Hi Arnau, Here is the easyconfig file I have but it is not working yet because it makes Boost instead of using the already installed one.
Cheers, Niek easyblock = 'ConfigureMake' name = 'Bridger' version = 'r2014-12-01' homepage = 'https://wiki.gacrc.uga.edu/wiki/Bridger' description = """Bridger is an efficient de novo trascriptome assembler for RNA-Seq data. """ toolchain = {'name': 'goolf', 'version': '1.7.20'} toolchainopts = {'pic': True, 'usempi': True} preconfigopts = 'export BOOST_ROOT=$EBROOTBOOST;' preconfigopts += 'export BOOST_INCLUDEDIR=$EBROOTBOOST/include;' preconfigopts += 'export BOOST_LIBRARYDIR=$EBROOTBOOST/lib;' configopts = '--with-boost=/apps/software/Boost/1.57.0-goolf-1.7.20-Python-2.7.9/' sources = ['%(name)s_%(version)s.tar.gz'] source_urls = [('http://downloads.sourceforge.net/project/rnaseqassembly')] dependencies = [ ('zlib', '1.2.8'), ('Boost', '1.57.0','-Python-2.7.9'), ] files_to_copy = [('Assemble','bin/')] moduleclass = 'bio' On Wed, Oct 7, 2015 at 10:39 AM, Arnau <[email protected]> wrote: > Hi Niek, > > would you mind sharing your easyconfig file for Bridger? :-) > > TIA, > Arnau > > 2015-09-24 11:20 GMT+02:00 Niek de Klein <[email protected]>: > >> That works, thanks! >> >> On Thu, Sep 24, 2015 at 11:11 AM, Jens Timmerman <[email protected] >> > wrote: >> >>> Hi Niek, >>> >>> SOURCELOWER_TAR_BZ2 results in 'bridger-r2014.12.01' >>> so this wil not work in the sources field. >>> >>> your version seems wrong aswell >>> This seems to work for me: >>> >>> >>> easyblock = 'MakeCp' >>> >>> name = 'Bridger' >>> version = 'r2014-12-01' >>> >>> homepage = 'https://wiki.gacrc.uga.edu/wiki/Bridger' >>> description = """Bridger is an efficient de novo trascriptome assembler >>> for RNA-Seq data. """ >>> >>> toolchain = {'name': 'goolf', 'version': '1.7.20'} >>> toolchainopts = {'pic': True, 'usempi': True} >>> >>> >>> sources = ['%(name)s_%(version)s.tar.gz'] >>> source_urls = [('http://downloads.sourceforge.net/project/rnaseqassembly >>> ')] >>> >>> >>> files_to_copy = [('Assemble','bin/')] >>> >>> moduleclass = 'bio' >>> >>> On 24/09/15 10:55, Niek de Klein wrote: >>> >>> Hi easybuild list, >>> >>> I'm trying to install Bridger from sourceforge. The sourceforge link is: >>> >>> >>> sourceforge.net/projects/rnaseqassembly/files/Bridger_r2014-12-01.tar.gz/download >>> >>> >>> >>> So I tried using >>> >>> name = 'Bridger' >>> version = 'r2014.12.01' >>> [..] >>> source_urls = [SOURCEFORGE_SOURCE] >>> sources = ['%%(name)s_%s.tar.gz' % '-'.join(version.split('.'))] >>> >>> but this does not find the file to download. Looking at other programs >>> installed from sourceforge it looks for this >>> >>> >>> sourceforge.net/projects/rnaseqassembly/files/bridger//2014.12.01/Bridger_2014-12-01.tar.gz/download >>> >>> so I think because this does not make use of >>> <tool>/<version>/<tool_version.tar.gz> SOURCEFORGE_SOURCE won't work, >>> correct? >>> >>> So then I tried with >>> >>> source_urls = ['sourceforge.net/projects/rnaseqassembly/files/'] >>> sources = ['%%(name)s_%s.tar.gz/download' % >>> '-'.join(version.split('.'))] >>> >>> But this gives the error >>> Unknown file type for file >>> /apps/sources/b/Bridger/Bridger_r2014-12-01.tar.gz/download (['download'])") >>> >>> Without /download at the end it doesn't find the url. >>> >>> Other things I have tried: >>> >>> source_urls = ['sourceforge.net/projects/rnaseqassembly/files/'] >>> sources = [('%%(name)s_%s.tar.gz' % >>> '-'.join(version.split('.')),'download')] >>> >>> >>> sources = [SOURCELOWER_TAR_BZ2] >>> source_urls = [('http://sourceforge.net/projects/rnaseqassembly/files/', >>> 'download')] >>> >>> and >>> >>> sources = [SOURCELOWER_TAR_BZ2] >>> source_urls = [('http://sourceforge.net/projects/rnaseqassembly/', >>> 'download')] >>> >>> But then the files can't be found. I don't know what else to try, how >>> can I get this downloaded from sourceforge? Below the full .eb file for >>> replication: >>> >>> easyblock = 'MakeCp' >>> >>> name = 'Bridger' >>> version = 'r2014.12.01' >>> >>> homepage = 'https://wiki.gacrc.uga.edu/wiki/Bridger' >>> description = """Bridger is an efficient de novo trascriptome assembler >>> for RNA-Seq data. """ >>> >>> toolchain = {'name': 'goolf', 'version': '1.7.20'} >>> toolchainopts = {'pic': True, 'usempi': True} >>> >>> >>> sources = [SOURCELOWER_TAR_BZ2] >>> source_urls = [('http://sourceforge.net/projects/rnaseqassembly/files', >>> 'download')] >>> >>> >>> files_to_copy = [('Assemble','bin/')] >>> >>> moduleclass = 'bio' >>> >>> >>> >>> >>> >>> >> >
