From jonathan_lim at merck.com Fri Sep 1 09:33:17 2006 From: jonathan_lim at merck.com (Lim, Jonathan) Date: Fri, 1 Sep 2006 09:33:17 -0400 Subject: [emboss-dev] FW: Perl parser for palindrome Message-ID: <95305ACDD8A44246A0720B446ED4D28A65D4C7@camtmx1100.merck.com> > Hello, > I've been trying to get the bioperl's Bio::Tools::EMBOSS::Palindrome > module to work with the palindrome program from EMBOSS 4. > I've had no luck so far - the output file is always empty. I'm using > the latest bioperl-live version, but it looks like there haven't been > any significant changes to the module since it was written back in > 2003. This leads me to believe that the module will only work with an > old version of palindrome. > I'm wondering if anyone has gotten this to work or knows of an > alternate perl parser/wrapper that would work with the newest > palindrome. > Thanks > > Jonathan > ------------------------------------------------------------------------------ Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. ------------------------------------------------------------------------------ From jison at ebi.ac.uk Mon Sep 4 07:29:31 2006 From: jison at ebi.ac.uk (Jon Ison) Date: Mon, 4 Sep 2006 12:29:31 +0100 (BST) Subject: [emboss-dev] FW: Perl parser for palindrome In-Reply-To: <95305ACDD8A44246A0720B446ED4D28A65D4C7@camtmx1100.merck.com> References: <95305ACDD8A44246A0720B446ED4D28A65D4C7@camtmx1100.merck.com> Message-ID: <48297.172.31.70.94.1157369371.squirrel@webmail.ebi.ac.uk> Hi Jonathan I haven't come across an updated Perl module. There have been some discussions about generating automatically foreign language bindings to the EMBOSS applications (which would keep things up to date) and you can expect some progress along these lines next year, but after the release. Cheers Jon > >> Hello, >> I've been trying to get the bioperl's Bio::Tools::EMBOSS::Palindrome >> module to work with the palindrome program from EMBOSS 4. >> I've had no luck so far - the output file is always empty. I'm using >> the latest bioperl-live version, but it looks like there haven't been >> any significant changes to the module since it was written back in >> 2003. This leads me to believe that the module will only work with an >> old version of palindrome. >> I'm wondering if anyone has gotten this to work or knows of an >> alternate perl parser/wrapper that would work with the newest >> palindrome. >> Thanks >> >> Jonathan >> > > ------------------------------------------------------------------------------ > Notice: This e-mail message, together with any attachments, contains > information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, > New Jersey, USA 08889), and/or its affiliates (which may be known > outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD > and in Japan, as Banyu - direct contact information for affiliates is > available at http://www.merck.com/contact/contacts.html) that may be > confidential, proprietary copyrighted and/or legally privileged. It is > intended solely for the use of the individual or entity named on this > message. If you are not the intended recipient, and have received this > message in error, please notify us immediately by reply e-mail and then > delete it from your system. > > ------------------------------------------------------------------------------ > _______________________________________________ > emboss-dev mailing list > emboss-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss-dev > From liushiyong at gmail.com Sun Sep 24 18:25:46 2006 From: liushiyong at gmail.com (Liu Shiyong) Date: Sun, 24 Sep 2006 17:25:46 -0500 Subject: [emboss-dev] help on building EMBOSS Message-ID: Dear all, I download CVS version and want to build EMBOSS in my Ubuntu(Linux protein 2.6.15-27-686 #1 SMP PREEMPT Sat Sep 16 02:13:27 UTC 2006 i686 GNU/Linux ) system. I got the following error information: gcc -O2 -o cons cons.o ../nucleus/.libs/libnucleus.a ../ajax/.libs/libajaxg.a ../ajax/.libs/libajax.a ../plplot/.libs/libplplot.a -L/usr/X11R6/lib -lX11 -lmgcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\" 4.0.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. -I. -I../nucleus -I../ajax -I../plplot -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -O2 -c cpgplot.c /bin/sh ../libtool --mode=link gcc -O2 -o cpgplot cpgplot.o../nucleus/libnucleus.la ../ajax/libajaxg.la ../ajax/libajax.la ../plplot/libplplot.la -L/usr/X11R6/lib -lX11 -lm gcc -O2 -o cpgplot cpgplot.o ../nucleus/.libs/libnucleus.a ../ajax/.libs/libajaxg.a ../ajax/.libs/libajax.a ../plplot/.libs/libplplot.a -L/usr/X11R6/lib -lX11 -lm cpgplot.o: In function `main':cpgplot.c:(.text+0xfed): undefined reference to `ajGraphDataReplaceI' :cpgplot.c:(.text+0x11e4): undefined reference to `ajGraphDataReplaceI' :cpgplot.c:(.text+0x135f): undefined reference to `ajGraphDataReplaceI' collect2: ld returned 1 exit status make[2]: *** [cpgplot] Error 1 make[2]: Leaving directory `/home/shiyong/Software/emboss/emboss/emboss' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/shiyong/Software/emboss/emboss/emboss' make: *** [all-recursive] Error 1 shiyong at protein:~/Software/emboss/emboss$ -- Shiyong Liu Research Assistant center for bioinformatics in the university of kansas Lab: (785)864-1962 Email: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu) Homepage: http://www.people.ku.edu/~syliu Lab: http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962 From jonathan_lim at merck.com Fri Sep 1 13:33:17 2006 From: jonathan_lim at merck.com (Lim, Jonathan) Date: Fri, 1 Sep 2006 09:33:17 -0400 Subject: [emboss-dev] FW: Perl parser for palindrome Message-ID: <95305ACDD8A44246A0720B446ED4D28A65D4C7@camtmx1100.merck.com> > Hello, > I've been trying to get the bioperl's Bio::Tools::EMBOSS::Palindrome > module to work with the palindrome program from EMBOSS 4. > I've had no luck so far - the output file is always empty. I'm using > the latest bioperl-live version, but it looks like there haven't been > any significant changes to the module since it was written back in > 2003. This leads me to believe that the module will only work with an > old version of palindrome. > I'm wondering if anyone has gotten this to work or knows of an > alternate perl parser/wrapper that would work with the newest > palindrome. > Thanks > > Jonathan > ------------------------------------------------------------------------------ Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. ------------------------------------------------------------------------------ From jison at ebi.ac.uk Mon Sep 4 11:29:31 2006 From: jison at ebi.ac.uk (Jon Ison) Date: Mon, 4 Sep 2006 12:29:31 +0100 (BST) Subject: [emboss-dev] FW: Perl parser for palindrome In-Reply-To: <95305ACDD8A44246A0720B446ED4D28A65D4C7@camtmx1100.merck.com> References: <95305ACDD8A44246A0720B446ED4D28A65D4C7@camtmx1100.merck.com> Message-ID: <48297.172.31.70.94.1157369371.squirrel@webmail.ebi.ac.uk> Hi Jonathan I haven't come across an updated Perl module. There have been some discussions about generating automatically foreign language bindings to the EMBOSS applications (which would keep things up to date) and you can expect some progress along these lines next year, but after the release. Cheers Jon > >> Hello, >> I've been trying to get the bioperl's Bio::Tools::EMBOSS::Palindrome >> module to work with the palindrome program from EMBOSS 4. >> I've had no luck so far - the output file is always empty. I'm using >> the latest bioperl-live version, but it looks like there haven't been >> any significant changes to the module since it was written back in >> 2003. This leads me to believe that the module will only work with an >> old version of palindrome. >> I'm wondering if anyone has gotten this to work or knows of an >> alternate perl parser/wrapper that would work with the newest >> palindrome. >> Thanks >> >> Jonathan >> > > ------------------------------------------------------------------------------ > Notice: This e-mail message, together with any attachments, contains > information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, > New Jersey, USA 08889), and/or its affiliates (which may be known > outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD > and in Japan, as Banyu - direct contact information for affiliates is > available at http://www.merck.com/contact/contacts.html) that may be > confidential, proprietary copyrighted and/or legally privileged. It is > intended solely for the use of the individual or entity named on this > message. If you are not the intended recipient, and have received this > message in error, please notify us immediately by reply e-mail and then > delete it from your system. > > ------------------------------------------------------------------------------ > _______________________________________________ > emboss-dev mailing list > emboss-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss-dev > From liushiyong at gmail.com Sun Sep 24 22:25:46 2006 From: liushiyong at gmail.com (Liu Shiyong) Date: Sun, 24 Sep 2006 17:25:46 -0500 Subject: [emboss-dev] help on building EMBOSS Message-ID: Dear all, I download CVS version and want to build EMBOSS in my Ubuntu(Linux protein 2.6.15-27-686 #1 SMP PREEMPT Sat Sep 16 02:13:27 UTC 2006 i686 GNU/Linux ) system. I got the following error information: gcc -O2 -o cons cons.o ../nucleus/.libs/libnucleus.a ../ajax/.libs/libajaxg.a ../ajax/.libs/libajax.a ../plplot/.libs/libplplot.a -L/usr/X11R6/lib -lX11 -lmgcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\" 4.0.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. -I. -I../nucleus -I../ajax -I../plplot -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -O2 -c cpgplot.c /bin/sh ../libtool --mode=link gcc -O2 -o cpgplot cpgplot.o../nucleus/libnucleus.la ../ajax/libajaxg.la ../ajax/libajax.la ../plplot/libplplot.la -L/usr/X11R6/lib -lX11 -lm gcc -O2 -o cpgplot cpgplot.o ../nucleus/.libs/libnucleus.a ../ajax/.libs/libajaxg.a ../ajax/.libs/libajax.a ../plplot/.libs/libplplot.a -L/usr/X11R6/lib -lX11 -lm cpgplot.o: In function `main':cpgplot.c:(.text+0xfed): undefined reference to `ajGraphDataReplaceI' :cpgplot.c:(.text+0x11e4): undefined reference to `ajGraphDataReplaceI' :cpgplot.c:(.text+0x135f): undefined reference to `ajGraphDataReplaceI' collect2: ld returned 1 exit status make[2]: *** [cpgplot] Error 1 make[2]: Leaving directory `/home/shiyong/Software/emboss/emboss/emboss' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/shiyong/Software/emboss/emboss/emboss' make: *** [all-recursive] Error 1 shiyong at protein:~/Software/emboss/emboss$ -- Shiyong Liu Research Assistant center for bioinformatics in the university of kansas Lab: (785)864-1962 Email: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu) Homepage: http://www.people.ku.edu/~syliu Lab: http://vakser.bioinformatics.ku.edu/people Phone: (785) 864-1962