On 12 Dec 2013, at 13:07, jens timmerman wrote:
> 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
Oh, that actually makes a lot of sense... Why didn't I realize this earlier. >_<
Thanks Jens!
Pablo: I now realize there's no bug after all, Jens is right, this is the
correct way of doing this.
regards,
Kenneth
>
>
> 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
>
