Hi Oliver, I tried to install that software doing "python setup.py install --user" and I cannot find anything in ~/.local/bin . I only get files in ~/.local/lib/python2.7/site-packages/ which is what easybuild is doing and then setting up PYTHONPATH in the modulefile, so when I load the misopy module I can import misopy in the python interpreter
[soft@login18 eb-test-installs]$ module load misopy [soft@login18 eb-test-installs]$ python Python 2.7.5 (default, Jun 20 2015, 21:57:09) [GCC 4.7.2] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import misopy >>> are you sure that misopy/0.5.3 is adding something to ~/.local/bin? At least in my system that's not the case.... I think what Niek suggests won't work for the PythonPackage easyblock. You can check all the available options in the PythonPackage easyblock by running "eb -a -e PythonPackage" and you can verify that those options are not avaiable by doing "eb -a -e PythonPackage| egrep 'executables|files_to_copy'". The option "files_to_copy" is only available in the MakeCp easyblock. $> eb -a -e MakeCp| egrep "executables|files_to_copy" files_to_copy* List of files or dirs to copy [default: []] regards, Pablo. 2015-06-23 19:11 GMT+02:00 Niek de Klein <[email protected]>: > HI Oliver, > > You can try the parameter executables and files_to_copy, like so: > > executables = ['binary_file_name'] > files_to_copy = [(executables, 'bin')] > > Cheers, > Niek > > > On Tue, Jun 23, 2015 at 5:29 PM, Stolpe, Oliver > <[email protected]> wrote: > > Hello list, > > > > I wrote an easyconfig file to install a python package. The installation > is > > successful besides the fact that easybuild throws away the binary that is > > generated (or main entrance point for the standalone). When I install the > > software on my machine with python setup.py build/install --user, it puts > > the binary to ~/.local/bin, but I don't know where easybuild puts this > file. > > When I look into the easybuild/software/MYSOFTWARE directory, there is no > > bin folder. > > > > Please help me save the binary :-) > > > > Thanks, > > Oliver > > > > The easyconfig file: > > > > easyblock = 'PythonPackage' > > > > name = 'misopy' > > version = '0.5.3' > > > > homepage = 'http://genes.mit.edu/burgelab/miso/index.html' > > description = """MISO (Mixture of Isoforms) is a probabilistic framework > > that > > quantitates the expression level of alternatively spliced genes from > > RNA-Seq > > data, and identifies differentially regulated isoforms or exons across > > samples. > > By modeling the generative process by which reads are produced from > > isoforms in > > RNA-Seq, the MISO model uses Bayesian inference to compute the > probability > > that > > a read originated from a particular isoform.""" > > > > toolchain = {'name': 'goolf', 'version': '1.4.10'} > > > > source_urls = ['http://pypi.python.org/packages/source/m/misopy'] > > sources = ['%(namelower)s-%(version)s.tar.gz'] > > > > python = 'Python' > > pythonver = '2.7.6' > > versionsuffix = '-%s-%s' % (python, pythonver) > > > > dependencies = [ > > ('matplotlib', '1.3.1', versionsuffix), > > (python, pythonver), > > ] > > > > moduleclass = 'bio' > > > -- Pablo Escobar López HPC systems engineer Biozentrum, University of Basel Swiss Institute of Bioinformatics SIB Email: [email protected] Phone: +41 61 267 21 80 http://www.biozentrum.unibas.ch
