C7E0C41.8721CD1@hgmp.mrc.ac.uk> Message-ID: <3C7E20BC.1033DDA1@uk.lionbioscience.com> "Gary Williams, Tel 01223 494522" wrote: > > David.Bauer at SCHERING.DE wrote: > > > > transeq -help says that -frame should be a list. > > But if I specify -frame=1,2,3 it crashes with segmentation fault > > and no visible error in the debug file. > > The last message there is that it correctly recognised the frame list. > > It seems frame can only be a character. > > In fact it is OK because there is the F as alias for 1,2,3 > > but -help should give the correct type. > > I have changed transeq's '-frame' qualifier so that it can take one or > more frame values: OK. I tested it. -frame=1,2,3 gives the same results as -frame=f > David has also suggested a change of the name of ACD type 'list' > to be 'menu'. > > This would break lots of parsers, but perhaps we could keep the > ACD type 'list' in the .acd files, but the name 'list' could be > changed to be 'menu' when displaying -help? Done. Lists will say 'menu list' in messages, and 'menu' in the help output. Selects will say 'selection list'. Also, the error message for a bad list or select option will include the valid options (for lists this is the short code). For example: % transeq tembl:paamir -frame=4 Translate nucleic acid sequences Error: '4' is not a valid menu option Accepted short codes are: 1,2,3,F,-1,-2,-3,R,6 Error: Bad menu option '4' The list and select options must be in a comma-separated list (-frame=1,2,3). White space was allowed up to now (-frame="1 2 3"), but I think is rarely used (it is easy to turn on again). Now you can use: % transeq -frame="Forward three frames" ... which is the long name for 'F' in the ACD file. Users never see these unless they are prompted for a required/optional value, as for example in msbar which has 3 prompted lists (menus). The list/menu and message changes are all in ajax/ajacd.c ... which can be added to the patchfiles although I suspect we are close to a new release anyway. Peter -- ------------------------------------------------ Peter Rice, LION Bioscience Ltd, Cambridge, UK peter.rice at uk.lionbioscience.com +44 1223 224723 From mad at biol.unlp.edu.ar Thu Feb 28 08:37:02 2002 From: mad at biol.unlp.edu.ar (Martin Sarachu) Date: Thu, 28 Feb 2002 11:37:02 +0300 Subject: Jemboss Message-ID: <3C7DEC2E.54789265@biol.unlp.edu.ar> I'm using EMBOSS-2.2.0 on Sparc/Solaris 8, with j2sdk1.4.0 besides the built-in java that came with solaris. When trying to compile Jemboss I do %/usr/j2sdk1.4.0/bin/javac org/emboss/jemboss/server/JembossServer.java I get >org/emboss/jemboss/server/JembossServer.java:499: cannot resolve symbol >symbol : class JembossThread >location: class org.emboss.jemboss.server.JembossServer > JembossThread jt = new JembossThread(rea.getProcess(),project); > ^ >org/emboss/jemboss/server/JembossServer.java:499: cannot resolve symbol >symbol : class JembossThread >location: class org.emboss.jemboss.server.JembossServer > JembossThread jt = new JembossThread(rea.getProcess(),project); > ^ >2 errors EMBOSS was configured --with-java=/usr/j2sdk1.4.0/include --with-javaos=/usr/j2sdk1.4.0/include/solaris, it compiled fine and runs ok. I didn't remove the java packages that came with solaris, I don't know if this can be a problem. martin -- Martin Sarachu ICQ: 123797358 EMBnet Argentina: http://www.ar.embnet.org