From christophe.caron at jouy.inra.fr Fri Jul 4 13:19:39 2008 From: christophe.caron at jouy.inra.fr (christophe caron) Date: Fri, 04 Jul 2008 19:19:39 +0200 Subject: [EMBOSS] fndadist : data read error Message-ID: <486E5BAB.7060408@jouy.inra.fr> Hello We run EMBOSS 5.0 and fdnadist on output files from mpi-clustalw (phylip format). Actually i could not post the original private data file. So I run # fdnadist -sequence nok2.phylip -outfile distance.matrix -method f But i get this message Nucleic acid sequence Distance Matrix program Error: Sequence is not nucleic Error: Unable to read sequence 'nok2.phylip' Died: fdnadist terminated: Bad value for '-sequence' and no prompt **Then i try with -debug option and from the debug file : - Phylip format seems to be correctly detected : ... Free: 0 Last: -1 seqRead:try format 22 (phylip) ++seqReadFmt format 22 (phylip) 'nok2.phylip' feat No seqReadPhylip seqin->Data 0 ajFileBuffBuff nok2.phylip buffsize: 5000 .... - Then i have this message: seqMsfTabDel key: 'lcl2X90834' item: 'lcl2X90834' Testing input buffer: IsBuff: Yes Eof: No Format 22 (phylip) failed, file buffer reset by seqReadFmt ++seqReadFmt failed - nothing read seqRead: (b1) seqReadFmt stat == FAIL *failed* Trace buffer file 'nok2.phylip' Pos: 0 Size: 5000 FreeSize: 0 Fpos: 339808 End: N Lines: Curr: 0 544e10 548200 < 3713 1453 > From: 0 544e10 548200 < 3713 1453 > To: 339808 5fbb20 0 < t--------- ------attt cat-ac-ttt -atgc-ta-a aaa------- > Free: 0 Last: -1 seqRead:try format 24 (acedb) ++seqReadFmt format 24 (acedb) 'nok2.phylip' feat No seqReadAcedb first line: ' 3713 1453 I think tha fdnadist could not read one line and then try others format (acedb...) How could i use the 3713/1453 information. Lines number ? **Finally the last 10 lines from the debug file EOF ajFileGetsL file nok2.phylip End of file - data in buffer - return ajFalse read 115137 lines ajFileBuffClear (0) Nobuff: No size 0: Lines: 5476c0 Curr: 1518600 Prev: 15185a0 Last: 1518600 Free: 5476c0 Freelast: 1518600 ajFileBuffClear 'nok2.phylip' (0 lines) N size: 0 pos: 0 removed 115137 lines add to free: 115137 Trace buffer file 'nok2.phylip' Pos: 0 Size: 0 FreeSize: 0 Fpos: 7388914 End: Y Free: 115137 Last: 115137 seqReadFmt success with format 43 (raw) seqQueryMatch '' id '' acc '' Sv '' Gi '' Des '' Key '' Org '' Case No Done No ajSeqTypeCheckIn type 'gapdnaphylo' found (DNA sequence with gaps and queries) Convert gaps to '-' ajSeqIsNuc Type '' ajSeqTypeGapnucS test seqTypeTest, len 5412078 goodchars 'ACGTUBDHKMNRSVWXY?.~O-' seqTypeTest, Sequence had bad character 'l' (6c) at 0 of 5412078/5412078 ajSeqIsNuc failed ajSeqTypeCheckIn: rejected - not nucleic seqRead: (a1) seqReadFmt stat == BADTYPE *failed* ajSeqRead: open buffer usa: 'nok2.phylip' returns: No Error with the sequence type ?? I have only 'l' in the header and not the sequence data (may be because fdnadist mode is RAW after the first error ?) And a last information: Phylip dnadist version runs fine on this file. Any clue ? thanks. cc -- ************************************************************************** Christophe Caron - INRA | T?l: (+33) 013465 2888 Mathematique, Informatique et Genome| Fax: (+33) 013465 2901 Domaine de Vilvert | Email: christophe.caron at jouy.inra.fr F-78350 Jouy-en-Josas | http://migale.jouy.inra.fr/ ************************************************************************** -------------- next part -------------- A non-text attachment was scrubbed... Name: christophe_caron.vcf Type: text/x-vcard Size: 160 bytes Desc: not available URL: From laura at mmb.pcb.ub.es Wed Jul 9 03:46:47 2008 From: laura at mmb.pcb.ub.es (laura) Date: Wed, 09 Jul 2008 09:46:47 +0200 Subject: [EMBOSS] problems with allversusall tool Message-ID: Dear emboss users, I am using allversus all tool for global sequence alignment. I am writing to you because I am obtaining perfect aligments between sequences that have a very different length.. for example if I have a 100 residues protein sequence and a 2 residues protein sequence I obtain a 100% identity when I perform the alignment, in which I would expect a very poor sequence identity. Is there any way to prevent it or it is a posible bug in the program?? I would thank you to answer me as soon as possible, Regards, Laura. From db60 at st-andrews.ac.uk Wed Jul 9 07:45:34 2008 From: db60 at st-andrews.ac.uk (Daniel Barker) Date: Wed, 09 Jul 2008 12:45:34 +0100 Subject: [EMBOSS] problems with allversusall tool In-Reply-To: References: Message-ID: <4874A4DE.1060406@st-andrews.ac.uk> Dear Laura, Which EMBOSS program are you using? I don't find this effect with EMBOSS needle: $ cat seq_a.fa >seq_a MGQMQIV $ cat seq_b.fa >seq_b IV $ needle Needleman-Wunsch global alignment. Input sequence: seq_a.fa Second sequence(s): seq_b.fa Gap opening penalty [10.0]: Gap extension penalty [0.5]: Output alignment [seq_a.needle]: $ cat seq_a.needle ######################################## # Program: needle # Rundate: Wed 9 Jul 2008 12:34:46 # Commandline: needle # -asequence seq_a.fa # -bsequence seq_b.fa # Align_format: srspair # Report_file: seq_a.needle ######################################## #======================================= # # Aligned_sequences: 2 # 1: seq_a # 2: seq_b # Matrix: EBLOSUM62 # Gap_penalty: 10.0 # Extend_penalty: 0.5 # # Length: 7 # Identity: 2/7 (28.6%) # Similarity: 2/7 (28.6%) # Gaps: 5/7 (71.4%) # Score: 8.0 # # #======================================= seq_a 1 MGQMQIV 7 || seq_b 1 -----IV 2 #--------------------------------------- #--------------------------------------- I'm not sure it's relevant to your question but note that, in EMBOSS needle, the score is unaffected by "hanging ends". I consider this odd, in fact not really a global alignment score. E.g. a protein with domain architecture -a-b-c-d- would get approx. the same score if aligned against a protein of domain architecture -c-d-, as it would when aligned against a protein of domain architecture -c-d-e-f-g-h-i-j-k-l-m-. In my view this goes against the spirit of global alignment - but this approach is briefly justified in the needle documentation, and I believe is not unusual for global"alignment programs. Here's what I mean: $ cat seq_c.fa >seq_c IVPPLKP bhmac-db60-2:~ db60$ needle Needleman-Wunsch global alignment. Input sequence: seq_a.fa Second sequence(s): seq_c.fa Gap opening penalty [10.0]: Gap extension penalty [0.5]: Output alignment [seq_a.needle]: $ cat seq_a.needle ######################################## # Program: needle # Rundate: Wed 9 Jul 2008 12:37:01 # Commandline: needle # -asequence seq_a.fa # -bsequence seq_c.fa # Align_format: srspair # Report_file: seq_a.needle ######################################## #======================================= # # Aligned_sequences: 2 # 1: seq_a # 2: seq_c # Matrix: EBLOSUM62 # Gap_penalty: 10.0 # Extend_penalty: 0.5 # # Length: 12 # Identity: 2/12 (16.7%) # Similarity: 2/12 (16.7%) # Gaps: 10/12 (83.3%) # Score: 8.0 # # #======================================= seq_a 1 MGQMQIV----- 7 || seq_c 1 -----IVPPLKP 7 #--------------------------------------- #--------------------------------------- Note that identity, similarity and gaps have all changed but score remains the same as when seq_a and seq_b were aligned, since the only difference is a "hanging end". Best regards, Daniel laura wrote: > Dear emboss users, > > I am using allversus all tool for global sequence alignment. I am writing > to you because I am obtaining perfect aligments between sequences that have > a very different length.. for example if I have a 100 residues protein > sequence and a 2 residues protein sequence I obtain a 100% identity when I > perform the alignment, in which I would expect a very poor sequence > identity. Is there any way to prevent it or it is a posible bug in the > program?? > > I would thank you to answer me as soon as possible, > > Regards, > > Laura. > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss -- Daniel Barker http://bio.st-andrews.ac.uk/staff/db60.htm The University of St Andrews is a charity registered in Scotland : No SC013532 From gbottu at vub.ac.be Thu Jul 10 09:44:08 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Thu, 10 Jul 2008 15:44:08 +0200 Subject: [EMBOSS] The location of the HTML manuals Message-ID: <48761228.40309@vub.ac.be> Dear Peter and Alan, We are currently working on a new version of wEMBOSS+wrappers4EMBOSS and on this occasion we were again disturbed by the location of the manuals in HTML format. Indeed, they once were all in one directory, but now they are partly in .../share/EMBOSS/doc/html/emboss/apps and partly in .../share/EMBOSS/doc/html/embassy/xxx. I actually wonder what problem you tried to solve by doing that. It certainly creates a problem for developers of Web interfaces, because popping up a manual by generating a hyperlink is not easy ; when all the manuals are in the same directory the interface program must just generate an hyperlink yyyyyy/xxx.html, where yyyyy is always the same thing and xxx is the name of the program. At the BEN site it works because I manually copied all the manuals to one location. This however does not make life easy for those who download+install wEMBOSS(+wrappers4EMBOSS). Regards, Guy Bottu, BEN From ajb at ebi.ac.uk Tue Jul 15 13:51:30 2008 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Tue, 15 Jul 2008 18:51:30 +0100 (BST) Subject: [EMBOSS] EMBOSS 6.0.0 released Message-ID: <49382.81.98.242.91.1216144290.squirrel@webmail.ebi.ac.uk> EMBOSS 6.0.0 is now available from: ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.0.0.tar.gz The associated EMBASSY packages are in the same directory. Note that, as usual, these are specific to the main package so versions downloaded for a previous release will not work with 6.0.0. Changes in 6.0.0 include new applications, improvement of existing applications, library API consistency changes, bugfixes etc. Most are described in the relevant section of the ChangeLog which is reproduced below. mEMBOSS-6.0.0 is available from: ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.0.0-setup.exe mEMBOSS contains all the EMBOSS changes plus improvements and bugfixes for the GUI (Jemboss). Also, this release of mEMBOSS contains the C runtime library files; these had to be installed separately in previous versions. Alan Version 6.0.0 New application aligncopy reads a set of aligned sequences and prints a report in one of the standard alignment formats that can accept the same number of sequences. Pairwise alignment formats can only be used if the input has exactly two sequences. New application aligncopypair reads a set of aigned sequences and prints a report or each pair of aligned sequences in one of the standard alignment formats. New application featreport reads a sequence and a feature table, and writes a report in and of the standard report formats. New application featcopy reads and writes a feature table to convert feature formats. New applications maskambignuc and maskambigprot replace ambiguity characters in nucleotide sequences with 'N' and in protein sequences with 'X'. New application consambig reports an alignment consensus sequence using ambiguity characters. The intended use cases are sequencing reads and SNP reporting. New application sizeseq sorts sequences in ascending or descending order of length. This is a port of the application seqsort from the domsearch EMBASSY package. New application skipredundant uses pairwise sequence matches to exclude sequences that are similar from an input set. This is a modified version of the application seqnr from the domsearch EMBASSY package. New applications provide utility functions for former GCG users: nohtml removes HTML tags, notab replaces tabs with spaces, nospace removes all whitespace from a file, skipspace removes extra whitespace from a file. Older EMBOSS applications can now generate a warning message stating that they are marked as 'obsolete' with an explanation and an indication of alternative programs in EMBOSS or in an EMBASSY package. This warning can be turned off by defining environment variable EMBOSS_WARNOBSOLETE with a value of "N" or by defining the same variable in the emboss.defaults or ~/.embossrc files. We will begin to mark applications as 'obsolete' in future releases. A new EMBASSY package "myembossdemo" contains the demonstration applications demoalign, demofeatures, demolist, demoreport, demosequence, demostring, demostringnew and demotable that illustrate how to use EMBOSS data types in your own applications. The myembossdemo package allows novice developers to try simple EMBOSS programming. The myemboss package is available for adding your own applications. The demo applications are no longer distributed with the main EMBOSS package. They were not installed and were only built with the "make check" option. Application short descriptions have been revised. The minimum length of application one line descriptions is increased from 60 to 70 characters. The descriptions are easier to write. Output from wossname can now be 90 characters wide. Interfaces that use the description in menus may need to allow some extra space. Function names in ajfile.c have been standardised. Old names are still accepted but are marked as "deprecated" and will generate warnings with the gcc compiler (see ajstr below). Other compilers will see no difference. New source files ajfiledata.c and ajfileio.c have been added. The buffered file data structures are renamed internally to be more consistent (AjPFileBuff to AjPFilebuff). notseq was unable to search for IDs containing '|' characters but uses string matching (not regular expressions) and these characters are valid in NCBI-style FASTA files if read with the "pearson" format which accepts the whole ID string without parsing. The sequence alignment code has been updated. Sequence alignments with low gap penalties failed to allow two gaps (one in each sequence) without a match in between. The embAlign functions are now simplified. Scores are returned by the PathCalc functions. The Walk functions that walk through the path and return the aligned sequences are faster and need fewer parameters. Profile alignments occasionally duplicated residues in the sequence around gap positions. Fast alignments around a limited width include additional residues at each end and require an offset rather than separate start positions. The offset if the difference between the two start positions used in 5.0.0 and earlier releases. Eprimer3 citations are corrected in the help text (from the ACD file) and in the documentation. The citation errors were traced to the original primer3_core documentation which has now been corrected. Wordmatch could confuse overlapping matches. It occasionally extended the wrong match and missed a corresponding new match. Seqmatchall results were correct with the default output format which reports match positions, but gave incorrect results with some other local alignment formats that include the sequence. Seqmatchall now stores alignments in the same way as other local alignment applications, and the alignment internals are corrected to ensure other applictaiopns will not have the same problem. Emma was officially supporting clustalw 1.83. Issues with clustalw 2.0 are now resolved and this version is supported if clustalw2 is installed. Emma executes an applications called clustalw (not clustalw2) so version 2.0 must be installed under this name or an environment variable EMBOSS_CLUSTALW needs to be defined to point to the executable clustalw2 file. Sequence format "selex" allows invalid sequence data files to be accepted as input. Selex format is still available but is no longer included in the formats that can be automatically detected. When reading selex format data, users need to put "-sformat selex" on the command line, or specify "selex::" at the from of the USA. See the HMMER (old version EMBASSY package) documentation for examples. HMMERNEW (recommended) examples use Stockholm format and so are unchanged. Program dbxfasta now defaults to a filename of "*.fasta" The previous default "*.dat" is not commonly used for FASTA format databases. Program msbar block mutations were 1 longer than the specified block and may crash if the block size was fixed (minimum and maximum block sizes the same). This off-by-one error is now corrected. In GenBank output format, multiple line KEYWORD sections were not formatted correctly. ACD list and select values (the menus that appear in the user prompt) can now have ACD variables. Although useful for local application development these are not used in EMBOSS distributed ACD files because the variables are difficult for web and GUI interfaces to resolve when presenting the menu text. List and Table internal data structures are now cached so that creating and deleting temporary lists and tables is more efficient. In emboss.default database definitions the filename and exclude values can be delimited by spaces, commas or semicolons. Previous releases used only spaces. Parsing is now consistent with the fields definition which allowed all the above characters. Protein sequences with pyrrolysine ('O') had 'O' converted to a gap because this was a gap character in early versions of Phylip. This was patched in 5.0.0 to allow 'O' in UniProt release 13. The gap character is upper case only, so 'o' was correctly read as pyrrolysine. Wordfinder used the same descriptions for two pairs of qualifiers. The descriptions are changed to make their meaning clear in commandline help and in web interfaces. New function ajTimeDiff returns the difference in seconds between two time values. Profiling tests showed that file reading and string handling can be made faster. String handling called functions many levels deep. Making this code inline and using macro versions improved performance for applications (e.g. database indexing) that use many string calls. File input requires each input line to be copied. Using copy-by-reference (ajStrAssignRef) often makes this more efficient. Existing macros now test for undefined strings: MAJSTRGETLEN, MAJSTRGETPTR, MAJSTRGETRES and MAJSTRGETUSE. New macros are added for string handling: MAJSTRDEL, MAJSTRGETUNIQUESTR, MAJSTRCMPC and MAJSTRCMPS. Memory management includes new macros AJCRESIZE0 and AJRESIZE0 provide resize functions that guarantee new memory is set to zero. The functions must be given the original allocated size. Using the GNU C run-time library, calls to mcheck and mprobe are available to test for memory corruption by examining the bytes before and after an address allocated by malloc. This can be turned on for any application, including Unix commands, with the environment variable MALLOC_CHECK_ which has values 0, 1, 2 or 3. 1 writes to standard error when a problem is found, 2 aborts the programs, 3 does both and 0 ignores errors. No recompilation is needed for this simple method. EMBOSS now has a ./configure option --enable-mprobe which enables two new functions. ajMemProbe, passed an address from malloc (AJNEW0, AJCNEW0, etc.) tests the bytes before and after and reports any errors. The advantage of using ajMemProbe rather than mprobe is that a macro MAJMEMPROBE also reports the file and line number where ist was called. To avoid large numbers of messages (when code has problems) a limit can be set with ajMemCheckSetLimit after which the program will exit. Note that enable-mprobe is incompatible with using valgrind to test for memory leaks - as mprobe and mcheck have to look at illegal bytes before and after allocated memory blocks. Memory checking is turned on by a call to mcheck, passing the function ajMemCheck, in ajnam.c before the first memory allocation. If any program calls malloc before calling embInit or embInitP this call will fail and issue a warning (if compiled with --enable-mprobe). A special call ajStrProbe tests any string with mprobe. Special calls ajListProbe and ajListProbeData test lists and their contents. For more details see http://www.gnu.org/software/libc/manual/ Protein sequences from the Staden package were read as nucleotide because they were missing information on the ID line to identify EMBL of SWISSPROT format. The sequences are now tested and correctly typed. Wordcount now accepts protein sequences as input. Previous releases only allowed nucleotide sequences. Wordfinder options had the same information prompt. These have been changed from "limit" to "minimum" and "maximum" to make their function clear. Prompting for values from the user now includes a test for standard input in use as an input file. If standard input is open, the default response is accepted and a message is written to the user. This is to avoid problems with command lines that use "stdin" as an input and do not include -auto. The acdpretty utility can now preserve comments in ACD files. Comments are maintained in blocks with blank lines before and after. Inline comments are started in column 50 unless they are exceptionally long. Comments themselves have white space cleaned up but otherwise are not reformatted. A new function ajAcdGetValueDefault is added to return the default value of an ACD qualifier. This can be combined with ajAcdIsUserdefined in wrappers to test for values changed by the user. Infile qualifiers in ACD have a new attribute "trydefault" which allows the default filename to fail. Any filename provided by the user has to exist. This was added to support the behaviour of the MIRA EMBASSY package. To allow an infile to fail the attribute "nullok" also must be set to "Y" Applications which produce an output file or graphics often created an empty output file when the plot was selected. The ACD files have been corrected to only create the file if it will be written to. Applications changed are charge, dan, freak, hmoment, iep and tcode. Whichdb only writes to its output file if -get is false. With -get it creates sequences. The outfile is no longer created when whichdb is in -get mode. String functions corrected so that Case in the name always means case-insensitive and works by converting to upper case. Some functions were defined the wrong way, with "Case" for the case-insensitive form. GFF3 format is now the default feature output. A new function ajFeatIsCds identifies protein coding nucleotide features (CDS) using the SO identifier. A new function ajFeattagIsNote identifies feature tags that are for the default feature tag. Protein features now use the new Sequence Ontology terms defined by BioSapiens. These are not yet accepted by GFF3 validators. The new SO identifiers are added to protein feature definitions and used internally. Feature format definitions (the Efeatures and Etags files) now allow #include references to other files. This allows a standard EMBL and Swissprot feature table definition to be included by the internal and GFF definitions. Redefinitions are allowed using + and - prefxes to add and remove tags for existing feature types. GFF3 format feature (and report) output is added. A new application "density" has been added. This reports the A+C+G+T and AT+GC densities of nucleic acid sequences within an adjustable sliding window. Plots of A+C+G+T or AT+GC are optionally produced. Molecular weight programs (e.g. digest, mowse) now have a -mono switch to allow use of monoisotopic weights. By default, average molecular weights are used. The Eamino.dat format has changed. Molecular weight information has been removed and put in its own Emolwt.dat file. This latter now allows specification of average and monoisotopic weights. Values for hydrogen and oxygen are specified as well as the amino acid weights. The library representation of amino acid property information has been changed. The EmbPropTable global table has been removed and replaced with EmbPPropAmino and EmbPPropMolwt objects. Pepcoil now produces a report (replacing a text output) in "motif" format. The default is changed to not report non coiled-coil regions as they are hard to distinguish in this format. The "motif" report format is extended to allow two score positions marked with "*" and "+" and labelled internally as "pos" and "pos2". No application uses pos2 (it was added for pepcoil, but both score maximum positions are always the same) A new function ajAcdIsUserdefined allows wrappers to test which qualifiers have values changed by the user so that they can use shorter command lines to launch the wrapped application. jaspscan application added. Scans sequences for transcription factors using the JASPAR matrices. jaspextract application added to move the JASPAR matrices into the EMBOSS data area subdirectories. Alignment format "trace" used to display internal data content, is renamed to "debug" to be consisten with other formats. A "debug" format is added for feature output. Application documentation has been updated to remove obsolete references to EMBL database identifiers. These are replaced with the correct accession numbers. Two new entries have been added to the "tembl" test EMBL database for use in the QA tests. Report output now checks the sequence and feature table type. Is the sequence is not a valid protein, protein-only formats (pir, swiss) will fail with an error message. Similarly, if the sequence is not a valid nucleotide sequence then nucleotide-only formats (embl, genbank) will fail with an error message. Garnier now uses the correct SwissProt and internal feature keys for protein secondary structure. The results will appear much better for example as a swissprot feature table. This required rewriting of the internals by recoding the secondary structure features with a "garnier" tag replacing the previous "helix", "sheet", "turns" and "coil" tags. The default output is unchanged. The results in other report formats will be changed. Silent no longer reports the "Dir" column. This is replaced by the new "Strand" column which reports "+" for a forward feature and "-" for a reverse feature. The following programs have changed default report output, with the strand included for nucleotide sequences: equicktandem, etandem, fuzznuc, fuzztran, recoder, restrict, silent, tcode, twofeat. The strand column can be removed with the new commandline associated qualifier -norstrandshow. Reports for nucleotide sequences have confusing ways to represent the start and end positions for features on the complementary strand. A strand column has been added to these reports, controlled by a new -rstrandshow qualifier and attribute. By default the strand is shown for all nucleotide reports (see a list of changed program outputs above). The start position is always lower than the end position for features on the complementary strand indicating the region that should be reversed. In past releases the seqtable report format (fuzznuc, dreg, dan) confusingly reversed start and end positions to indicate the unreported strand. For all report formats (nametable, table) the start and end positions are now consistent with nucleotide feature formats (gff, embl, genbank). Reports from dreg incorrectly reported sequences reversed with the -sreverse qualifier. Report headers now include the text "(Reversed)" when the input sequence(s) are reverse complemented. Phylogenetic trees in newick format are now parsed into internal trees and converted back for use by Phylip. This allows us to read other tree formats and pass them to Phylip (e.g. Nexus) Some ACD data types did not allow the input to be NULL because extra tests were carried out on the results. These are all cleaned up and tested so that they can safely be set to nullok and missing in local applications. New sequence reading formats for PDB files. By default the ATOM records are used (format "pdb"). An alternative format "pdbseq" will read the SEQRES records which give the original sequence. The ATOM records give the sequence determined from the structure. Improved the help text for the -stdout and -filter options to explain output files are written to standard output. Some users expected graphics output (from plplot) to be controlled. From ajb at ebi.ac.uk Tue Jul 15 15:49:46 2008 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Tue, 15 Jul 2008 20:49:46 +0100 (BST) Subject: [EMBOSS] EMBOSS 6.0.0: please download again Message-ID: <54508.81.98.242.91.1216151386.squirrel@webmail.ebi.ac.uk> There was a problem with the original upload of EMBOSS 6.0.0 and mEMBOSS-6.0.0 to the open-bio server. If you have downloaded either prior to receiving this message then please download again. Apologies for the error. Alan From ajb at ebi.ac.uk Wed Jul 16 15:29:21 2008 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Wed, 16 Jul 2008 20:29:21 +0100 (BST) Subject: [EMBOSS] EMBOSS 6.0.1 released Message-ID: <34749.81.98.242.91.1216236561.squirrel@webmail.ebi.ac.uk> A couple of problems were noticed by the EMBOSS community in 6.0.0 prompting us to produce another release rather than just a patch. So, a day later: EMBOSS 6.0.1 is now available from: ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.0.1.tar.gz mEMBOSS-6.0.1 is available from: ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.0.1-setup.exe This is a maintenance release and fixes missing graphics output in a range of applications (e.g. plotorf). In mEMBOSS it additionally fixes the "Load Sequence Attributes" button failure. Apologies for any inconvenience. The phrase "That could have gone better" springs to mind. Alan From niels at genomics.dk Thu Jul 17 05:23:21 2008 From: niels at genomics.dk (Niels Larsen) Date: Thu, 17 Jul 2008 11:23:21 +0200 Subject: [EMBOSS] X-dependency optional? In-Reply-To: <20070723003321.GA10302@kunpuu.plessy.org> References: <54666.81.98.241.17.1184486717.squirrel@webmail.ebi.ac.uk> <20070722105517.GC21806@kunpuu.plessy.org> <20070723003321.GA10302@kunpuu.plessy.org> Message-ID: <487F0F89.7030402@genomics.dk> Greetings, I get this error with 6.0.1, http://emboss.open-bio.org/pipermail/emboss/2007-July/003056.html and could probably silence it by installing libx-dev as suggested in the next post. But I am planning to include EMBOSS in a free distributable software package, and so the libx-dev package may or may not be on the target machines (and the package should install under regular users). I wont be using anything X. I could not make the error go away with any ./configure option .. did i overlook it or perhaps there isnt one? Niels L From ajb at ebi.ac.uk Thu Jul 17 06:16:11 2008 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 17 Jul 2008 11:16:11 +0100 (BST) Subject: [EMBOSS] X-dependency optional? In-Reply-To: <487F0F89.7030402@genomics.dk> References: <54666.81.98.241.17.1184486717.squirrel@webmail.ebi.ac.uk> <20070722105517.GC21806@kunpuu.plessy.org> <20070723003321.GA10302@kunpuu.plessy.org> <487F0F89.7030402@genomics.dk> Message-ID: <40852.81.98.242.91.1216289771.squirrel@webmail.ebi.ac.uk> Dear Nils, It can be tricky to remove that dependency. The configuration switch --without-x works on some systems. The FAQ mentions the problem briefly Q) I have a Linux system and compilation ends prematurely saying that it can't find the -lX11 libraries ... but I know I have X11 installed. A) You may well have the X11 server installed but you haven't installed the X11 development files. For example, on RPM distributions, you need to install: xorg-x11-devel (xorg-based X11 distros) or XFree86-devel (XFree86-based X11 distros) It could do with updating to reflect the package name in Debian-based distros and the new name for xorg-based distros. It does give a hint though. The books we're writing (1st proof stage) certainly give more information - the web pages will soon be updated using the material from the latter. I intend revisiting that area of configuration at some stage. Alan > Greetings, > > I get this error with 6.0.1, > > http://emboss.open-bio.org/pipermail/emboss/2007-July/003056.html > > and could probably silence it by installing libx-dev as suggested > in the next post. But I am planning to include EMBOSS in a free > distributable software package, and so the libx-dev package may or > may not be on the target machines (and the package should install > under regular users). I wont be using anything X. I could not make > the error go away with any ./configure option .. did i overlook it > or perhaps there isnt one? > > Niels L > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From niels at genomics.dk Thu Jul 17 16:12:54 2008 From: niels at genomics.dk (Niels Larsen) Date: Thu, 17 Jul 2008 22:12:54 +0200 Subject: [EMBOSS] X-dependency optional? In-Reply-To: <40852.81.98.242.91.1216289771.squirrel@webmail.ebi.ac.uk> References: <54666.81.98.241.17.1184486717.squirrel@webmail.ebi.ac.uk> <20070722105517.GC21806@kunpuu.plessy.org> <20070723003321.GA10302@kunpuu.plessy.org> <487F0F89.7030402@genomics.dk> <40852.81.98.242.91.1216289771.squirrel@webmail.ebi.ac.uk> Message-ID: <487FA7C6.3030109@genomics.dk> Dear Alan, Yes, the first couple of systems I tried on (an old Mandrake 2005 and Ubuntu 6.06) failed with the --without-x option. I might try including all libx-dev variants, or if that turns out difficult wait for your configuration update (such update is not critical for me at present, but I will be happy whenever its there.) Niels L ajb at ebi.ac.uk wrote: > Dear Nils, > > It can be tricky to remove that dependency. The configuration > switch --without-x works on some systems. The FAQ mentions > the problem briefly > > Q) I have a Linux system and compilation ends prematurely saying that > it can't find the -lX11 libraries ... but I know I have X11 > installed. > > A) You may well have the X11 server installed but you haven't installed > the X11 development files. For example, on RPM distributions, you need > to install: > xorg-x11-devel (xorg-based X11 distros) or > XFree86-devel (XFree86-based X11 distros) > > It could do with updating to reflect the package name in Debian-based > distros and the new name for xorg-based distros. It does give a > hint though. The books we're writing (1st proof stage) certainly give > more information - the web pages will soon be updated using the material > from the latter. > > I intend revisiting that area of configuration at some stage. > > Alan From staffa at niehs.nih.gov Thu Jul 17 18:24:22 2008 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS)) Date: Thu, 17 Jul 2008 18:24:22 -0400 Subject: [EMBOSS] SeaView In-Reply-To: <487F0F89.7030402@genomics.dk> Message-ID: I would really appreciate any evaluation of the editor SEAVIEW by anyone reading this. In reading the paper by Galtier,Gouy and Gautier, I see that it has been around quite a while. They make a passing reference to Smith's GDE, which was the foundation for GCG's SeqLab editor. Do you think SeaView is as good as SeqLab; better; worse? Thank you for your attention. Nick Staffa Telephone: 919-316-4569 (NIEHS: 6-4569) Scientific Computing Support Group NIEHS Enterprise-Wide Information Technology Support Contract (Science Task Monitor: Roy W. Reter (reter at niehs.nih.gov) National Institute of Environmental Health Sciences National Institutes of Health Research Triangle Park, North Carolina From peter.robinson at t-online.de Fri Jul 18 00:24:14 2008 From: peter.robinson at t-online.de (Peter Robinson) Date: Fri, 18 Jul 2008 06:24:14 +0200 Subject: [EMBOSS] SeaView In-Reply-To: References: Message-ID: <48801AEE.9090208@t-online.de> Staffa, Nick (NIH/NIEHS) wrote: Seaview has perhaps few bells and whistles but is easy to use and effective, I like it very much! -peter > I would really appreciate any evaluation of the editor SEAVIEW by anyone > reading this. In reading the paper by Galtier,Gouy and Gautier, > I see that it has been around quite a while. > They make a passing reference to Smith's GDE, which was the foundation for > GCG's SeqLab editor. Do you think SeaView is as good as SeqLab; better; > worse? > > Thank you for your attention. > > > > Nick Staffa > Telephone: 919-316-4569 (NIEHS: 6-4569) > Scientific Computing Support Group > NIEHS Enterprise-Wide Information Technology Support Contract > (Science Task Monitor: Roy W. Reter (reter at niehs.nih.gov) > National Institute of Environmental Health Sciences > National Institutes of Health > Research Triangle Park, North Carolina > > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > > From gbottu at vub.ac.be Fri Jul 18 08:48:50 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Fri, 18 Jul 2008 14:48:50 +0200 Subject: [EMBOSS] SeaView In-Reply-To: References: Message-ID: <48809132.5040907@vub.ac.be> Staffa, Nick (NIH/NIEHS) wrote: > I would really appreciate any evaluation of the editor SEAVIEW by anyone > reading this. > Do you think SeaView is as good as SeqLab Dear Nick, Well, at the BEN site I installed SeaView as replacement, when we lost GCG+SeqLab. SeqLab does multiple sequence editing + graphical display of features + allows to execute programs on sequence (ranges). SeaView is basically just an editor (although it can call clustal or muscle to re-align portions of the aligment, and make a dotplot). What I find a great loss is that in SeqLab you can with the mouse select a block and then with one click delete it, while with SeaView you need to press as many time the as there are columns to delete. But if you have nothing else SeaView is certainly not bad. It has the advantage to be freeware and that there are versions for several platforms. You can install it and test it yourself. It is in principle easy to install (although there might be problems with prerequisite libraries). You can obtain it from ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview (and in some LINUX distributions like Gentoo it is actually vailable). If you run into trouble I am willing to give some advice. Regards, Guy Bottu, Belgian EMBnet Node From andrespinzon at gmail.com Fri Jul 18 10:19:36 2008 From: andrespinzon at gmail.com (Andres Pinzon) Date: Fri, 18 Jul 2008 09:19:36 -0500 Subject: [EMBOSS] SeaView In-Reply-To: <48809132.5040907@vub.ac.be> References: <48809132.5040907@vub.ac.be> Message-ID: <8968fc7e0807180719r4700ecb3qbed32f0912e1c127@mail.gmail.com> Hi Nick, It is also available on Ubuntu hardy. Have you ever used CLC sequence viewer? http://www.clcbio.com/index.php?id=28 Thats the editor we use here at the Colombia node, and I think it is one of the most intuitive tools I have ever tried. It has most of the seaview features (plus some others) runs under several platforms, is free and is really easy to install (no dependencies, just java). The following address lists all the available features (for this and other CLC versions): http://www.clcbio.com/index.php?id=89 Best, On Fri, Jul 18, 2008 at 7:48 AM, Guy Bottu wrote: > Staffa, Nick (NIH/NIEHS) wrote: > >> I would really appreciate any evaluation of the editor SEAVIEW by anyone >> reading this. >> Do you think SeaView is as good as SeqLab >> > > Dear Nick, > > Well, at the BEN site I installed SeaView as replacement, when we lost > GCG+SeqLab. SeqLab does multiple sequence editing + graphical display of > features + allows to execute programs on sequence (ranges). SeaView is > basically just an editor (although it can call clustal or muscle to re-align > portions of the aligment, and make a dotplot). What I find a great loss is > that in SeqLab you can with the mouse select a block and then with one click > delete it, while with SeaView you need to press as many time the > as there are columns to delete. But if you have nothing else SeaView is > certainly not bad. It has the advantage to be freeware and that there are > versions for several platforms. > You can install it and test it yourself. It is in principle easy to install > (although there might be problems with prerequisite libraries). You can > obtain it from ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview (and in > some LINUX distributions like Gentoo it is actually vailable). If you run > into trouble I am willing to give some advice. > > Regards, > Guy Bottu, > Belgian EMBnet Node > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > -- Andr?s Pinz?n http://bioinf.ibun.unal.edu.co/~apinzon/ Bioinformatics Center, Colombia EMBnet node http://bioinf.ibun.unal.edu.co Tel +57 3165000 ext 16961 Fax +571 3165415 Micology and Phytopathology Laboratory - Los Andes University. http://bioinf.uniandes.edu.co Tel +571 3394949 ext. 2768 From david at compbio.dundee.ac.uk Fri Jul 18 10:31:20 2008 From: david at compbio.dundee.ac.uk (David Martin) Date: Fri, 18 Jul 2008 15:31:20 +0100 Subject: [EMBOSS] SeaView In-Reply-To: <48809132.5040907@vub.ac.be> Message-ID: On 18/7/08 13:48, "Guy Bottu" wrote: > Staffa, Nick (NIH/NIEHS) wrote: >> I would really appreciate any evaluation of the editor SEAVIEW by anyone >> reading this. >> Do you think SeaView is as good as SeqLab > > Dear Nick, > > Well, at the BEN site I installed SeaView as replacement, when we lost > GCG+SeqLab. SeqLab does multiple sequence editing + graphical display of > features + allows to execute programs on sequence (ranges). SeaView is > basically > just an editor (although it can call clustal or muscle to re-align portions of > the aligment, and make a dotplot). What I find a great loss is that in SeqLab > you can with the mouse select a block and then with one click delete it, while > with SeaView you need to press as many time the as there are > columns > to delete. But if you have nothing else SeaView is certainly not bad. It has > the > advantage to be freeware and that there are versions for several platforms. > You can install it and test it yourself. It is in principle easy to install > (although there might be problems with prerequisite libraries). You can obtain > it from ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview (and in some LINUX > distributions like Gentoo it is actually vailable). If you run into trouble I > am > willing to give some advice. You might want to take a look at Jalview 2 which will do editing, MSA, feature display and more. OK, I am a little biased (it is developed in our group) but a quick rundown of the key features: * edit on blocks/ranges * edit using representative sequences * Multiple views on the same alignment * features from arbitrary DAS servers (even map protein features onto DNA.) * integration with jmol for structure viewing * hide/display arbitrary columns/rows. * Multiple sequence alignment (Clustal, MAFFT, Muscle) * Tree construction on arbitrary regions. Available from Jalview.org ..d -- David Martin PhD Post-Genomics and Molecular Interactions Centre University of Dundee http://www.compbio.dundee.ac.uk/ The University of Dundee is a registered Scottish charity, No: SC015096 From charles-listes-emboss at plessy.org Fri Jul 18 11:13:32 2008 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Sat, 19 Jul 2008 00:13:32 +0900 Subject: [EMBOSS] SeaView Message-ID: <20080718151332.GH3227@kunpuu.plessy.org> Le Fri, Jul 18, 2008 at 02:48:50PM +0200, Guy Bottu a ?crit : > SeaView is certainly not bad. It has the advantage to be freeware and that > there are versions for several platforms. > You can install it and test it yourself. It is in principle easy to install > (although there might be problems with prerequisite libraries). Hi all, Indeed, to get PDF export requires the PDFlib, which is not free software. However, Manolo Gouy, the upstream author, kindly provided compilation options to replace the PDF support by a simple PS support. It is with this option that Seaview is built on Debian and its derivatives. As a bonus, on FreeDesktop compliant window managers (like GNOME, KDE, Xfce), alignments in Clustal?W format will be recognised as being openable with SeaView. Have a nice weekend, -- Charles Plessy Debian-Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From breedaditi at yahoo.com Fri Jul 18 15:49:40 2008 From: breedaditi at yahoo.com (Aditi Breed) Date: Fri, 18 Jul 2008 12:49:40 -0700 (PDT) Subject: [EMBOSS] Installation (make ) error Message-ID: <945780.72408.qm@web35903.mail.mud.yahoo.com> Hello , I get the following error when i try to make EMBOSS. Can some one guide me as to what i need to do , to get rid of this error . xwin.c:3378: error: 'XwDisplay' has no member named 'display' xwin.c:3378: error: 'XwDev' has no member named 'window' xwin.c:3378: error: 'XwDev' has no member named 'gc' xwin.c:3379: error: 'XwDev' has no member named 'width' xwin.c:3379: error: 'XwDev' has no member named 'height' xwin.c: In function 'imageops': xwin.c:3394: error: 'XwDev' has no member named 'write_to_window' xwin.c:3398: error: 'XwDev' has no member named 'write_to_window' xwin.c:3402: error: 'XwDev' has no member named 'write_to_pixmap' xwin.c:3406: error: 'XwDisplay' has no member named 'display' xwin.c:3407: error: 'XwDev' has no member named 'write_to_pixmap' make[2]: *** [xwin.lo] Error 1 make[2]: Leaving directory `/home/akhunovlab/DOWNLOADS/EMBOSS/EMBOSS-6.0.1/plplot' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/akhunovlab/DOWNLOADS/EMBOSS/EMBOSS-6.0.1/plplot' make: *** [all-recursive] Error 1 I shall be grateful if someone could please help .. Regards, Aditi "Great spirits often meet violent opposition with mediocre minds" - Albert Einstein From staffa at niehs.nih.gov Fri Jul 18 16:39:19 2008 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS)) Date: Fri, 18 Jul 2008 16:39:19 -0400 Subject: [EMBOSS] SeaView In-Reply-To: <8968fc7e0807180719r4700ecb3qbed32f0912e1c127@mail.gmail.com> Message-ID: Thanks. I didn?t know CLC gave away anything. I printed out the manual(179 pages!), and it looks real spiffy. Must say that SeaView?s gray background makes reading sequence difficult. On 7/18/08 10:19 AM, "Andres Pinzon" wrote: > Hi Nick, > It is also available on Ubuntu hardy. Have you ever used CLC sequence viewer? > > http://www.clcbio.com/index.php?id=28 > > Thats the editor we use here at the Colombia node, and I think it is one of > the most > intuitive tools I have ever tried. It has most of the seaview features (plus > some others) runs > under several platforms, is free and is really easy to install (no > dependencies, just java). > > The following address lists all the available features (for this and other CLC > versions): > > http://www.clcbio.com/index.php?id=89 > > Best, > > On Fri, Jul 18, 2008 at 7:48 AM, Guy Bottu wrote: >> Staffa, Nick (NIH/NIEHS) wrote: >>> I would really appreciate any evaluation of the editor SEAVIEW by anyone >>> reading this. >>> Do you think SeaView is as good as SeqLab >> >> Dear Nick, >> >> Well, at the BEN site I installed SeaView as replacement, when we lost >> GCG+SeqLab. SeqLab does multiple sequence editing + graphical display of >> features + allows to execute programs on sequence (ranges). SeaView is >> basically just an editor (although it can call clustal or muscle to re-align >> portions of the aligment, and make a dotplot). What I find a great loss is >> that in SeqLab you can with the mouse select a block and then with one click >> delete it, while with SeaView you need to press as many time the >> as there are columns to delete. But if you have nothing else SeaView is >> certainly not bad. It has the advantage to be freeware and that there are >> versions for several platforms. >> You can install it and test it yourself. It is in principle easy to install >> (although there might be problems with prerequisite libraries). You can >> obtain it from ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview (and in >> some LINUX distributions like Gentoo it is actually vailable). If you run >> into trouble I am willing to give some advice. >> >> Regards, >> Guy Bottu, >> Belgian EMBnet Node >> _______________________________________________ >> EMBOSS mailing list >> EMBOSS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss > > From ajb at ebi.ac.uk Fri Jul 18 16:53:05 2008 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Fri, 18 Jul 2008 21:53:05 +0100 (BST) Subject: [EMBOSS] Installation (make ) error In-Reply-To: <945780.72408.qm@web35903.mail.mud.yahoo.com> References: <945780.72408.qm@web35903.mail.mud.yahoo.com> Message-ID: <58327.81.98.242.91.1216414385.squirrel@webmail.ebi.ac.uk> You need to install the X11 development files for your operating system. You did not say which OS and version you are using. I would guess from the output that it is some sort of Debian-based Linux one. If that is the case then you need to install the libx11-dev package from your distribution. If you are using an RPM-based Linux distribution then the RPM you need to install will be called something like xorg-x11-proto-devel After you have installed the correct package then you will need to do a 'make clean' in EMBOSS and then do the configuration step again. HTH Alan > Hello , > I get the following error when i try to make EMBOSS. > Can some one guide me as to what i need to do , to get rid of this error . > > > xwin.c:3378: error: 'XwDisplay' has no member named 'display' > xwin.c:3378: error: 'XwDev' has no member named 'window' > xwin.c:3378: error: 'XwDev' has no member named 'gc' > xwin.c:3379: error: 'XwDev' has no member named 'width' > xwin.c:3379: error: 'XwDev' has no member named 'height' > xwin.c: In function 'imageops': > xwin.c:3394: error: 'XwDev' has no member named 'write_to_window' > xwin.c:3398: error: 'XwDev' has no member named 'write_to_window' > xwin.c:3402: error: 'XwDev' has no member named 'write_to_pixmap' > xwin.c:3406: error: 'XwDisplay' has no member named 'display' > xwin.c:3407: error: 'XwDev' has no member named 'write_to_pixmap' > make[2]: *** [xwin.lo] Error 1 > make[2]: Leaving directory > `/home/akhunovlab/DOWNLOADS/EMBOSS/EMBOSS-6.0.1/plplot' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory > `/home/akhunovlab/DOWNLOADS/EMBOSS/EMBOSS-6.0.1/plplot' > make: *** [all-recursive] Error 1 > > > I shall be grateful if someone could please help .. > > Regards, > Aditi > > > "Great spirits often meet violent opposition with mediocre minds" - Albert > Einstein > > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From charles-listes-emboss at plessy.org Fri Jul 18 20:26:49 2008 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Sat, 19 Jul 2008 09:26:49 +0900 Subject: [EMBOSS] Installation (make ) error In-Reply-To: <58327.81.98.242.91.1216414385.squirrel@webmail.ebi.ac.uk> References: <945780.72408.qm@web35903.mail.mud.yahoo.com> <58327.81.98.242.91.1216414385.squirrel@webmail.ebi.ac.uk> Message-ID: <20080719002649.GB20577@kunpuu.plessy.org> Le Fri, Jul 18, 2008 at 09:53:05PM +0100, ajb at ebi.ac.uk a ?crit : > You need to install the X11 development files for your > operating system. > > You did not say which OS and version you are using. > > I would guess from the output that it is some sort of Debian-based Linux > one. If that is the case then you need to install the libx11-dev > package from your distribution. Hello, The packages on to install on Debian for building EMBOSS are: libx11-dev, x11proto-core-dev, libgdchart-gd2-xpm-dev, zlib1g-dev, libpng12-dev and libpcre3-dev. Have a nice day, -- Charles Plessy Debian-Med packaging team http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From kvddrift at earthlink.net Sun Jul 20 18:17:38 2008 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sun, 20 Jul 2008 18:17:38 -0400 Subject: [EMBOSS] EMBOSS 6.0.1 released In-Reply-To: <34749.81.98.242.91.1216236561.squirrel@webmail.ebi.ac.uk> References: <34749.81.98.242.91.1216236561.squirrel@webmail.ebi.ac.uk> Message-ID: <7EF664A9-8456-4778-9A99-30FCBD6A6C82@earthlink.net> Hi, I noticed that a libplplot is being created (on Mac OS X - using fink): /sw/src/fink.build/root-emboss-6.0.1-1/sw/lib/libplplot.dylib -> EMBOSS/libplplot.dylib There is afaik no mention of libplplot in the fink package for EMBOSS. Also the build log doesn't show it. Is this correct, I thought all libs were now called libeplplot? cheers, - Koen. On Jul 16, 2008, at 3:29 PM, ajb at ebi.ac.uk wrote: > A couple of problems were noticed by the EMBOSS community > in 6.0.0 prompting us to produce another release rather than just a > patch. > > So, a day later: > > EMBOSS 6.0.1 is now available from: > > ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.0.1.tar.gz > > mEMBOSS-6.0.1 is available from: > > ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.0.1-setup.exe > > > This is a maintenance release and fixes missing graphics output > in a range of applications (e.g. plotorf). > > In mEMBOSS it additionally fixes the "Load Sequence Attributes" button > failure. > > Apologies for any inconvenience. > > The phrase "That could have gone better" springs to mind. > > Alan > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From ajb at ebi.ac.uk Mon Jul 21 04:25:56 2008 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 21 Jul 2008 09:25:56 +0100 (BST) Subject: [EMBOSS] EMBOSS 6.0.1 released In-Reply-To: <7EF664A9-8456-4778-9A99-30FCBD6A6C82@earthlink.net> References: <34749.81.98.242.91.1216236561.squirrel@webmail.ebi.ac.uk> <7EF664A9-8456-4778-9A99-30FCBD6A6C82@earthlink.net> Message-ID: <43484.81.98.242.91.1216628756.squirrel@webmail.ebi.ac.uk> Hi Koen, It is correct that EMBOSS uses the name 'libeplplot' for the graphics library throughout therefore no libraries called 'libplplot' are produced. The change to the name libeplplot was made, as you're probably aware, in EMBOSS 5.0.0. There is no mention of 'libplplot' in the source code (though it may be mentioned in documentation) and, verifying what you said, no 'libplplot' libraries are produced using a standard configure/make/make install of EMBOSS on a MacBook Pro here running 10.4.11 We therefore plead not guilty M'lud. HTH Alan > Hi, > > I noticed that a libplplot is being created (on Mac OS X - using fink): > > /sw/src/fink.build/root-emboss-6.0.1-1/sw/lib/libplplot.dylib -> > EMBOSS/libplplot.dylib > > There is afaik no mention of libplplot in the fink package for EMBOSS. > Also the build log doesn't show it. > > > Is this correct, I thought all libs were now called libeplplot? > > cheers, > > - Koen. > > > > On Jul 16, 2008, at 3:29 PM, ajb at ebi.ac.uk wrote: > >> A couple of problems were noticed by the EMBOSS community >> in 6.0.0 prompting us to produce another release rather than just a >> patch. >> >> So, a day later: >> >> EMBOSS 6.0.1 is now available from: >> >> ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.0.1.tar.gz >> >> mEMBOSS-6.0.1 is available from: >> >> ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.0.1-setup.exe >> >> >> This is a maintenance release and fixes missing graphics output >> in a range of applications (e.g. plotorf). >> >> In mEMBOSS it additionally fixes the "Load Sequence Attributes" button >> failure. >> >> Apologies for any inconvenience. >> >> The phrase "That could have gone better" springs to mind. >> >> Alan >> >> >> _______________________________________________ >> EMBOSS mailing list >> EMBOSS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss > From kvddrift at earthlink.net Mon Jul 21 18:09:55 2008 From: kvddrift at earthlink.net (Koen van der Drift) Date: Mon, 21 Jul 2008 18:09:55 -0400 Subject: [EMBOSS] EMBOSS 6.0.1 released In-Reply-To: <43484.81.98.242.91.1216628756.squirrel@webmail.ebi.ac.uk> References: <34749.81.98.242.91.1216236561.squirrel@webmail.ebi.ac.uk> <7EF664A9-8456-4778-9A99-30FCBD6A6C82@earthlink.net> <43484.81.98.242.91.1216628756.squirrel@webmail.ebi.ac.uk> Message-ID: <14E52975-99BD-4AE5-AA82-1785185F5111@earthlink.net> On Jul 21, 2008, at 4:25 AM, ajb at ebi.ac.uk wrote: > We therefore plead not guilty M'lud. I found the problem. Mea culpa :) FYI, there was a line in the fink package that made symlinks to all the dynamic libraries as follows: ln -s EMBOSS/lib{ajax,ajaxg,nucleus,plplot}.dylib /lib So I never found that when I searched for the string libplplot. It's all fixed now. Sorry for the noise, - Koen. From shrish at ccmb.res.in Wed Jul 23 02:50:05 2008 From: shrish at ccmb.res.in (Shrish Tiwari) Date: Wed, 23 Jul 2008 12:20:05 +0530 (IST) Subject: [EMBOSS] requests for backtranseq Message-ID: <129447317.1216795805530.JavaMail.root@127.0.0.1> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From prija.ponnan at gmail.com Thu Jul 24 05:08:44 2008 From: prija.ponnan at gmail.com (Prija Ponnan) Date: Thu, 24 Jul 2008 15:08:44 +0600 Subject: [EMBOSS] Installation (configure) error Message-ID: <67b1a92d0807240208h22084c7cv8c0135f11eb2faf8@mail.gmail.com> hello I encounter the following error while trying to *configure EMBOSS* checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for gawk... (cached) gawk checking for gcc... no checking for cc... no checking for cl.exe... no configure: error: no acceptable C compiler found in $PATH I'm using fedora-based linux OS Please guide me as to what I have to do to get rid of the error Thanx in advance -- Prija From ajb at ebi.ac.uk Thu Jul 24 05:51:36 2008 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 24 Jul 2008 10:51:36 +0100 (BST) Subject: [EMBOSS] Installation (configure) error In-Reply-To: <67b1a92d0807240208h22084c7cv8c0135f11eb2faf8@mail.gmail.com> References: <67b1a92d0807240208h22084c7cv8c0135f11eb2faf8@mail.gmail.com> Message-ID: <36902.86.9.126.186.1216893096.squirrel@webmail.ebi.ac.uk> Hi, You've obviously installed Fedora without any of the software development packages and you therefore need to install the C compiler. You can try doing: yum install gcc yum install gd-devel yum install xorg-x11-proto-devel Then try the emboss configuration again. It may be the case that you're still missing a few packages but the above is a reasonable start and should automatically download other needed development software. HTH Alan > hello > > I encounter the following error while trying to *configure EMBOSS* > > checking for gawk... gawk > checking whether make sets $(MAKE)... yes > checking for gawk... (cached) gawk > checking for gcc... no > checking for cc... no > checking for cl.exe... no > configure: error: no acceptable C compiler found in $PATH > > I'm using fedora-based linux OS > > Please guide me as to what I have to do to get rid of the error > > Thanx in advance > > -- > Prija > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From gbottu at vub.ac.be Thu Jul 24 12:11:37 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Thu, 24 Jul 2008 18:11:37 +0200 Subject: [EMBOSS] wEMBOSS 1.8.0 and wrappers4EMBOSS 2.2.0 released Message-ID: <4888A9B9.1030209@vub.ac.be> Dear users of wEMBOSS, We have the pleasure to announce that the new version of wEMBOSS has been released. It contains important bug and feature fixes : - wEMBOSS allows you to type in your Email address, so that the program is started "in the background" and you are warned by Email when it has finished. The idea was that you could then start other programs or close your Web browser. At a certain moment however a bug has appeared that made that on many systems the program crashed when you tried that. This bug has been fixed. - wEMBOSS did not work under Mac OSX unless a small change was made in the code (in the SETUID part). To relieve wEMBOSS site managers from the burden of having to "hack" the code themselves, we now distribute separate versions for Mac OSX and for other UNIX flavours. - The "Search for programs" function retrieved a huge number of irrelevant program names. This number has been drastically reduced by avoiding to search in the "See also" section of the program manuals. - The on-line manuals in HTML format are installed at different locations, depending on EMBOSS version and whether it is a standard EMBOSS or an EMBASSY program. wEMBOSS can now always find the manual, wherever it is installed by default. For a complete list of the changes you can look at the Changelog : http://sourceforge.net/project/shownotes.php?group_id=170030&release_id=615018 wEMBOSS 1.8.0 is released together with the new version 2.1.0 of wrappers4EMBOSS. Besides a lot of fixes, refreshments and enhancements it addresses the following important issues : - Those who installed the EBI Web Services module will have noticed that it stopped functioning. The reason is that the EBI upgraded its SOAP server without backwards compatibility. The new version of the wrapper contains upgraded versions of the clients. - This some were asking for : a tool to use a remote MRS server as sequence access mechanism under EMBOSS (using Web Services). - The PHYLIP suite (available under EMBOSS as an EMBASSY package) handles quite well the parsimony and distances methods, but is very weak for Maximum Likelihood (only 1 model, slow on big datasets). To address this deficiency we have added wrappers for PhyML and ModelGenerator. For a complete list of the changes you can look at the Changelog : http://sourceforge.net/project/shownotes.php?group_id=170030&release_id=615013 Regards, Belgian EMBnet Node - wEMBOSS development team, Guy Bottu From prija.ponnan at gmail.com Mon Jul 28 09:04:04 2008 From: prija.ponnan at gmail.com (Prija Ponnan) Date: Mon, 28 Jul 2008 18:34:04 +0530 Subject: [EMBOSS] Installation (make) error Message-ID: <67b1a92d0807280604o72fb878bo936952dfc12013e0@mail.gmail.com> Hello I'd encountered following error while trying to "make" EMBOSS gd.c:601: structure has no member named `palette' gd.c:602: structure has no member named `truecolour' gd.c: In function `plD_eop_gif': gd.c:1530: warning: assignment makes pointer from integer without a cast make[2]: *** [gd.lo] Error 1 make[2]: Leaving directory `/home/acbr/prija/EMBOSS-6.0.1/plplot' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/acbr/prija/EMBOSS-6.0.1/plplot' make: *** [all-recursive] Error 1 I'm using REDHAT linux OS Please guide me to get rid of this error Thanks in advance -- Prija From prija.ponnan at gmail.com Tue Jul 29 09:28:10 2008 From: prija.ponnan at gmail.com (Prija Ponnan) Date: Tue, 29 Jul 2008 18:58:10 +0530 Subject: [EMBOSS] EMBOSS installation Message-ID: <67b1a92d0807290628q3c541a0dv3e2e0261d4da4b17@mail.gmail.com> Hello I've finally installed EMBOSS 6.0.1 Thank You for your valuable guidance -- Prija From benys at usp.br Tue Jul 29 10:41:19 2008 From: benys at usp.br (Beny Spira) Date: Tue, 29 Jul 2008 11:41:19 -0300 Subject: [EMBOSS] gui Message-ID: <21e884180807290741l1d1913b8mfd66e4a21002037e@mail.gmail.com> Dear all, I wish to install emboss-explorer on both Debian and Mandriva. Installing in Debian is straightforward, there is an apt package. However, in Mandriva I tried to install it, but it needs configuration at the web server level, which I am not familiar with. Another problem is that in Debian it worked at first, but not anymore. My question is if there a simple protocol on how to configure the web-server (including what packages need to be installed) to use with emboss-explorer. My EMBOSS version is 5.0.0 Thanks Beny -- Beny Spira Departamento de Microbiologia Instituto de Ci?ncias Biom?dicas Universidade de S?o Paulo Av. Prof. Lineu Prestes 1374 S?o Paulo-SP CEP:05508-900 Brasil Tel: 5511-3091-7347 FAX: 5511-3091-7354 E-mail: benys at usp.br Homepage: www.icb.usp.br/~benys From charles-listes-emboss at plessy.org Tue Jul 29 11:13:58 2008 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Wed, 30 Jul 2008 00:13:58 +0900 Subject: [EMBOSS] gui In-Reply-To: <21e884180807290741l1d1913b8mfd66e4a21002037e@mail.gmail.com> References: <21e884180807290741l1d1913b8mfd66e4a21002037e@mail.gmail.com> Message-ID: <20080729151358.GF20143@kunpuu.plessy.org> Le Tue, Jul 29, 2008 at 11:41:19AM -0300, Beny Spira a ?crit : > In Debian it worked at first, but not anymore. Dear Beny, I made the last update of the Debian package for EMBOSS Explorer. Some files were moved but it does not restart apache automatically. Can you retry after restarting apache (or reloading its configuration, it is lighter)? If it still does not work, please give me details about the problem, and I will try to solve it. Have a a nice day, -- Charles Plessy Debian Med packaging team http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From christophe.caron at jouy.inra.fr Fri Jul 4 17:19:39 2008 From: christophe.caron at jouy.inra.fr (christophe caron) Date: Fri, 04 Jul 2008 19:19:39 +0200 Subject: [EMBOSS] fndadist : data read error Message-ID: <486E5BAB.7060408@jouy.inra.fr> Hello We run EMBOSS 5.0 and fdnadist on output files from mpi-clustalw (phylip format). Actually i could not post the original private data file. So I run # fdnadist -sequence nok2.phylip -outfile distance.matrix -method f But i get this message Nucleic acid sequence Distance Matrix program Error: Sequence is not nucleic Error: Unable to read sequence 'nok2.phylip' Died: fdnadist terminated: Bad value for '-sequence' and no prompt **Then i try with -debug option and from the debug file : - Phylip format seems to be correctly detected : ... Free: 0 Last: -1 seqRead:try format 22 (phylip) ++seqReadFmt format 22 (phylip) 'nok2.phylip' feat No seqReadPhylip seqin->Data 0 ajFileBuffBuff nok2.phylip buffsize: 5000 .... - Then i have this message: seqMsfTabDel key: 'lcl2X90834' item: 'lcl2X90834' Testing input buffer: IsBuff: Yes Eof: No Format 22 (phylip) failed, file buffer reset by seqReadFmt ++seqReadFmt failed - nothing read seqRead: (b1) seqReadFmt stat == FAIL *failed* Trace buffer file 'nok2.phylip' Pos: 0 Size: 5000 FreeSize: 0 Fpos: 339808 End: N Lines: Curr: 0 544e10 548200 < 3713 1453 > From: 0 544e10 548200 < 3713 1453 > To: 339808 5fbb20 0 < t--------- ------attt cat-ac-ttt -atgc-ta-a aaa------- > Free: 0 Last: -1 seqRead:try format 24 (acedb) ++seqReadFmt format 24 (acedb) 'nok2.phylip' feat No seqReadAcedb first line: ' 3713 1453 I think tha fdnadist could not read one line and then try others format (acedb...) How could i use the 3713/1453 information. Lines number ? **Finally the last 10 lines from the debug file EOF ajFileGetsL file nok2.phylip End of file - data in buffer - return ajFalse read 115137 lines ajFileBuffClear (0) Nobuff: No size 0: Lines: 5476c0 Curr: 1518600 Prev: 15185a0 Last: 1518600 Free: 5476c0 Freelast: 1518600 ajFileBuffClear 'nok2.phylip' (0 lines) N size: 0 pos: 0 removed 115137 lines add to free: 115137 Trace buffer file 'nok2.phylip' Pos: 0 Size: 0 FreeSize: 0 Fpos: 7388914 End: Y Free: 115137 Last: 115137 seqReadFmt success with format 43 (raw) seqQueryMatch '' id '' acc '' Sv '' Gi '' Des '' Key '' Org '' Case No Done No ajSeqTypeCheckIn type 'gapdnaphylo' found (DNA sequence with gaps and queries) Convert gaps to '-' ajSeqIsNuc Type '' ajSeqTypeGapnucS test seqTypeTest, len 5412078 goodchars 'ACGTUBDHKMNRSVWXY?.~O-' seqTypeTest, Sequence had bad character 'l' (6c) at 0 of 5412078/5412078 ajSeqIsNuc failed ajSeqTypeCheckIn: rejected - not nucleic seqRead: (a1) seqReadFmt stat == BADTYPE *failed* ajSeqRead: open buffer usa: 'nok2.phylip' returns: No Error with the sequence type ?? I have only 'l' in the header and not the sequence data (may be because fdnadist mode is RAW after the first error ?) And a last information: Phylip dnadist version runs fine on this file. Any clue ? thanks. cc -- ************************************************************************** Christophe Caron - INRA | T?l: (+33) 013465 2888 Mathematique, Informatique et Genome| Fax: (+33) 013465 2901 Domaine de Vilvert | Email: christophe.caron at jouy.inra.fr F-78350 Jouy-en-Josas | http://migale.jouy.inra.fr/ ************************************************************************** -------------- next part -------------- A non-text attachment was scrubbed... Name: christophe_caron.vcf Type: text/x-vcard Size: 160 bytes Desc: not available URL: From laura at mmb.pcb.ub.es Wed Jul 9 07:46:47 2008 From: laura at mmb.pcb.ub.es (laura) Date: Wed, 09 Jul 2008 09:46:47 +0200 Subject: [EMBOSS] problems with allversusall tool Message-ID: Dear emboss users, I am using allversus all tool for global sequence alignment. I am writing to you because I am obtaining perfect aligments between sequences that have a very different length.. for example if I have a 100 residues protein sequence and a 2 residues protein sequence I obtain a 100% identity when I perform the alignment, in which I would expect a very poor sequence identity. Is there any way to prevent it or it is a posible bug in the program?? I would thank you to answer me as soon as possible, Regards, Laura. From db60 at st-andrews.ac.uk Wed Jul 9 11:45:34 2008 From: db60 at st-andrews.ac.uk (Daniel Barker) Date: Wed, 09 Jul 2008 12:45:34 +0100 Subject: [EMBOSS] problems with allversusall tool In-Reply-To: References: Message-ID: <4874A4DE.1060406@st-andrews.ac.uk> Dear Laura, Which EMBOSS program are you using? I don't find this effect with EMBOSS needle: $ cat seq_a.fa >seq_a MGQMQIV $ cat seq_b.fa >seq_b IV $ needle Needleman-Wunsch global alignment. Input sequence: seq_a.fa Second sequence(s): seq_b.fa Gap opening penalty [10.0]: Gap extension penalty [0.5]: Output alignment [seq_a.needle]: $ cat seq_a.needle ######################################## # Program: needle # Rundate: Wed 9 Jul 2008 12:34:46 # Commandline: needle # -asequence seq_a.fa # -bsequence seq_b.fa # Align_format: srspair # Report_file: seq_a.needle ######################################## #======================================= # # Aligned_sequences: 2 # 1: seq_a # 2: seq_b # Matrix: EBLOSUM62 # Gap_penalty: 10.0 # Extend_penalty: 0.5 # # Length: 7 # Identity: 2/7 (28.6%) # Similarity: 2/7 (28.6%) # Gaps: 5/7 (71.4%) # Score: 8.0 # # #======================================= seq_a 1 MGQMQIV 7 || seq_b 1 -----IV 2 #--------------------------------------- #--------------------------------------- I'm not sure it's relevant to your question but note that, in EMBOSS needle, the score is unaffected by "hanging ends". I consider this odd, in fact not really a global alignment score. E.g. a protein with domain architecture -a-b-c-d- would get approx. the same score if aligned against a protein of domain architecture -c-d-, as it would when aligned against a protein of domain architecture -c-d-e-f-g-h-i-j-k-l-m-. In my view this goes against the spirit of global alignment - but this approach is briefly justified in the needle documentation, and I believe is not unusual for global"alignment programs. Here's what I mean: $ cat seq_c.fa >seq_c IVPPLKP bhmac-db60-2:~ db60$ needle Needleman-Wunsch global alignment. Input sequence: seq_a.fa Second sequence(s): seq_c.fa Gap opening penalty [10.0]: Gap extension penalty [0.5]: Output alignment [seq_a.needle]: $ cat seq_a.needle ######################################## # Program: needle # Rundate: Wed 9 Jul 2008 12:37:01 # Commandline: needle # -asequence seq_a.fa # -bsequence seq_c.fa # Align_format: srspair # Report_file: seq_a.needle ######################################## #======================================= # # Aligned_sequences: 2 # 1: seq_a # 2: seq_c # Matrix: EBLOSUM62 # Gap_penalty: 10.0 # Extend_penalty: 0.5 # # Length: 12 # Identity: 2/12 (16.7%) # Similarity: 2/12 (16.7%) # Gaps: 10/12 (83.3%) # Score: 8.0 # # #======================================= seq_a 1 MGQMQIV----- 7 || seq_c 1 -----IVPPLKP 7 #--------------------------------------- #--------------------------------------- Note that identity, similarity and gaps have all changed but score remains the same as when seq_a and seq_b were aligned, since the only difference is a "hanging end". Best regards, Daniel laura wrote: > Dear emboss users, > > I am using allversus all tool for global sequence alignment. I am writing > to you because I am obtaining perfect aligments between sequences that have > a very different length.. for example if I have a 100 residues protein > sequence and a 2 residues protein sequence I obtain a 100% identity when I > perform the alignment, in which I would expect a very poor sequence > identity. Is there any way to prevent it or it is a posible bug in the > program?? > > I would thank you to answer me as soon as possible, > > Regards, > > Laura. > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss -- Daniel Barker http://bio.st-andrews.ac.uk/staff/db60.htm The University of St Andrews is a charity registered in Scotland : No SC013532 From gbottu at vub.ac.be Thu Jul 10 13:44:08 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Thu, 10 Jul 2008 15:44:08 +0200 Subject: [EMBOSS] The location of the HTML manuals Message-ID: <48761228.40309@vub.ac.be> Dear Peter and Alan, We are currently working on a new version of wEMBOSS+wrappers4EMBOSS and on this occasion we were again disturbed by the location of the manuals in HTML format. Indeed, they once were all in one directory, but now they are partly in .../share/EMBOSS/doc/html/emboss/apps and partly in .../share/EMBOSS/doc/html/embassy/xxx. I actually wonder what problem you tried to solve by doing that. It certainly creates a problem for developers of Web interfaces, because popping up a manual by generating a hyperlink is not easy ; when all the manuals are in the same directory the interface program must just generate an hyperlink yyyyyy/xxx.html, where yyyyy is always the same thing and xxx is the name of the program. At the BEN site it works because I manually copied all the manuals to one location. This however does not make life easy for those who download+install wEMBOSS(+wrappers4EMBOSS). Regards, Guy Bottu, BEN From ajb at ebi.ac.uk Tue Jul 15 17:51:30 2008 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Tue, 15 Jul 2008 18:51:30 +0100 (BST) Subject: [EMBOSS] EMBOSS 6.0.0 released Message-ID: <49382.81.98.242.91.1216144290.squirrel@webmail.ebi.ac.uk> EMBOSS 6.0.0 is now available from: ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.0.0.tar.gz The associated EMBASSY packages are in the same directory. Note that, as usual, these are specific to the main package so versions downloaded for a previous release will not work with 6.0.0. Changes in 6.0.0 include new applications, improvement of existing applications, library API consistency changes, bugfixes etc. Most are described in the relevant section of the ChangeLog which is reproduced below. mEMBOSS-6.0.0 is available from: ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.0.0-setup.exe mEMBOSS contains all the EMBOSS changes plus improvements and bugfixes for the GUI (Jemboss). Also, this release of mEMBOSS contains the C runtime library files; these had to be installed separately in previous versions. Alan Version 6.0.0 New application aligncopy reads a set of aligned sequences and prints a report in one of the standard alignment formats that can accept the same number of sequences. Pairwise alignment formats can only be used if the input has exactly two sequences. New application aligncopypair reads a set of aigned sequences and prints a report or each pair of aligned sequences in one of the standard alignment formats. New application featreport reads a sequence and a feature table, and writes a report in and of the standard report formats. New application featcopy reads and writes a feature table to convert feature formats. New applications maskambignuc and maskambigprot replace ambiguity characters in nucleotide sequences with 'N' and in protein sequences with 'X'. New application consambig reports an alignment consensus sequence using ambiguity characters. The intended use cases are sequencing reads and SNP reporting. New application sizeseq sorts sequences in ascending or descending order of length. This is a port of the application seqsort from the domsearch EMBASSY package. New application skipredundant uses pairwise sequence matches to exclude sequences that are similar from an input set. This is a modified version of the application seqnr from the domsearch EMBASSY package. New applications provide utility functions for former GCG users: nohtml removes HTML tags, notab replaces tabs with spaces, nospace removes all whitespace from a file, skipspace removes extra whitespace from a file. Older EMBOSS applications can now generate a warning message stating that they are marked as 'obsolete' with an explanation and an indication of alternative programs in EMBOSS or in an EMBASSY package. This warning can be turned off by defining environment variable EMBOSS_WARNOBSOLETE with a value of "N" or by defining the same variable in the emboss.defaults or ~/.embossrc files. We will begin to mark applications as 'obsolete' in future releases. A new EMBASSY package "myembossdemo" contains the demonstration applications demoalign, demofeatures, demolist, demoreport, demosequence, demostring, demostringnew and demotable that illustrate how to use EMBOSS data types in your own applications. The myembossdemo package allows novice developers to try simple EMBOSS programming. The myemboss package is available for adding your own applications. The demo applications are no longer distributed with the main EMBOSS package. They were not installed and were only built with the "make check" option. Application short descriptions have been revised. The minimum length of application one line descriptions is increased from 60 to 70 characters. The descriptions are easier to write. Output from wossname can now be 90 characters wide. Interfaces that use the description in menus may need to allow some extra space. Function names in ajfile.c have been standardised. Old names are still accepted but are marked as "deprecated" and will generate warnings with the gcc compiler (see ajstr below). Other compilers will see no difference. New source files ajfiledata.c and ajfileio.c have been added. The buffered file data structures are renamed internally to be more consistent (AjPFileBuff to AjPFilebuff). notseq was unable to search for IDs containing '|' characters but uses string matching (not regular expressions) and these characters are valid in NCBI-style FASTA files if read with the "pearson" format which accepts the whole ID string without parsing. The sequence alignment code has been updated. Sequence alignments with low gap penalties failed to allow two gaps (one in each sequence) without a match in between. The embAlign functions are now simplified. Scores are returned by the PathCalc functions. The Walk functions that walk through the path and return the aligned sequences are faster and need fewer parameters. Profile alignments occasionally duplicated residues in the sequence around gap positions. Fast alignments around a limited width include additional residues at each end and require an offset rather than separate start positions. The offset if the difference between the two start positions used in 5.0.0 and earlier releases. Eprimer3 citations are corrected in the help text (from the ACD file) and in the documentation. The citation errors were traced to the original primer3_core documentation which has now been corrected. Wordmatch could confuse overlapping matches. It occasionally extended the wrong match and missed a corresponding new match. Seqmatchall results were correct with the default output format which reports match positions, but gave incorrect results with some other local alignment formats that include the sequence. Seqmatchall now stores alignments in the same way as other local alignment applications, and the alignment internals are corrected to ensure other applictaiopns will not have the same problem. Emma was officially supporting clustalw 1.83. Issues with clustalw 2.0 are now resolved and this version is supported if clustalw2 is installed. Emma executes an applications called clustalw (not clustalw2) so version 2.0 must be installed under this name or an environment variable EMBOSS_CLUSTALW needs to be defined to point to the executable clustalw2 file. Sequence format "selex" allows invalid sequence data files to be accepted as input. Selex format is still available but is no longer included in the formats that can be automatically detected. When reading selex format data, users need to put "-sformat selex" on the command line, or specify "selex::" at the from of the USA. See the HMMER (old version EMBASSY package) documentation for examples. HMMERNEW (recommended) examples use Stockholm format and so are unchanged. Program dbxfasta now defaults to a filename of "*.fasta" The previous default "*.dat" is not commonly used for FASTA format databases. Program msbar block mutations were 1 longer than the specified block and may crash if the block size was fixed (minimum and maximum block sizes the same). This off-by-one error is now corrected. In GenBank output format, multiple line KEYWORD sections were not formatted correctly. ACD list and select values (the menus that appear in the user prompt) can now have ACD variables. Although useful for local application development these are not used in EMBOSS distributed ACD files because the variables are difficult for web and GUI interfaces to resolve when presenting the menu text. List and Table internal data structures are now cached so that creating and deleting temporary lists and tables is more efficient. In emboss.default database definitions the filename and exclude values can be delimited by spaces, commas or semicolons. Previous releases used only spaces. Parsing is now consistent with the fields definition which allowed all the above characters. Protein sequences with pyrrolysine ('O') had 'O' converted to a gap because this was a gap character in early versions of Phylip. This was patched in 5.0.0 to allow 'O' in UniProt release 13. The gap character is upper case only, so 'o' was correctly read as pyrrolysine. Wordfinder used the same descriptions for two pairs of qualifiers. The descriptions are changed to make their meaning clear in commandline help and in web interfaces. New function ajTimeDiff returns the difference in seconds between two time values. Profiling tests showed that file reading and string handling can be made faster. String handling called functions many levels deep. Making this code inline and using macro versions improved performance for applications (e.g. database indexing) that use many string calls. File input requires each input line to be copied. Using copy-by-reference (ajStrAssignRef) often makes this more efficient. Existing macros now test for undefined strings: MAJSTRGETLEN, MAJSTRGETPTR, MAJSTRGETRES and MAJSTRGETUSE. New macros are added for string handling: MAJSTRDEL, MAJSTRGETUNIQUESTR, MAJSTRCMPC and MAJSTRCMPS. Memory management includes new macros AJCRESIZE0 and AJRESIZE0 provide resize functions that guarantee new memory is set to zero. The functions must be given the original allocated size. Using the GNU C run-time library, calls to mcheck and mprobe are available to test for memory corruption by examining the bytes before and after an address allocated by malloc. This can be turned on for any application, including Unix commands, with the environment variable MALLOC_CHECK_ which has values 0, 1, 2 or 3. 1 writes to standard error when a problem is found, 2 aborts the programs, 3 does both and 0 ignores errors. No recompilation is needed for this simple method. EMBOSS now has a ./configure option --enable-mprobe which enables two new functions. ajMemProbe, passed an address from malloc (AJNEW0, AJCNEW0, etc.) tests the bytes before and after and reports any errors. The advantage of using ajMemProbe rather than mprobe is that a macro MAJMEMPROBE also reports the file and line number where ist was called. To avoid large numbers of messages (when code has problems) a limit can be set with ajMemCheckSetLimit after which the program will exit. Note that enable-mprobe is incompatible with using valgrind to test for memory leaks - as mprobe and mcheck have to look at illegal bytes before and after allocated memory blocks. Memory checking is turned on by a call to mcheck, passing the function ajMemCheck, in ajnam.c before the first memory allocation. If any program calls malloc before calling embInit or embInitP this call will fail and issue a warning (if compiled with --enable-mprobe). A special call ajStrProbe tests any string with mprobe. Special calls ajListProbe and ajListProbeData test lists and their contents. For more details see http://www.gnu.org/software/libc/manual/ Protein sequences from the Staden package were read as nucleotide because they were missing information on the ID line to identify EMBL of SWISSPROT format. The sequences are now tested and correctly typed. Wordcount now accepts protein sequences as input. Previous releases only allowed nucleotide sequences. Wordfinder options had the same information prompt. These have been changed from "limit" to "minimum" and "maximum" to make their function clear. Prompting for values from the user now includes a test for standard input in use as an input file. If standard input is open, the default response is accepted and a message is written to the user. This is to avoid problems with command lines that use "stdin" as an input and do not include -auto. The acdpretty utility can now preserve comments in ACD files. Comments are maintained in blocks with blank lines before and after. Inline comments are started in column 50 unless they are exceptionally long. Comments themselves have white space cleaned up but otherwise are not reformatted. A new function ajAcdGetValueDefault is added to return the default value of an ACD qualifier. This can be combined with ajAcdIsUserdefined in wrappers to test for values changed by the user. Infile qualifiers in ACD have a new attribute "trydefault" which allows the default filename to fail. Any filename provided by the user has to exist. This was added to support the behaviour of the MIRA EMBASSY package. To allow an infile to fail the attribute "nullok" also must be set to "Y" Applications which produce an output file or graphics often created an empty output file when the plot was selected. The ACD files have been corrected to only create the file if it will be written to. Applications changed are charge, dan, freak, hmoment, iep and tcode. Whichdb only writes to its output file if -get is false. With -get it creates sequences. The outfile is no longer created when whichdb is in -get mode. String functions corrected so that Case in the name always means case-insensitive and works by converting to upper case. Some functions were defined the wrong way, with "Case" for the case-insensitive form. GFF3 format is now the default feature output. A new function ajFeatIsCds identifies protein coding nucleotide features (CDS) using the SO identifier. A new function ajFeattagIsNote identifies feature tags that are for the default feature tag. Protein features now use the new Sequence Ontology terms defined by BioSapiens. These are not yet accepted by GFF3 validators. The new SO identifiers are added to protein feature definitions and used internally. Feature format definitions (the Efeatures and Etags files) now allow #include references to other files. This allows a standard EMBL and Swissprot feature table definition to be included by the internal and GFF definitions. Redefinitions are allowed using + and - prefxes to add and remove tags for existing feature types. GFF3 format feature (and report) output is added. A new application "density" has been added. This reports the A+C+G+T and AT+GC densities of nucleic acid sequences within an adjustable sliding window. Plots of A+C+G+T or AT+GC are optionally produced. Molecular weight programs (e.g. digest, mowse) now have a -mono switch to allow use of monoisotopic weights. By default, average molecular weights are used. The Eamino.dat format has changed. Molecular weight information has been removed and put in its own Emolwt.dat file. This latter now allows specification of average and monoisotopic weights. Values for hydrogen and oxygen are specified as well as the amino acid weights. The library representation of amino acid property information has been changed. The EmbPropTable global table has been removed and replaced with EmbPPropAmino and EmbPPropMolwt objects. Pepcoil now produces a report (replacing a text output) in "motif" format. The default is changed to not report non coiled-coil regions as they are hard to distinguish in this format. The "motif" report format is extended to allow two score positions marked with "*" and "+" and labelled internally as "pos" and "pos2". No application uses pos2 (it was added for pepcoil, but both score maximum positions are always the same) A new function ajAcdIsUserdefined allows wrappers to test which qualifiers have values changed by the user so that they can use shorter command lines to launch the wrapped application. jaspscan application added. Scans sequences for transcription factors using the JASPAR matrices. jaspextract application added to move the JASPAR matrices into the EMBOSS data area subdirectories. Alignment format "trace" used to display internal data content, is renamed to "debug" to be consisten with other formats. A "debug" format is added for feature output. Application documentation has been updated to remove obsolete references to EMBL database identifiers. These are replaced with the correct accession numbers. Two new entries have been added to the "tembl" test EMBL database for use in the QA tests. Report output now checks the sequence and feature table type. Is the sequence is not a valid protein, protein-only formats (pir, swiss) will fail with an error message. Similarly, if the sequence is not a valid nucleotide sequence then nucleotide-only formats (embl, genbank) will fail with an error message. Garnier now uses the correct SwissProt and internal feature keys for protein secondary structure. The results will appear much better for example as a swissprot feature table. This required rewriting of the internals by recoding the secondary structure features with a "garnier" tag replacing the previous "helix", "sheet", "turns" and "coil" tags. The default output is unchanged. The results in other report formats will be changed. Silent no longer reports the "Dir" column. This is replaced by the new "Strand" column which reports "+" for a forward feature and "-" for a reverse feature. The following programs have changed default report output, with the strand included for nucleotide sequences: equicktandem, etandem, fuzznuc, fuzztran, recoder, restrict, silent, tcode, twofeat. The strand column can be removed with the new commandline associated qualifier -norstrandshow. Reports for nucleotide sequences have confusing ways to represent the start and end positions for features on the complementary strand. A strand column has been added to these reports, controlled by a new -rstrandshow qualifier and attribute. By default the strand is shown for all nucleotide reports (see a list of changed program outputs above). The start position is always lower than the end position for features on the complementary strand indicating the region that should be reversed. In past releases the seqtable report format (fuzznuc, dreg, dan) confusingly reversed start and end positions to indicate the unreported strand. For all report formats (nametable, table) the start and end positions are now consistent with nucleotide feature formats (gff, embl, genbank). Reports from dreg incorrectly reported sequences reversed with the -sreverse qualifier. Report headers now include the text "(Reversed)" when the input sequence(s) are reverse complemented. Phylogenetic trees in newick format are now parsed into internal trees and converted back for use by Phylip. This allows us to read other tree formats and pass them to Phylip (e.g. Nexus) Some ACD data types did not allow the input to be NULL because extra tests were carried out on the results. These are all cleaned up and tested so that they can safely be set to nullok and missing in local applications. New sequence reading formats for PDB files. By default the ATOM records are used (format "pdb"). An alternative format "pdbseq" will read the SEQRES records which give the original sequence. The ATOM records give the sequence determined from the structure. Improved the help text for the -stdout and -filter options to explain output files are written to standard output. Some users expected graphics output (from plplot) to be controlled. From ajb at ebi.ac.uk Tue Jul 15 19:49:46 2008 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Tue, 15 Jul 2008 20:49:46 +0100 (BST) Subject: [EMBOSS] EMBOSS 6.0.0: please download again Message-ID: <54508.81.98.242.91.1216151386.squirrel@webmail.ebi.ac.uk> There was a problem with the original upload of EMBOSS 6.0.0 and mEMBOSS-6.0.0 to the open-bio server. If you have downloaded either prior to receiving this message then please download again. Apologies for the error. Alan From ajb at ebi.ac.uk Wed Jul 16 19:29:21 2008 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Wed, 16 Jul 2008 20:29:21 +0100 (BST) Subject: [EMBOSS] EMBOSS 6.0.1 released Message-ID: <34749.81.98.242.91.1216236561.squirrel@webmail.ebi.ac.uk> A couple of problems were noticed by the EMBOSS community in 6.0.0 prompting us to produce another release rather than just a patch. So, a day later: EMBOSS 6.0.1 is now available from: ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.0.1.tar.gz mEMBOSS-6.0.1 is available from: ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.0.1-setup.exe This is a maintenance release and fixes missing graphics output in a range of applications (e.g. plotorf). In mEMBOSS it additionally fixes the "Load Sequence Attributes" button failure. Apologies for any inconvenience. The phrase "That could have gone better" springs to mind. Alan From niels at genomics.dk Thu Jul 17 09:23:21 2008 From: niels at genomics.dk (Niels Larsen) Date: Thu, 17 Jul 2008 11:23:21 +0200 Subject: [EMBOSS] X-dependency optional? In-Reply-To: <20070723003321.GA10302@kunpuu.plessy.org> References: <54666.81.98.241.17.1184486717.squirrel@webmail.ebi.ac.uk> <20070722105517.GC21806@kunpuu.plessy.org> <20070723003321.GA10302@kunpuu.plessy.org> Message-ID: <487F0F89.7030402@genomics.dk> Greetings, I get this error with 6.0.1, http://emboss.open-bio.org/pipermail/emboss/2007-July/003056.html and could probably silence it by installing libx-dev as suggested in the next post. But I am planning to include EMBOSS in a free distributable software package, and so the libx-dev package may or may not be on the target machines (and the package should install under regular users). I wont be using anything X. I could not make the error go away with any ./configure option .. did i overlook it or perhaps there isnt one? Niels L From ajb at ebi.ac.uk Thu Jul 17 10:16:11 2008 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 17 Jul 2008 11:16:11 +0100 (BST) Subject: [EMBOSS] X-dependency optional? In-Reply-To: <487F0F89.7030402@genomics.dk> References: <54666.81.98.241.17.1184486717.squirrel@webmail.ebi.ac.uk> <20070722105517.GC21806@kunpuu.plessy.org> <20070723003321.GA10302@kunpuu.plessy.org> <487F0F89.7030402@genomics.dk> Message-ID: <40852.81.98.242.91.1216289771.squirrel@webmail.ebi.ac.uk> Dear Nils, It can be tricky to remove that dependency. The configuration switch --without-x works on some systems. The FAQ mentions the problem briefly Q) I have a Linux system and compilation ends prematurely saying that it can't find the -lX11 libraries ... but I know I have X11 installed. A) You may well have the X11 server installed but you haven't installed the X11 development files. For example, on RPM distributions, you need to install: xorg-x11-devel (xorg-based X11 distros) or XFree86-devel (XFree86-based X11 distros) It could do with updating to reflect the package name in Debian-based distros and the new name for xorg-based distros. It does give a hint though. The books we're writing (1st proof stage) certainly give more information - the web pages will soon be updated using the material from the latter. I intend revisiting that area of configuration at some stage. Alan > Greetings, > > I get this error with 6.0.1, > > http://emboss.open-bio.org/pipermail/emboss/2007-July/003056.html > > and could probably silence it by installing libx-dev as suggested > in the next post. But I am planning to include EMBOSS in a free > distributable software package, and so the libx-dev package may or > may not be on the target machines (and the package should install > under regular users). I wont be using anything X. I could not make > the error go away with any ./configure option .. did i overlook it > or perhaps there isnt one? > > Niels L > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From niels at genomics.dk Thu Jul 17 20:12:54 2008 From: niels at genomics.dk (Niels Larsen) Date: Thu, 17 Jul 2008 22:12:54 +0200 Subject: [EMBOSS] X-dependency optional? In-Reply-To: <40852.81.98.242.91.1216289771.squirrel@webmail.ebi.ac.uk> References: <54666.81.98.241.17.1184486717.squirrel@webmail.ebi.ac.uk> <20070722105517.GC21806@kunpuu.plessy.org> <20070723003321.GA10302@kunpuu.plessy.org> <487F0F89.7030402@genomics.dk> <40852.81.98.242.91.1216289771.squirrel@webmail.ebi.ac.uk> Message-ID: <487FA7C6.3030109@genomics.dk> Dear Alan, Yes, the first couple of systems I tried on (an old Mandrake 2005 and Ubuntu 6.06) failed with the --without-x option. I might try including all libx-dev variants, or if that turns out difficult wait for your configuration update (such update is not critical for me at present, but I will be happy whenever its there.) Niels L ajb at ebi.ac.uk wrote: > Dear Nils, > > It can be tricky to remove that dependency. The configuration > switch --without-x works on some systems. The FAQ mentions > the problem briefly > > Q) I have a Linux system and compilation ends prematurely saying that > it can't find the -lX11 libraries ... but I know I have X11 > installed. > > A) You may well have the X11 server installed but you haven't installed > the X11 development files. For example, on RPM distributions, you need > to install: > xorg-x11-devel (xorg-based X11 distros) or > XFree86-devel (XFree86-based X11 distros) > > It could do with updating to reflect the package name in Debian-based > distros and the new name for xorg-based distros. It does give a > hint though. The books we're writing (1st proof stage) certainly give > more information - the web pages will soon be updated using the material > from the latter. > > I intend revisiting that area of configuration at some stage. > > Alan From staffa at niehs.nih.gov Thu Jul 17 22:24:22 2008 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS)) Date: Thu, 17 Jul 2008 18:24:22 -0400 Subject: [EMBOSS] SeaView In-Reply-To: <487F0F89.7030402@genomics.dk> Message-ID: I would really appreciate any evaluation of the editor SEAVIEW by anyone reading this. In reading the paper by Galtier,Gouy and Gautier, I see that it has been around quite a while. They make a passing reference to Smith's GDE, which was the foundation for GCG's SeqLab editor. Do you think SeaView is as good as SeqLab; better; worse? Thank you for your attention. Nick Staffa Telephone: 919-316-4569 (NIEHS: 6-4569) Scientific Computing Support Group NIEHS Enterprise-Wide Information Technology Support Contract (Science Task Monitor: Roy W. Reter (reter at niehs.nih.gov) National Institute of Environmental Health Sciences National Institutes of Health Research Triangle Park, North Carolina From peter.robinson at t-online.de Fri Jul 18 04:24:14 2008 From: peter.robinson at t-online.de (Peter Robinson) Date: Fri, 18 Jul 2008 06:24:14 +0200 Subject: [EMBOSS] SeaView In-Reply-To: References: Message-ID: <48801AEE.9090208@t-online.de> Staffa, Nick (NIH/NIEHS) wrote: Seaview has perhaps few bells and whistles but is easy to use and effective, I like it very much! -peter > I would really appreciate any evaluation of the editor SEAVIEW by anyone > reading this. In reading the paper by Galtier,Gouy and Gautier, > I see that it has been around quite a while. > They make a passing reference to Smith's GDE, which was the foundation for > GCG's SeqLab editor. Do you think SeaView is as good as SeqLab; better; > worse? > > Thank you for your attention. > > > > Nick Staffa > Telephone: 919-316-4569 (NIEHS: 6-4569) > Scientific Computing Support Group > NIEHS Enterprise-Wide Information Technology Support Contract > (Science Task Monitor: Roy W. Reter (reter at niehs.nih.gov) > National Institute of Environmental Health Sciences > National Institutes of Health > Research Triangle Park, North Carolina > > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > > From gbottu at vub.ac.be Fri Jul 18 12:48:50 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Fri, 18 Jul 2008 14:48:50 +0200 Subject: [EMBOSS] SeaView In-Reply-To: References: Message-ID: <48809132.5040907@vub.ac.be> Staffa, Nick (NIH/NIEHS) wrote: > I would really appreciate any evaluation of the editor SEAVIEW by anyone > reading this. > Do you think SeaView is as good as SeqLab Dear Nick, Well, at the BEN site I installed SeaView as replacement, when we lost GCG+SeqLab. SeqLab does multiple sequence editing + graphical display of features + allows to execute programs on sequence (ranges). SeaView is basically just an editor (although it can call clustal or muscle to re-align portions of the aligment, and make a dotplot). What I find a great loss is that in SeqLab you can with the mouse select a block and then with one click delete it, while with SeaView you need to press as many time the as there are columns to delete. But if you have nothing else SeaView is certainly not bad. It has the advantage to be freeware and that there are versions for several platforms. You can install it and test it yourself. It is in principle easy to install (although there might be problems with prerequisite libraries). You can obtain it from ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview (and in some LINUX distributions like Gentoo it is actually vailable). If you run into trouble I am willing to give some advice. Regards, Guy Bottu, Belgian EMBnet Node From andrespinzon at gmail.com Fri Jul 18 14:19:36 2008 From: andrespinzon at gmail.com (Andres Pinzon) Date: Fri, 18 Jul 2008 09:19:36 -0500 Subject: [EMBOSS] SeaView In-Reply-To: <48809132.5040907@vub.ac.be> References: <48809132.5040907@vub.ac.be> Message-ID: <8968fc7e0807180719r4700ecb3qbed32f0912e1c127@mail.gmail.com> Hi Nick, It is also available on Ubuntu hardy. Have you ever used CLC sequence viewer? http://www.clcbio.com/index.php?id=28 Thats the editor we use here at the Colombia node, and I think it is one of the most intuitive tools I have ever tried. It has most of the seaview features (plus some others) runs under several platforms, is free and is really easy to install (no dependencies, just java). The following address lists all the available features (for this and other CLC versions): http://www.clcbio.com/index.php?id=89 Best, On Fri, Jul 18, 2008 at 7:48 AM, Guy Bottu wrote: > Staffa, Nick (NIH/NIEHS) wrote: > >> I would really appreciate any evaluation of the editor SEAVIEW by anyone >> reading this. >> Do you think SeaView is as good as SeqLab >> > > Dear Nick, > > Well, at the BEN site I installed SeaView as replacement, when we lost > GCG+SeqLab. SeqLab does multiple sequence editing + graphical display of > features + allows to execute programs on sequence (ranges). SeaView is > basically just an editor (although it can call clustal or muscle to re-align > portions of the aligment, and make a dotplot). What I find a great loss is > that in SeqLab you can with the mouse select a block and then with one click > delete it, while with SeaView you need to press as many time the > as there are columns to delete. But if you have nothing else SeaView is > certainly not bad. It has the advantage to be freeware and that there are > versions for several platforms. > You can install it and test it yourself. It is in principle easy to install > (although there might be problems with prerequisite libraries). You can > obtain it from ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview (and in > some LINUX distributions like Gentoo it is actually vailable). If you run > into trouble I am willing to give some advice. > > Regards, > Guy Bottu, > Belgian EMBnet Node > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > -- Andr?s Pinz?n http://bioinf.ibun.unal.edu.co/~apinzon/ Bioinformatics Center, Colombia EMBnet node http://bioinf.ibun.unal.edu.co Tel +57 3165000 ext 16961 Fax +571 3165415 Micology and Phytopathology Laboratory - Los Andes University. http://bioinf.uniandes.edu.co Tel +571 3394949 ext. 2768 From david at compbio.dundee.ac.uk Fri Jul 18 14:31:20 2008 From: david at compbio.dundee.ac.uk (David Martin) Date: Fri, 18 Jul 2008 15:31:20 +0100 Subject: [EMBOSS] SeaView In-Reply-To: <48809132.5040907@vub.ac.be> Message-ID: On 18/7/08 13:48, "Guy Bottu" wrote: > Staffa, Nick (NIH/NIEHS) wrote: >> I would really appreciate any evaluation of the editor SEAVIEW by anyone >> reading this. >> Do you think SeaView is as good as SeqLab > > Dear Nick, > > Well, at the BEN site I installed SeaView as replacement, when we lost > GCG+SeqLab. SeqLab does multiple sequence editing + graphical display of > features + allows to execute programs on sequence (ranges). SeaView is > basically > just an editor (although it can call clustal or muscle to re-align portions of > the aligment, and make a dotplot). What I find a great loss is that in SeqLab > you can with the mouse select a block and then with one click delete it, while > with SeaView you need to press as many time the as there are > columns > to delete. But if you have nothing else SeaView is certainly not bad. It has > the > advantage to be freeware and that there are versions for several platforms. > You can install it and test it yourself. It is in principle easy to install > (although there might be problems with prerequisite libraries). You can obtain > it from ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview (and in some LINUX > distributions like Gentoo it is actually vailable). If you run into trouble I > am > willing to give some advice. You might want to take a look at Jalview 2 which will do editing, MSA, feature display and more. OK, I am a little biased (it is developed in our group) but a quick rundown of the key features: * edit on blocks/ranges * edit using representative sequences * Multiple views on the same alignment * features from arbitrary DAS servers (even map protein features onto DNA.) * integration with jmol for structure viewing * hide/display arbitrary columns/rows. * Multiple sequence alignment (Clustal, MAFFT, Muscle) * Tree construction on arbitrary regions. Available from Jalview.org ..d -- David Martin PhD Post-Genomics and Molecular Interactions Centre University of Dundee http://www.compbio.dundee.ac.uk/ The University of Dundee is a registered Scottish charity, No: SC015096 From charles-listes-emboss at plessy.org Fri Jul 18 15:13:32 2008 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Sat, 19 Jul 2008 00:13:32 +0900 Subject: [EMBOSS] SeaView Message-ID: <20080718151332.GH3227@kunpuu.plessy.org> Le Fri, Jul 18, 2008 at 02:48:50PM +0200, Guy Bottu a ?crit : > SeaView is certainly not bad. It has the advantage to be freeware and that > there are versions for several platforms. > You can install it and test it yourself. It is in principle easy to install > (although there might be problems with prerequisite libraries). Hi all, Indeed, to get PDF export requires the PDFlib, which is not free software. However, Manolo Gouy, the upstream author, kindly provided compilation options to replace the PDF support by a simple PS support. It is with this option that Seaview is built on Debian and its derivatives. As a bonus, on FreeDesktop compliant window managers (like GNOME, KDE, Xfce), alignments in Clustal?W format will be recognised as being openable with SeaView. Have a nice weekend, -- Charles Plessy Debian-Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From breedaditi at yahoo.com Fri Jul 18 19:49:40 2008 From: breedaditi at yahoo.com (Aditi Breed) Date: Fri, 18 Jul 2008 12:49:40 -0700 (PDT) Subject: [EMBOSS] Installation (make ) error Message-ID: <945780.72408.qm@web35903.mail.mud.yahoo.com> Hello , I get the following error when i try to make EMBOSS. Can some one guide me as to what i need to do , to get rid of this error . xwin.c:3378: error: 'XwDisplay' has no member named 'display' xwin.c:3378: error: 'XwDev' has no member named 'window' xwin.c:3378: error: 'XwDev' has no member named 'gc' xwin.c:3379: error: 'XwDev' has no member named 'width' xwin.c:3379: error: 'XwDev' has no member named 'height' xwin.c: In function 'imageops': xwin.c:3394: error: 'XwDev' has no member named 'write_to_window' xwin.c:3398: error: 'XwDev' has no member named 'write_to_window' xwin.c:3402: error: 'XwDev' has no member named 'write_to_pixmap' xwin.c:3406: error: 'XwDisplay' has no member named 'display' xwin.c:3407: error: 'XwDev' has no member named 'write_to_pixmap' make[2]: *** [xwin.lo] Error 1 make[2]: Leaving directory `/home/akhunovlab/DOWNLOADS/EMBOSS/EMBOSS-6.0.1/plplot' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/akhunovlab/DOWNLOADS/EMBOSS/EMBOSS-6.0.1/plplot' make: *** [all-recursive] Error 1 I shall be grateful if someone could please help .. Regards, Aditi "Great spirits often meet violent opposition with mediocre minds" - Albert Einstein From staffa at niehs.nih.gov Fri Jul 18 20:39:19 2008 From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS)) Date: Fri, 18 Jul 2008 16:39:19 -0400 Subject: [EMBOSS] SeaView In-Reply-To: <8968fc7e0807180719r4700ecb3qbed32f0912e1c127@mail.gmail.com> Message-ID: Thanks. I didn?t know CLC gave away anything. I printed out the manual(179 pages!), and it looks real spiffy. Must say that SeaView?s gray background makes reading sequence difficult. On 7/18/08 10:19 AM, "Andres Pinzon" wrote: > Hi Nick, > It is also available on Ubuntu hardy. Have you ever used CLC sequence viewer? > > http://www.clcbio.com/index.php?id=28 > > Thats the editor we use here at the Colombia node, and I think it is one of > the most > intuitive tools I have ever tried. It has most of the seaview features (plus > some others) runs > under several platforms, is free and is really easy to install (no > dependencies, just java). > > The following address lists all the available features (for this and other CLC > versions): > > http://www.clcbio.com/index.php?id=89 > > Best, > > On Fri, Jul 18, 2008 at 7:48 AM, Guy Bottu wrote: >> Staffa, Nick (NIH/NIEHS) wrote: >>> I would really appreciate any evaluation of the editor SEAVIEW by anyone >>> reading this. >>> Do you think SeaView is as good as SeqLab >> >> Dear Nick, >> >> Well, at the BEN site I installed SeaView as replacement, when we lost >> GCG+SeqLab. SeqLab does multiple sequence editing + graphical display of >> features + allows to execute programs on sequence (ranges). SeaView is >> basically just an editor (although it can call clustal or muscle to re-align >> portions of the aligment, and make a dotplot). What I find a great loss is >> that in SeqLab you can with the mouse select a block and then with one click >> delete it, while with SeaView you need to press as many time the >> as there are columns to delete. But if you have nothing else SeaView is >> certainly not bad. It has the advantage to be freeware and that there are >> versions for several platforms. >> You can install it and test it yourself. It is in principle easy to install >> (although there might be problems with prerequisite libraries). You can >> obtain it from ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview (and in >> some LINUX distributions like Gentoo it is actually vailable). If you run >> into trouble I am willing to give some advice. >> >> Regards, >> Guy Bottu, >> Belgian EMBnet Node >> _______________________________________________ >> EMBOSS mailing list >> EMBOSS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss > > From ajb at ebi.ac.uk Fri Jul 18 20:53:05 2008 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Fri, 18 Jul 2008 21:53:05 +0100 (BST) Subject: [EMBOSS] Installation (make ) error In-Reply-To: <945780.72408.qm@web35903.mail.mud.yahoo.com> References: <945780.72408.qm@web35903.mail.mud.yahoo.com> Message-ID: <58327.81.98.242.91.1216414385.squirrel@webmail.ebi.ac.uk> You need to install the X11 development files for your operating system. You did not say which OS and version you are using. I would guess from the output that it is some sort of Debian-based Linux one. If that is the case then you need to install the libx11-dev package from your distribution. If you are using an RPM-based Linux distribution then the RPM you need to install will be called something like xorg-x11-proto-devel After you have installed the correct package then you will need to do a 'make clean' in EMBOSS and then do the configuration step again. HTH Alan > Hello , > I get the following error when i try to make EMBOSS. > Can some one guide me as to what i need to do , to get rid of this error . > > > xwin.c:3378: error: 'XwDisplay' has no member named 'display' > xwin.c:3378: error: 'XwDev' has no member named 'window' > xwin.c:3378: error: 'XwDev' has no member named 'gc' > xwin.c:3379: error: 'XwDev' has no member named 'width' > xwin.c:3379: error: 'XwDev' has no member named 'height' > xwin.c: In function 'imageops': > xwin.c:3394: error: 'XwDev' has no member named 'write_to_window' > xwin.c:3398: error: 'XwDev' has no member named 'write_to_window' > xwin.c:3402: error: 'XwDev' has no member named 'write_to_pixmap' > xwin.c:3406: error: 'XwDisplay' has no member named 'display' > xwin.c:3407: error: 'XwDev' has no member named 'write_to_pixmap' > make[2]: *** [xwin.lo] Error 1 > make[2]: Leaving directory > `/home/akhunovlab/DOWNLOADS/EMBOSS/EMBOSS-6.0.1/plplot' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory > `/home/akhunovlab/DOWNLOADS/EMBOSS/EMBOSS-6.0.1/plplot' > make: *** [all-recursive] Error 1 > > > I shall be grateful if someone could please help .. > > Regards, > Aditi > > > "Great spirits often meet violent opposition with mediocre minds" - Albert > Einstein > > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From charles-listes-emboss at plessy.org Sat Jul 19 00:26:49 2008 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Sat, 19 Jul 2008 09:26:49 +0900 Subject: [EMBOSS] Installation (make ) error In-Reply-To: <58327.81.98.242.91.1216414385.squirrel@webmail.ebi.ac.uk> References: <945780.72408.qm@web35903.mail.mud.yahoo.com> <58327.81.98.242.91.1216414385.squirrel@webmail.ebi.ac.uk> Message-ID: <20080719002649.GB20577@kunpuu.plessy.org> Le Fri, Jul 18, 2008 at 09:53:05PM +0100, ajb at ebi.ac.uk a ?crit : > You need to install the X11 development files for your > operating system. > > You did not say which OS and version you are using. > > I would guess from the output that it is some sort of Debian-based Linux > one. If that is the case then you need to install the libx11-dev > package from your distribution. Hello, The packages on to install on Debian for building EMBOSS are: libx11-dev, x11proto-core-dev, libgdchart-gd2-xpm-dev, zlib1g-dev, libpng12-dev and libpcre3-dev. Have a nice day, -- Charles Plessy Debian-Med packaging team http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From kvddrift at earthlink.net Sun Jul 20 22:17:38 2008 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sun, 20 Jul 2008 18:17:38 -0400 Subject: [EMBOSS] EMBOSS 6.0.1 released In-Reply-To: <34749.81.98.242.91.1216236561.squirrel@webmail.ebi.ac.uk> References: <34749.81.98.242.91.1216236561.squirrel@webmail.ebi.ac.uk> Message-ID: <7EF664A9-8456-4778-9A99-30FCBD6A6C82@earthlink.net> Hi, I noticed that a libplplot is being created (on Mac OS X - using fink): /sw/src/fink.build/root-emboss-6.0.1-1/sw/lib/libplplot.dylib -> EMBOSS/libplplot.dylib There is afaik no mention of libplplot in the fink package for EMBOSS. Also the build log doesn't show it. Is this correct, I thought all libs were now called libeplplot? cheers, - Koen. On Jul 16, 2008, at 3:29 PM, ajb at ebi.ac.uk wrote: > A couple of problems were noticed by the EMBOSS community > in 6.0.0 prompting us to produce another release rather than just a > patch. > > So, a day later: > > EMBOSS 6.0.1 is now available from: > > ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.0.1.tar.gz > > mEMBOSS-6.0.1 is available from: > > ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.0.1-setup.exe > > > This is a maintenance release and fixes missing graphics output > in a range of applications (e.g. plotorf). > > In mEMBOSS it additionally fixes the "Load Sequence Attributes" button > failure. > > Apologies for any inconvenience. > > The phrase "That could have gone better" springs to mind. > > Alan > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss From ajb at ebi.ac.uk Mon Jul 21 08:25:56 2008 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 21 Jul 2008 09:25:56 +0100 (BST) Subject: [EMBOSS] EMBOSS 6.0.1 released In-Reply-To: <7EF664A9-8456-4778-9A99-30FCBD6A6C82@earthlink.net> References: <34749.81.98.242.91.1216236561.squirrel@webmail.ebi.ac.uk> <7EF664A9-8456-4778-9A99-30FCBD6A6C82@earthlink.net> Message-ID: <43484.81.98.242.91.1216628756.squirrel@webmail.ebi.ac.uk> Hi Koen, It is correct that EMBOSS uses the name 'libeplplot' for the graphics library throughout therefore no libraries called 'libplplot' are produced. The change to the name libeplplot was made, as you're probably aware, in EMBOSS 5.0.0. There is no mention of 'libplplot' in the source code (though it may be mentioned in documentation) and, verifying what you said, no 'libplplot' libraries are produced using a standard configure/make/make install of EMBOSS on a MacBook Pro here running 10.4.11 We therefore plead not guilty M'lud. HTH Alan > Hi, > > I noticed that a libplplot is being created (on Mac OS X - using fink): > > /sw/src/fink.build/root-emboss-6.0.1-1/sw/lib/libplplot.dylib -> > EMBOSS/libplplot.dylib > > There is afaik no mention of libplplot in the fink package for EMBOSS. > Also the build log doesn't show it. > > > Is this correct, I thought all libs were now called libeplplot? > > cheers, > > - Koen. > > > > On Jul 16, 2008, at 3:29 PM, ajb at ebi.ac.uk wrote: > >> A couple of problems were noticed by the EMBOSS community >> in 6.0.0 prompting us to produce another release rather than just a >> patch. >> >> So, a day later: >> >> EMBOSS 6.0.1 is now available from: >> >> ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.0.1.tar.gz >> >> mEMBOSS-6.0.1 is available from: >> >> ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.0.1-setup.exe >> >> >> This is a maintenance release and fixes missing graphics output >> in a range of applications (e.g. plotorf). >> >> In mEMBOSS it additionally fixes the "Load Sequence Attributes" button >> failure. >> >> Apologies for any inconvenience. >> >> The phrase "That could have gone better" springs to mind. >> >> Alan >> >> >> _______________________________________________ >> EMBOSS mailing list >> EMBOSS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss > From kvddrift at earthlink.net Mon Jul 21 22:09:55 2008 From: kvddrift at earthlink.net (Koen van der Drift) Date: Mon, 21 Jul 2008 18:09:55 -0400 Subject: [EMBOSS] EMBOSS 6.0.1 released In-Reply-To: <43484.81.98.242.91.1216628756.squirrel@webmail.ebi.ac.uk> References: <34749.81.98.242.91.1216236561.squirrel@webmail.ebi.ac.uk> <7EF664A9-8456-4778-9A99-30FCBD6A6C82@earthlink.net> <43484.81.98.242.91.1216628756.squirrel@webmail.ebi.ac.uk> Message-ID: <14E52975-99BD-4AE5-AA82-1785185F5111@earthlink.net> On Jul 21, 2008, at 4:25 AM, ajb at ebi.ac.uk wrote: > We therefore plead not guilty M'lud. I found the problem. Mea culpa :) FYI, there was a line in the fink package that made symlinks to all the dynamic libraries as follows: ln -s EMBOSS/lib{ajax,ajaxg,nucleus,plplot}.dylib /lib So I never found that when I searched for the string libplplot. It's all fixed now. Sorry for the noise, - Koen. From shrish at ccmb.res.in Wed Jul 23 06:50:05 2008 From: shrish at ccmb.res.in (Shrish Tiwari) Date: Wed, 23 Jul 2008 12:20:05 +0530 (IST) Subject: [EMBOSS] requests for backtranseq Message-ID: <129447317.1216795805530.JavaMail.root@127.0.0.1> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From prija.ponnan at gmail.com Thu Jul 24 09:08:44 2008 From: prija.ponnan at gmail.com (Prija Ponnan) Date: Thu, 24 Jul 2008 15:08:44 +0600 Subject: [EMBOSS] Installation (configure) error Message-ID: <67b1a92d0807240208h22084c7cv8c0135f11eb2faf8@mail.gmail.com> hello I encounter the following error while trying to *configure EMBOSS* checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for gawk... (cached) gawk checking for gcc... no checking for cc... no checking for cl.exe... no configure: error: no acceptable C compiler found in $PATH I'm using fedora-based linux OS Please guide me as to what I have to do to get rid of the error Thanx in advance -- Prija From ajb at ebi.ac.uk Thu Jul 24 09:51:36 2008 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 24 Jul 2008 10:51:36 +0100 (BST) Subject: [EMBOSS] Installation (configure) error In-Reply-To: <67b1a92d0807240208h22084c7cv8c0135f11eb2faf8@mail.gmail.com> References: <67b1a92d0807240208h22084c7cv8c0135f11eb2faf8@mail.gmail.com> Message-ID: <36902.86.9.126.186.1216893096.squirrel@webmail.ebi.ac.uk> Hi, You've obviously installed Fedora without any of the software development packages and you therefore need to install the C compiler. You can try doing: yum install gcc yum install gd-devel yum install xorg-x11-proto-devel Then try the emboss configuration again. It may be the case that you're still missing a few packages but the above is a reasonable start and should automatically download other needed development software. HTH Alan > hello > > I encounter the following error while trying to *configure EMBOSS* > > checking for gawk... gawk > checking whether make sets $(MAKE)... yes > checking for gawk... (cached) gawk > checking for gcc... no > checking for cc... no > checking for cl.exe... no > configure: error: no acceptable C compiler found in $PATH > > I'm using fedora-based linux OS > > Please guide me as to what I have to do to get rid of the error > > Thanx in advance > > -- > Prija > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From gbottu at vub.ac.be Thu Jul 24 16:11:37 2008 From: gbottu at vub.ac.be (Guy Bottu) Date: Thu, 24 Jul 2008 18:11:37 +0200 Subject: [EMBOSS] wEMBOSS 1.8.0 and wrappers4EMBOSS 2.2.0 released Message-ID: <4888A9B9.1030209@vub.ac.be> Dear users of wEMBOSS, We have the pleasure to announce that the new version of wEMBOSS has been released. It contains important bug and feature fixes : - wEMBOSS allows you to type in your Email address, so that the program is started "in the background" and you are warned by Email when it has finished. The idea was that you could then start other programs or close your Web browser. At a certain moment however a bug has appeared that made that on many systems the program crashed when you tried that. This bug has been fixed. - wEMBOSS did not work under Mac OSX unless a small change was made in the code (in the SETUID part). To relieve wEMBOSS site managers from the burden of having to "hack" the code themselves, we now distribute separate versions for Mac OSX and for other UNIX flavours. - The "Search for programs" function retrieved a huge number of irrelevant program names. This number has been drastically reduced by avoiding to search in the "See also" section of the program manuals. - The on-line manuals in HTML format are installed at different locations, depending on EMBOSS version and whether it is a standard EMBOSS or an EMBASSY program. wEMBOSS can now always find the manual, wherever it is installed by default. For a complete list of the changes you can look at the Changelog : http://sourceforge.net/project/shownotes.php?group_id=170030&release_id=615018 wEMBOSS 1.8.0 is released together with the new version 2.1.0 of wrappers4EMBOSS. Besides a lot of fixes, refreshments and enhancements it addresses the following important issues : - Those who installed the EBI Web Services module will have noticed that it stopped functioning. The reason is that the EBI upgraded its SOAP server without backwards compatibility. The new version of the wrapper contains upgraded versions of the clients. - This some were asking for : a tool to use a remote MRS server as sequence access mechanism under EMBOSS (using Web Services). - The PHYLIP suite (available under EMBOSS as an EMBASSY package) handles quite well the parsimony and distances methods, but is very weak for Maximum Likelihood (only 1 model, slow on big datasets). To address this deficiency we have added wrappers for PhyML and ModelGenerator. For a complete list of the changes you can look at the Changelog : http://sourceforge.net/project/shownotes.php?group_id=170030&release_id=615013 Regards, Belgian EMBnet Node - wEMBOSS development team, Guy Bottu From prija.ponnan at gmail.com Mon Jul 28 13:04:04 2008 From: prija.ponnan at gmail.com (Prija Ponnan) Date: Mon, 28 Jul 2008 18:34:04 +0530 Subject: [EMBOSS] Installation (make) error Message-ID: <67b1a92d0807280604o72fb878bo936952dfc12013e0@mail.gmail.com> Hello I'd encountered following error while trying to "make" EMBOSS gd.c:601: structure has no member named `palette' gd.c:602: structure has no member named `truecolour' gd.c: In function `plD_eop_gif': gd.c:1530: warning: assignment makes pointer from integer without a cast make[2]: *** [gd.lo] Error 1 make[2]: Leaving directory `/home/acbr/prija/EMBOSS-6.0.1/plplot' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/acbr/prija/EMBOSS-6.0.1/plplot' make: *** [all-recursive] Error 1 I'm using REDHAT linux OS Please guide me to get rid of this error Thanks in advance -- Prija From prija.ponnan at gmail.com Tue Jul 29 13:28:10 2008 From: prija.ponnan at gmail.com (Prija Ponnan) Date: Tue, 29 Jul 2008 18:58:10 +0530 Subject: [EMBOSS] EMBOSS installation Message-ID: <67b1a92d0807290628q3c541a0dv3e2e0261d4da4b17@mail.gmail.com> Hello I've finally installed EMBOSS 6.0.1 Thank You for your valuable guidance -- Prija From benys at usp.br Tue Jul 29 14:41:19 2008 From: benys at usp.br (Beny Spira) Date: Tue, 29 Jul 2008 11:41:19 -0300 Subject: [EMBOSS] gui Message-ID: <21e884180807290741l1d1913b8mfd66e4a21002037e@mail.gmail.com> Dear all, I wish to install emboss-explorer on both Debian and Mandriva. Installing in Debian is straightforward, there is an apt package. However, in Mandriva I tried to install it, but it needs configuration at the web server level, which I am not familiar with. Another problem is that in Debian it worked at first, but not anymore. My question is if there a simple protocol on how to configure the web-server (including what packages need to be installed) to use with emboss-explorer. My EMBOSS version is 5.0.0 Thanks Beny -- Beny Spira Departamento de Microbiologia Instituto de Ci?ncias Biom?dicas Universidade de S?o Paulo Av. Prof. Lineu Prestes 1374 S?o Paulo-SP CEP:05508-900 Brasil Tel: 5511-3091-7347 FAX: 5511-3091-7354 E-mail: benys at usp.br Homepage: www.icb.usp.br/~benys From charles-listes-emboss at plessy.org Tue Jul 29 15:13:58 2008 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Wed, 30 Jul 2008 00:13:58 +0900 Subject: [EMBOSS] gui In-Reply-To: <21e884180807290741l1d1913b8mfd66e4a21002037e@mail.gmail.com> References: <21e884180807290741l1d1913b8mfd66e4a21002037e@mail.gmail.com> Message-ID: <20080729151358.GF20143@kunpuu.plessy.org> Le Tue, Jul 29, 2008 at 11:41:19AM -0300, Beny Spira a ?crit : > In Debian it worked at first, but not anymore. Dear Beny, I made the last update of the Debian package for EMBOSS Explorer. Some files were moved but it does not restart apache automatically. Can you retry after restarting apache (or reloading its configuration, it is lighter)? If it still does not work, please give me details about the problem, and I will try to solve it. Have a a nice day, -- Charles Plessy Debian Med packaging team http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan