From cjfields at illinois.edu Tue Dec 1 14:56:24 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 1 Dec 2009 13:56:24 -0600 Subject: [BioLib-dev] EMBOSS mapping in Biolib In-Reply-To: <20091128101220.GA16682@thebird.nl> References: <20091125162731.GA3589@thebird.nl> <20091128101220.GA16682@thebird.nl> Message-ID: <37132A0B-B891-4C67-BDB9-B278507201E5@illinois.edu> Thanks Pjotr. I'll pull it off github and test it out this week (Mac OS X and Ubuntu Feisty). chris On Nov 28, 2009, at 4:12 AM, Pjotr Prins wrote: > I just executed the EMBOSS mapping for Perl (and Python). The writeup at: > > http://biolib.open-bio.org/wiki/Mapping_EMBOSS#Mapping_EMBOSS_Perl_and_Python > > It took three hours, and was a bit harder than normal after a succesful > Ruby mapping. > > Pj. > _______________________________________________ > BioLib-dev mailing list > BioLib-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biolib-dev From pjotr.public14 at thebird.nl Wed Dec 2 11:28:04 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 2 Dec 2009 17:28:04 +0100 Subject: [BioLib-dev] EMBOSS mapping in Biolib In-Reply-To: <37132A0B-B891-4C67-BDB9-B278507201E5@illinois.edu> References: <20091125162731.GA3589@thebird.nl> <20091128101220.GA16682@thebird.nl> <37132A0B-B891-4C67-BDB9-B278507201E5@illinois.edu> Message-ID: <20091202162804.GA9692@thebird.nl> Hi Chris, If you pull the emboss branch on github it should build with ./configure --with-perl --with-emboss make make test Note you need the submodules - it should read git submodules 713800c4aa08ddf70b87f245a524c1a0b30c0942 contrib/EMBOSS (heads/biolib) 3f05266254664f08f6e4f11c6ee005b6a8e083b3 tools/cmake-support (heads/master) 4016e6040efa2b09659ef034ebe3c127fe0137c0 tools/rubydoctest (REL-1.0-10-g4016e60) perhaps with git submodule update --init all three are on my github account. The submodules read cat .gitmodules [submodule "src/clibs/rqtl"] path = src/clibs/rqtl url = git://github.com/pjotrp/rqtl.git [submodule "tools/cmake-support"] path = tools/cmake-support url = git://github.com/pjotrp/cmake-support.git [submodule "tools/rubydoctest"] path = tools/rubydoctest url = git://github.com/pjotrp/rubydoctest.git [submodule "contrib/libsequence-1.6.6"] path = contrib/libsequence-1.6.6 url = git://github.com/pjotrp/libsequence.git [submodule "contrib/boost"] path = contrib/boost url = git://gitorious.org/boost/svn.git [submodule "contrib/EMBOSS"] path = contrib/EMBOSS url = git://github.com/pjotrp/EMBOSS.git Pj. On Tue, Dec 01, 2009 at 01:56:24PM -0600, Chris Fields wrote: > Thanks Pjotr. I'll pull it off github and test it out this week (Mac OS X and Ubuntu Feisty). > > chris > > On Nov 28, 2009, at 4:12 AM, Pjotr Prins wrote: > > > I just executed the EMBOSS mapping for Perl (and Python). The writeup at: > > > > http://biolib.open-bio.org/wiki/Mapping_EMBOSS#Mapping_EMBOSS_Perl_and_Python > > > > It took three hours, and was a bit harder than normal after a succesful > > Ruby mapping. > > > > Pj. > > _______________________________________________ > > BioLib-dev mailing list > > BioLib-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biolib-dev > From cjfields at illinois.edu Tue Dec 1 19:56:24 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 1 Dec 2009 13:56:24 -0600 Subject: [BioLib-dev] EMBOSS mapping in Biolib In-Reply-To: <20091128101220.GA16682@thebird.nl> References: <20091125162731.GA3589@thebird.nl> <20091128101220.GA16682@thebird.nl> Message-ID: <37132A0B-B891-4C67-BDB9-B278507201E5@illinois.edu> Thanks Pjotr. I'll pull it off github and test it out this week (Mac OS X and Ubuntu Feisty). chris On Nov 28, 2009, at 4:12 AM, Pjotr Prins wrote: > I just executed the EMBOSS mapping for Perl (and Python). The writeup at: > > http://biolib.open-bio.org/wiki/Mapping_EMBOSS#Mapping_EMBOSS_Perl_and_Python > > It took three hours, and was a bit harder than normal after a succesful > Ruby mapping. > > Pj. > _______________________________________________ > BioLib-dev mailing list > BioLib-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biolib-dev From pjotr.public14 at thebird.nl Wed Dec 2 16:28:04 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 2 Dec 2009 17:28:04 +0100 Subject: [BioLib-dev] EMBOSS mapping in Biolib In-Reply-To: <37132A0B-B891-4C67-BDB9-B278507201E5@illinois.edu> References: <20091125162731.GA3589@thebird.nl> <20091128101220.GA16682@thebird.nl> <37132A0B-B891-4C67-BDB9-B278507201E5@illinois.edu> Message-ID: <20091202162804.GA9692@thebird.nl> Hi Chris, If you pull the emboss branch on github it should build with ./configure --with-perl --with-emboss make make test Note you need the submodules - it should read git submodules 713800c4aa08ddf70b87f245a524c1a0b30c0942 contrib/EMBOSS (heads/biolib) 3f05266254664f08f6e4f11c6ee005b6a8e083b3 tools/cmake-support (heads/master) 4016e6040efa2b09659ef034ebe3c127fe0137c0 tools/rubydoctest (REL-1.0-10-g4016e60) perhaps with git submodule update --init all three are on my github account. The submodules read cat .gitmodules [submodule "src/clibs/rqtl"] path = src/clibs/rqtl url = git://github.com/pjotrp/rqtl.git [submodule "tools/cmake-support"] path = tools/cmake-support url = git://github.com/pjotrp/cmake-support.git [submodule "tools/rubydoctest"] path = tools/rubydoctest url = git://github.com/pjotrp/rubydoctest.git [submodule "contrib/libsequence-1.6.6"] path = contrib/libsequence-1.6.6 url = git://github.com/pjotrp/libsequence.git [submodule "contrib/boost"] path = contrib/boost url = git://gitorious.org/boost/svn.git [submodule "contrib/EMBOSS"] path = contrib/EMBOSS url = git://github.com/pjotrp/EMBOSS.git Pj. On Tue, Dec 01, 2009 at 01:56:24PM -0600, Chris Fields wrote: > Thanks Pjotr. I'll pull it off github and test it out this week (Mac OS X and Ubuntu Feisty). > > chris > > On Nov 28, 2009, at 4:12 AM, Pjotr Prins wrote: > > > I just executed the EMBOSS mapping for Perl (and Python). The writeup at: > > > > http://biolib.open-bio.org/wiki/Mapping_EMBOSS#Mapping_EMBOSS_Perl_and_Python > > > > It took three hours, and was a bit harder than normal after a succesful > > Ruby mapping. > > > > Pj. > > _______________________________________________ > > BioLib-dev mailing list > > BioLib-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biolib-dev >