From maj at fortinbras.us Mon Jul 20 15:47:38 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 20 Jul 2009 15:47:38 -0400 Subject: [BioLib-dev] a CMake walkthrough on the wiki Message-ID: <1EDF8F97CAF24F0698E618C6A7723E24@NewLife> Hi All, I've been plowing through the build, and made some notes on what's going on when during "cmake .". I've attempted to organize these at http://biolib.open-bio.org/wiki/CMake_Walkthrough Feel free to correct and amplify--might be useful to all- cheers, Mark From pmr at ebi.ac.uk Mon Jul 27 06:30:33 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 27 Jul 2009 11:30:33 +0100 Subject: [BioLib-dev] Open-bio cross-project issues Message-ID: <4A6D81C9.2040607@ebi.ac.uk> Peter C. wrote (to bioperl-l, biopython-l, emboss-dev): > Hi all, > > Peter Rice kindly said he will look into an OBF cross project mailing > list, but in the meantime this has been cross posted to the Biopython, > BioPerl, and EMBOSS development lists. There is a list already for this purpose - open-bio-l I think we will also need a cross-project wiki space on the OBF site. Is there something already used by other projects or should we set something up? I am cross-posting this to other OBF project lists to encourage developers interested in combining efforts to address common problems. This started with FASTQ short read formats, and open-bio-l (a low volume list) has also seen discussion of common test data sets. Please sign up to open-bio-l (if you are not there already) and post suggestions for cross-project issues there. The list subscription page is: http://lists.open-bio.org/mailman/listinfo/open-bio-l Please feel free to forward this to any other projects I may have missed (I picked the obvious addresses from the list.open-bio-org server) regards, Peter Rice _______________________________________________ emboss-dev mailing list emboss-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss-dev From pjotr.public14 at thebird.nl Tue Jul 28 07:25:26 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 28 Jul 2009 13:25:26 +0200 Subject: [BioLib-dev] File location Message-ID: <20090728112526.GA5826@thebird.nl> Hi Adam, Nice to see the progression. Currently your SWIG files are in biolib/src/mappings/swig/python this conflicts with other mappings like: biolib/src/mappings/swig/affyio biolib/src/mappings/swig/staden_io_lib biolib/src/mappings/swig/... Do you mind moving the biopp specific interface files into its own subdir. E.g.: biolib/src/mappings/swig/biopp Thanks, Pj. From pjotr.public14 at thebird.nl Fri Jul 31 03:58:10 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 31 Jul 2009 09:58:10 +0200 Subject: [BioLib-dev] Merging libsequence into main Message-ID: <20090731075810.GA8052@thebird.nl> Hi Xin, I have started merging your tree into the release candidate. I have pulled from your master_conflict branch (a bit odd name ;) and adjusted one major thing. Since libsequence needs the Boost++ libraries I have added those as a git submodule. After pulling from my libsequence branch at git at github.com:pjotrp/biolib.git (using git remote) you should see commit 8aa0e29ced45f24463f78804b718119c4412005a. Next update the submodules. Like this: git submodule -i update it will pull boost into root contrib directory ./contrib/boost/... I had to adjust some of your make files to match the new layout. So when you do: cd src/clibs/libsequence-1.6.6/src rm CMakeCache.txt cmake . make it should build the library in ../build fine. Next go to your Python mappings cd src/mappings/swig/python/libsequence rm CMakeCache.txt cmake . make and I get the error: /home/wrk/izip/git/opensource/biolib-libsequence/src/mappings/swig/python/libsequence/../../../../../contrib/libsequence-1.6.6/Sequence/AlignStream.hpp:65: Error: Syntax error in input(3). After pulling my tree, can you have a look into this? Do you see the same? Pj. From maj at fortinbras.us Mon Jul 20 19:47:38 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 20 Jul 2009 15:47:38 -0400 Subject: [BioLib-dev] a CMake walkthrough on the wiki Message-ID: <1EDF8F97CAF24F0698E618C6A7723E24@NewLife> Hi All, I've been plowing through the build, and made some notes on what's going on when during "cmake .". I've attempted to organize these at http://biolib.open-bio.org/wiki/CMake_Walkthrough Feel free to correct and amplify--might be useful to all- cheers, Mark From pmr at ebi.ac.uk Mon Jul 27 10:30:33 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 27 Jul 2009 11:30:33 +0100 Subject: [BioLib-dev] Open-bio cross-project issues Message-ID: <4A6D81C9.2040607@ebi.ac.uk> Peter C. wrote (to bioperl-l, biopython-l, emboss-dev): > Hi all, > > Peter Rice kindly said he will look into an OBF cross project mailing > list, but in the meantime this has been cross posted to the Biopython, > BioPerl, and EMBOSS development lists. There is a list already for this purpose - open-bio-l I think we will also need a cross-project wiki space on the OBF site. Is there something already used by other projects or should we set something up? I am cross-posting this to other OBF project lists to encourage developers interested in combining efforts to address common problems. This started with FASTQ short read formats, and open-bio-l (a low volume list) has also seen discussion of common test data sets. Please sign up to open-bio-l (if you are not there already) and post suggestions for cross-project issues there. The list subscription page is: http://lists.open-bio.org/mailman/listinfo/open-bio-l Please feel free to forward this to any other projects I may have missed (I picked the obvious addresses from the list.open-bio-org server) regards, Peter Rice _______________________________________________ emboss-dev mailing list emboss-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss-dev From pjotr.public14 at thebird.nl Tue Jul 28 11:25:26 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 28 Jul 2009 13:25:26 +0200 Subject: [BioLib-dev] File location Message-ID: <20090728112526.GA5826@thebird.nl> Hi Adam, Nice to see the progression. Currently your SWIG files are in biolib/src/mappings/swig/python this conflicts with other mappings like: biolib/src/mappings/swig/affyio biolib/src/mappings/swig/staden_io_lib biolib/src/mappings/swig/... Do you mind moving the biopp specific interface files into its own subdir. E.g.: biolib/src/mappings/swig/biopp Thanks, Pj. From pjotr.public14 at thebird.nl Fri Jul 31 07:58:10 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 31 Jul 2009 09:58:10 +0200 Subject: [BioLib-dev] Merging libsequence into main Message-ID: <20090731075810.GA8052@thebird.nl> Hi Xin, I have started merging your tree into the release candidate. I have pulled from your master_conflict branch (a bit odd name ;) and adjusted one major thing. Since libsequence needs the Boost++ libraries I have added those as a git submodule. After pulling from my libsequence branch at git at github.com:pjotrp/biolib.git (using git remote) you should see commit 8aa0e29ced45f24463f78804b718119c4412005a. Next update the submodules. Like this: git submodule -i update it will pull boost into root contrib directory ./contrib/boost/... I had to adjust some of your make files to match the new layout. So when you do: cd src/clibs/libsequence-1.6.6/src rm CMakeCache.txt cmake . make it should build the library in ../build fine. Next go to your Python mappings cd src/mappings/swig/python/libsequence rm CMakeCache.txt cmake . make and I get the error: /home/wrk/izip/git/opensource/biolib-libsequence/src/mappings/swig/python/libsequence/../../../../../contrib/libsequence-1.6.6/Sequence/AlignStream.hpp:65: Error: Syntax error in input(3). After pulling my tree, can you have a look into this? Do you see the same? Pj.