Re: [easybuild] Sourceforge download

2015-10-08 Thread Niek de Klein 
Hi Martin,


Thanks for making the .eb file. However, I am getting the below error for
the plugin patch, do you know how to fix this?

Thanks,
Niek

== 2015-10-08 21:23:25,613 main ERROR cmd "patch -b -p1 -i
/apps/sources/EasyBuild/custom/Bridger-r2014-12-01-fix-plugin-Makefiles.patch"
exited with exitcode 1 and output:
patching file plugins/fastool/Makefile
Hunk #1 FAILED at 1.
1 out of 1 hunk FAILED -- saving rejects to file
plugins/fastool/Makefile.rej
patching file plugins/rsem/makefile
Hunk #2 FAILED at 50.
Hunk #3 FAILED at 83.
Hunk #4 FAILED at 93.
Hunk #5 FAILED at 127.
4 out of 5 hunks FAILED -- saving rejects to file plugins/rsem/makefile.rej
patching file plugins/rsem/sam/Makefile
Hunk #1 FAILED at 1.
Hunk #2 FAILED at 25.
Hunk #3 FAILED at 48.
3 out of 3 hunks FAILED -- saving rejects to file
plugins/rsem/sam/Makefile.rej
patching file plugins/rsem/sam/bcftools/Makefile
Hunk #1 FAILED at 1.
Hunk #2 FAILED at 11.
Hunk #3 FAILED at 31.
3 out of 3 hunks FAILED -- saving rejects to file
plugins/rsem/sam/bcftools/Makefile.rej
patching file plugins/rsem/sam/misc/Makefile
Hunk #1 FAILED at 1.
Hunk #2 FAILED at 11.
Hunk #3 FAILED at 20.
Hunk #4 FAILED at 28.
4 out of 4 hunks FAILED -- saving rejects to file
plugins/rsem/sam/misc/Makefile.rej
 (at easybuild/tools/run.py:359 in parse_cmd_output)
== 2015-10-08 21:23:25,647 main.easyblock WARNING build failed (first 300
chars): cmd "patch -b -p1 -i
/apps/sources/EasyBuild/custom/Bridger-r2014-12-01-fix-plugin-Makefiles.patch"
exited with exitcode 1 and output:
patching file plugins/fastool/Makefile
Hunk #1 FAILED at 1.
1 out of 1 hunk FAILED -- saving rejects to file
plugins/fastool/Makefile.rej
patching file plugins/rsem/
== 2015-10-08 21:23:25,647 main.MakeCp INFO Closing log for application
name Bridger version r2014-12-01

On Thu, Oct 8, 2015 at 5:49 PM, Martin  wrote:

> The software derives stuff from BOOST_ROOT existing as an environment
> variable
>
> Anyhow I put some work into it as we also needed Bridger, sorry for it not
> being a pull request but maybe it is of some use to Niek de Klein.
>
> Mind you: Not my best piece of work, but it gets the job done. Also Kudos
> to Arnau for beating me to it :)
>
> best,
> Martin
>
>
> Files are attached
> On Wed, Oct 7, 2015 at 5:11 PM, Kenneth Hoste 
> wrote:
>
>> Why the $BOOST_ROOT, and not just use
>> --configopts="--with-boost=$EBROOTBOOST" ?
>>
>
>
>
>
> --
> http://www.xing.com/profile/Martin_Marcher
> http://www.linkedin.com/in/martinmarcher
> Mobil: +43 / 660 / 62 45 103
> UID: ATU68801424
>

Re: [easybuild] Sourceforge download

2015-10-08 Thread Martin 
The software derives stuff from BOOST_ROOT existing as an environment
variable

Anyhow I put some work into it as we also needed Bridger, sorry for it not
being a pull request but maybe it is of some use to Niek de Klein.

Mind you: Not my best piece of work, but it gets the job done. Also Kudos
to Arnau for beating me to it :)

best,
Martin


Files are attached
On Wed, Oct 7, 2015 at 5:11 PM, Kenneth Hoste 
wrote:

> Why the $BOOST_ROOT, and not just use
> --configopts="--with-boost=$EBROOTBOOST" ?
>




-- 
http://www.xing.com/profile/Martin_Marcher
http://www.linkedin.com/in/martinmarcher
Mobil: +43 / 660 / 62 45 103
UID: ATU68801424
<>

Re: [easybuild] Sourceforge download

2015-10-07 Thread Kenneth Hoste 
Why the $BOOST_ROOT, and not just use 
--configopts="--with-boost=$EBROOTBOOST" ?



K.

On 07/10/15 14:58, Martin wrote:

The point was exactly to _not_ hardcode it :)

On Wed, Oct 7, 2015 at 2:08 PM, Niek de Klein > 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 > 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
> 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
> 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
>:

That works, thanks!

On Thu, Sep 24, 2015 at 11:11 AM, Jens Timmerman
> 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

Re: [easybuild] Sourceforge download

2015-10-07 Thread Niek de Klein 
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  wrote:

> If you go thru creating a BOOST_ROOT shouldn't you do this also:
>
> configopts = '--with-boost=$BOOST_ROOT'
>
>
> /Martin
>
> On Wed, Oct 7, 2015 at 10:49 AM, Niek de Klein 
> wrote:
>
>> Hi Arnau,
>>
>> Here is the easyconfig file I have but it is not working yet because it
>> makes Boost instead of using the already installed one.
>>
>> Cheers,
>> Niek
>>
>>
>> easyblock = 'ConfigureMake'
>>
>> name = 'Bridger'
>> version = 'r2014-12-01'
>>
>> homepage = 'https://wiki.gacrc.uga.edu/wiki/Bridger'
>> description = """Bridger is an efficient de novo trascriptome assembler
>> for RNA-Seq data. """
>>
>> toolchain = {'name': 'goolf', 'version': '1.7.20'}
>> toolchainopts = {'pic': True, 'usempi': True}
>>
>> preconfigopts = 'export BOOST_ROOT=$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  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 :
>>>
 That works, thanks!

 On Thu, Sep 24, 2015 at 11:11 AM, Jens Timmerman <
 jens.timmer...@ugent.be> 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
> // 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

Re: [easybuild] Sourceforge download

2015-10-07 Thread Martin 
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 
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  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 :
>>
>>> That works, thanks!
>>>
>>> On Thu, Sep 24, 2015 at 11:11 AM, Jens Timmerman <
>>> jens.timmer...@ugent.be> 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
 // 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'

Re: [easybuild] Sourceforge download

2015-10-07 Thread Arnau 
Thanks!

2015-10-07 10:49 GMT+02:00 Niek de Klein :

> 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  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 :
>>
>>> That works, thanks!
>>>
>>> On Thu, Sep 24, 2015 at 11:11 AM, Jens Timmerman <
>>> jens.timmer...@ugent.be> 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
 // 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'






>>>
>>
>

Re: [easybuild] Sourceforge download

2015-10-07 Thread Niek de Klein 
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  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 :
>
>> That works, thanks!
>>
>> On Thu, Sep 24, 2015 at 11:11 AM, Jens Timmerman > > 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
>>> // 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'
>>>
>>>
>>>
>>>
>>>
>>>
>>
>

Re: [easybuild] Sourceforge download

2015-10-07 Thread Arnau 
Hi Niek,

would you mind sharing your easyconfig file for Bridger? :-)

TIA,
Arnau

2015-09-24 11:20 GMT+02:00 Niek de Klein :

> That works, thanks!
>
> On Thu, Sep 24, 2015 at 11:11 AM, Jens Timmerman 
> 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
>> // 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'
>>
>>
>>
>>
>>
>>
>

Re: [easybuild] Sourceforge download

2015-09-24 Thread Jens Timmerman 

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 
// 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'

Re: [easybuild] Sourceforge download

2015-09-24 Thread Ward Poelmans 
What about:

sources= ['%(name)s_%(version)s.tar.gz']
source_urls = [('http://sourceforge.net/projects/rnaseqassembly/files/',
'download')]

Ward

On Thu, Sep 24, 2015 at 10:55 AM, 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
> // 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/',
> 'download')]
>
>
> files_to_copy = [('Assemble','bin/')]
>
> moduleclass = 'bio'
>
>
>
>



-- 
dr. ir. Ward Poelmans
Center for Molecular Modeling
Ghent University
Technologiepark 903,
B-9052 Zwijnaarde
Belgium
Tel: +32 9 264 65 76
E-mail: ward.poelm...@ugent.be
http://molmod.UGent.be/

[easybuild] Sourceforge download

2015-09-24 Thread Niek de Klein 
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
// 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/',
'download')]


files_to_copy = [('Assemble','bin/')]

moduleclass = 'bio'