The point was exactly to _not_ hardcode it :) On Wed, Oct 7, 2015 at 2:08 PM, Niek de Klein <[email protected]> wrote:
> 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 >> > > -- http://www.xing.com/profile/Martin_Marcher http://www.linkedin.com/in/martinmarcher Mobil: +43 / 660 / 62 45 103 UID: ATU68801424
