Hi Oliver,
(you're not subscribed to this mailing list with the email address you
used, but I did accept your mail since you're subscribed with another
mail address and this is clearly a useful post; I added that in CC just
to make sure you get this)
On 23/06/15 17:29, Stolpe, Oliver 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 :-)
Welcome to the tarpit that is Python packaging...
There's good news (twice) and bad news.
The 1st good news is that I fixed your problem.
The bad news is that I had to patch something in the misopy 'sources'
(well, the setup.py script).
The 2nd good news is that the patch is trivial. :-)
The problem is that misopy is using something called 'entry points', but
not doing it 100% correctly.
See
https://chriswarrick.com/blog/2014/09/15/python-apps-the-right-way-entry_points-and-scripts/
.
The key phrase on that page is "You must use setuptools, otherwise this
won’t work."
The setup.py of misopy has this though:
from distutils.core import setup, Extension
This should actually be:
from setuptools import setup, Extension
EasyBuild installs Python packages using "python setup.py build" and
"python setup.py install".
In other words, it trusts that the setup.py script is doing what it
should be doing. And in this case, it's not.
If you use pip to install misopy, you're unknowingly dancing around this
problem, since pip apparently 'fixes' this by itself by providing
something different than setuptools when importing from distutils.core .
Ah, the joys of having 100 different ways of installing Python packages...
Anyway, the problem is fixed using the slightly modified easyconfig file
and trivial patch file in attachment.
Note that I also made EasyBuild check that the 'bin/miso' script is
actually being installed.
If you would comment out the patch, you'll notice that EasyBuild
complains that 'bin/miso' is missing, and thus that the installation is
incomplete.
(behind the scenes, it's already making sure that "python -c 'import
misopy' " works too)
I've reported this issue to the MISO developers, see
https://github.com/yarden/MISO/pull/78 .
Please consider contributing back your working easyconfig file, see
https://github.com/hpcugent/easybuild/wiki/Contributing-back .
If you're not up for that, let me know if it's OK if I do this for you
instead.
regards,
Kenneth
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'
|
--- misopy-0.5.3/setup.py.orig 2015-06-23 21:19:18.523951057 +0300
+++ misopy-0.5.3/setup.py 2015-06-23 21:19:37.714662822 +0300
@@ -1,4 +1,4 @@
-from distutils.core import setup, Extension
+from setuptools import setup, Extension
import distutils.ccompiler
import glob
import os
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']
patches = ['misopy-%(version)s_setup-fix.patch']
python = 'Python'
pythonver = '2.7.6'
versionsuffix = '-%s-%s' % (python, pythonver)
dependencies = [
('matplotlib', '1.3.1', versionsuffix),
(python, pythonver),
]
sanity_check_paths = {
'files': ['bin/miso'],
'dirs': [],
}
moduleclass = 'bio'
