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' >> >> >> >> >> >> >
