Hi Pablo
On 12/11/2013 10:44 PM, Pablo Escobar Lopez wrote:
> As suggested by Kenneth I tried this
>
> ('BioPython', '1.62', {
> 'source_urls': ['http://biopython.org/DIST'],
> 'options': {'modulename': 'Bio'},
> }),
>
This should be
('BioPython', '1.62', {
'source_urls': ['http://biopython.org/DIST'],
'modulename': 'Bio',
}),
As en example you can see pycrypto here
https://github.com/hpcugent/easybuild-easyconfigs/pull/563/files#r8009224
Regards
Jens Timmerman
> But still getting the same problem :|
>
> $> grep -i "import bio" /scratch/easybuild-Su7OiF.log
>
> == 2013-12-11 22:39:25,559 main.filetools DEBUG run_cmd: running cmd
> python -c "import BioPython" (in /tmp/easybuild/Python/2.7.5/goolf-1.4.10)
> == 2013-12-11 22:40:26,207 main.filetools DEBUG run_cmd: running cmd
> python -c "import biopython" (in /tmp/easybuild)
> == 2013-12-11 22:40:26,239 main.EB_Python WARNING Extension: BioPython
> failed to install, cmd 'python -c "import biopython"' (stdin: None)
> output: Traceback (most recent call last):
> == 2013-12-11 22:40:26,240 main.EB_Python WARNING Sanity check for
> BioPython failed: BioPython failed to install, cmd 'python -c "import
> biopython"' (stdin: None) output: Traceback (most recent call last):
>
>
>
> 2013/12/11 Pablo Escobar Lopez <[email protected]
> <mailto:[email protected]>>
>
> Hi,
>
> I am trying to add an extra library (extension) to my python
> install. For this I have edited my eb file adding this to the
> extensions section
>
> ('biopython', '1.62', {
> 'source_urls': ['http://biopython.org/DIST'],
> 'options': {'modulename': 'Bio'},
> }),
>
> But when trying to run eb python.eb --force -k I get this error:
>
> == installing...
> == taking care of extensions...
> == packaging...
> == postprocessing...
> == sanity checking...
> ERROR: EasyBuild encountered an exception (at easybuild/main.py:770
> in build_and_install_software): autoBuild Failed (last 300 chars):
> EasyBuild crashed with an error (at
> easybuild/framework/easyblock.py:1547 in sanity_check_step): Sanity
> check failed: sanity checks for ['biopython'] extensions failed!
>
> The problem seem that eb is trying to do "import biopython" for
> sanity check instead of "import Bio" as set in the options. You can
> find this in the debug log (attached)
>
> == 2013-12-11 22:01:02,748 main.EB_Python WARNING Sanity check for
> biopython failed: biopython failed to install, cmd 'python -c
> "import biopython"' (stdin: None) output: Traceback (most recent
> call last):
> File "<string>", line 1, in <module>
> ImportError: No module named biopython
>
> By now I have workarounded it by temporally disabling sanity check
> in the python easyblock and enabling it again after install.
>
> do you how this could be done without tweaking the easyblock?
>
> maybe would be nice to have some cli option to do something like
> --no-sanity-check?
>
> regards,
> pablo.
>
>
> --
> Pablo Escobar López
> HPC systems engineer
> Biozentrum, University of Basel
> Email: [email protected]
> <mailto:[email protected]>
> Phone: +41 61 267 15 82 <tel:%2B41%2061%20267%2015%2082>
> http://www.biozentrum.unibas.ch
>
>
>
>
> --
> Pablo Escobar López
> HPC systems engineer
> Biozentrum, University of Basel
> Email: [email protected] <mailto:[email protected]>
> Phone: +41 61 267 15 82
> http://www.biozentrum.unibas.ch
