It's in there, albeit hard coded: configopts = '--with-boost=/apps/software/Boost/1.57.0-goolf-1.7.20-Python-2.7.9/'
On Wed, Oct 7, 2015 at 1:49 PM, Martin <[email protected]> wrote: > If you go thru creating a BOOST_ROOT shouldn't you do this also: > > configopts = '--with-boost=$BOOST_ROOT' > > > /Martin > > On Wed, Oct 7, 2015 at 10:49 AM, Niek de Klein <[email protected]> > wrote: > >> Hi Arnau, >> >> Here is the easyconfig file I have but it is not working yet because it >> makes Boost instead of using the already installed one. >> >> Cheers, >> Niek >> >> >> easyblock = 'ConfigureMake' >> >> name = 'Bridger' >> version = 'r2014-12-01' >> >> homepage = 'https://wiki.gacrc.uga.edu/wiki/Bridger' >> description = """Bridger is an efficient de novo trascriptome assembler >> for RNA-Seq data. """ >> >> toolchain = {'name': 'goolf', 'version': '1.7.20'} >> toolchainopts = {'pic': True, 'usempi': True} >> >> preconfigopts = 'export BOOST_ROOT=$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' >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>> >> > > > -- > http://www.xing.com/profile/Martin_Marcher > http://www.linkedin.com/in/martinmarcher > Mobil: +43 / 660 / 62 45 103 > UID: ATU68801424 >
