Thanks! 2015-10-07 10:49 GMT+02:00 Niek de Klein <[email protected]>:
> 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' >>>> >>>> >>>> >>>> >>>> >>>> >>> >> >
