From pmr at ebi.ac.uk Fri Apr 13 06:09:52 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 13 Apr 2007 11:09:52 +0100 Subject: [emboss-dev] Profiling and testing water In-Reply-To: References: Message-ID: <461F56F0.3000707@ebi.ac.uk> Vivek Menon wrote: > Hello all, I am having issues compiling the water and needle programs from > the EMBOSS package. That makes 3 related requests in the past week! It seems profiling and looking at the code for water is becoming popular. For those who want to play with the code, it may be helpful to describe how the EMBOSS QA testing works. So far this has just been run internally to check that code changes have not broken anything. Firstly, edit file test/.embossrc to set the locations of the source test directory (emboss_qadata) and the installed test directory (emboss_testdata). The install directory is used for the test databases tsw, tembl (etc.) provided with the EMBOSS distribution. The source test directory is used so that the results of one test can be used in another. cd to the source test directory. cd to the qa subdirectory. Run all the QA tests using: ../../scripts/qatest.pl -without=srs (the command line option turns off tests that require SRS installed locally) Run one selected QA test: ../../scripts/qatest.pl water-ex Tests run in a subdirectory with the name of the test (test/qa/water-ex) If the test succeeds, the directory is removed (the command line option -kk keeps the directory). New tests are easy to define - add them to test/qatest.dat Each test has to have a unique name. Descriptions of the definition line types are in the top of the file. Tests assume files stderr and stdout are created and empty. All other output files must be included in the test definition (getting a surprise new file is an error). The .embossrc file defines the date to be 15-jul-2006 so do not be surprised if you see that date in your output - we use it to keep the results constant when updating the documentation. All the *-ex tests are examples for the manuals. Have fun!!! Peter From paul.guermonprez at intel.com Tue Apr 17 07:17:32 2007 From: paul.guermonprez at intel.com (Guermonprez, Paul) Date: Tue, 17 Apr 2007 12:17:32 +0100 Subject: [emboss-dev] Profiling and testing water References: <461F56F0.3000707@ebi.ac.uk> Message-ID: <48F17FCD4E8AB449BD956AF127AE4FD40158BF46@irsmsx411.ger.corp.intel.com> hello, you can find an software optimisation note for water here : http://www.guermonprez.net/projects/emboss/emboss-EBI_06_06.pdf http://www.guermonprez.net/projects/emboss/emboss-runsh.tar.gz the sources are last year emboss release. 11-12x speedup on regular servers (serially). feel free to send comments. regards, paul. -----Original Message----- From: emboss-dev-bounces at lists.open-bio.org on behalf of Peter Rice Sent: Fri 4/13/2007 11:09 AM To: emboss at emboss.open-bio.org Cc: emboss-dev at emboss.open-bio.org Subject: [emboss-dev] Profiling and testing water Vivek Menon wrote: > Hello all, I am having issues compiling the water and needle programs from > the EMBOSS package. That makes 3 related requests in the past week! It seems profiling and looking at the code for water is becoming popular. For those who want to play with the code, it may be helpful to describe how the EMBOSS QA testing works. So far this has just been run internally to check that code changes have not broken anything. Firstly, edit file test/.embossrc to set the locations of the source test directory (emboss_qadata) and the installed test directory (emboss_testdata). The install directory is used for the test databases tsw, tembl (etc.) provided with the EMBOSS distribution. The source test directory is used so that the results of one test can be used in another. cd to the source test directory. cd to the qa subdirectory. Run all the QA tests using: ../../scripts/qatest.pl -without=srs (the command line option turns off tests that require SRS installed locally) Run one selected QA test: ../../scripts/qatest.pl water-ex Tests run in a subdirectory with the name of the test (test/qa/water-ex) If the test succeeds, the directory is removed (the command line option -kk keeps the directory). New tests are easy to define - add them to test/qatest.dat Each test has to have a unique name. Descriptions of the definition line types are in the top of the file. Tests assume files stderr and stdout are created and empty. All other output files must be included in the test definition (getting a surprise new file is an error). The .embossrc file defines the date to be 15-jul-2006 so do not be surprised if you see that date in your output - we use it to keep the results constant when updating the documentation. All the *-ex tests are examples for the manuals. Have fun!!! Peter _______________________________________________ emboss-dev mailing list emboss-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss-dev From pmr at ebi.ac.uk Thu Apr 26 07:53:47 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 26 Apr 2007 12:53:47 +0100 Subject: [emboss-dev] TeX or LaTeX experts? Message-ID: <463092CB.3090307@ebi.ac.uk> Quick plea for help ... does anyone know a reliable way to convert TeX documentation into HTML? The reason for asking is that someone asked about an error in the HTML version (now rather ancient) of the EMBOSS admin guide ... and I noticed it has a word deleted throughout. The word is "EMBOSS" where it appears as bold text in the postscript and PDF versions! We are working on the new admin guide (the HTML one on the website was for EMBOSS 2.5.0) so this is just an interim fix. Peter From pmr at ebi.ac.uk Thu Apr 26 11:58:35 2007 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 26 Apr 2007 16:58:35 +0100 Subject: [emboss-dev] TeX or LaTeX experts? In-Reply-To: <463092CB.3090307@ebi.ac.uk> References: <463092CB.3090307@ebi.ac.uk> Message-ID: <4630CC2B.7040801@ebi.ac.uk> Peter Rice wrote: > Quick plea for help ... does anyone know a reliable way to convert TeX documentation > into HTML? Thanks for the help everyone. The trouble turned out to be that Latex2html ignores all style files, and that is where the bold "EMBOSS" text is defined. Style files have to be rewritten as very horrible perl functions. I think it worked - at least it now has "EMBOSS" in the right places and I've removed some HGMP (or uk.embnet.org) references. regards, Peter From jrvalverde at cnb.uam.es Fri Apr 27 06:01:43 2007 From: jrvalverde at cnb.uam.es (Jose R. Valverde) Date: Fri, 27 Apr 2007 12:01:43 +0200 Subject: [emboss-dev] TeX or LaTeX experts? In-Reply-To: <4630CC2B.7040801@ebi.ac.uk> References: <463092CB.3090307@ebi.ac.uk> <4630CC2B.7040801@ebi.ac.uk> Message-ID: <20070427120143.5cd7dc13@veda.cnb.uam.es> Eric Raymond has a TeX/LaTeX to SGML conversion utility set up in his home page (look under Software). I can't remember the address right now but a Google search should point it. I'm not sure if that will do, but is worth a try. j On Thu, 26 Apr 2007 16:58:35 +0100 Peter Rice wrote: > Peter Rice wrote: > > Quick plea for help ... does anyone know a reliable way to convert TeX documentation > > into HTML? > > Thanks for the help everyone. > > The trouble turned out to be that Latex2html ignores all style files, and that > is where the bold "EMBOSS" text is defined. > > Style files have to be rewritten as very horrible perl functions. I think it > worked - at least it now has "EMBOSS" in the right places and I've removed some > HGMP (or uk.embnet.org) references. > > regards, > > Peter > _______________________________________________ > emboss-dev mailing list > emboss-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss-dev -- These opinions are mine and only mine. Hey man, I saw them first! Jos? R. Valverde De nada sirve la Inteligencia Artificial cuando falta la Natural -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 189 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss-dev/attachments/20070427/17bfeaa3/attachment.bin