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
<http://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
<http://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/
<http://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/
<http://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'
