The point was exactly to _not_ hardcode it :)
On Wed, Oct 7, 2015 at 2:08 PM, Niek de Klein <[email protected]
<mailto:[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]
<mailto:[email protected]>> wrote:
If you go thru creating a BOOST_ROOT shouldn't you do this also:
configopts = '--with-boost=$BOOST_ROOT'
/Martin
On Wed, Oct 7, 2015 at 10:49 AM, Niek de Klein
<[email protected] <mailto:[email protected]>> wrote:
Hi Arnau,
Here is the easyconfig file I have but it is not working
yet because it makes Boost instead of using the already
installed one.
Cheers,
Niek
easyblock = 'ConfigureMake'
name = 'Bridger'
version = 'r2014-12-01'
homepage = 'https://wiki.gacrc.uga.edu/wiki/Bridger'
description = """Bridger is an efficient de novo
trascriptome assembler for RNA-Seq data. """
toolchain = {'name': 'goolf', 'version': '1.7.20'}
toolchainopts = {'pic': True, 'usempi': True}
preconfigopts = 'export BOOST_ROOT=$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'
<http://downloads.sourceforge.net/project/rnaseqassembly%27>)]
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] <mailto:[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] <mailto:[email protected]>>:
That works, thanks!
On Thu, Sep 24, 2015 at 11:11 AM, Jens Timmerman
<[email protected]
<mailto:[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
<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'
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