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kylessmith / SomVarIUS

Somatic variant identification from unpaired samples
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ImportError: No module named cfaidx #2

Closed mingyi-wang closed 7 years ago

mingyi-wang commented 7 years ago

I've installed the SomVarIUS and pysam is also included in python. But when I ran "SomVarIUS -h", I got the error likes followings. Could you let me know how to fix that?

Traceback (most recent call last): File "/DCEG/Resources/Tools/python/2.7.8-shared/bin/SomVarIUS", line 4, in import('pkg_resources').run_script('SomVarIUS==1.2', 'SomVarIUS') File "/DCEG/Resources/Tools/python/2.7.8-shared/lib/python2.7/site-packages/pkg_resources/init.py", line 746, in run_script self.require(requires)[0].run_script(script_name, ns) File "/DCEG/Resources/Tools/python/2.7.8-shared/lib/python2.7/site-packages/pkg_resources/init.py", line 1508, in run_script exec(script_code, namespace, namespace) File "/DCEG/Resources/Tools/python/2.7.8-shared/lib/python2.7/site-packages/SomVarIUS-1.2-py2.7-linux-x86_64.egg/EGG-INFO/scripts/SomVarIUS", line 3, in requires = 'SomVarIUS==1.2' File "build/bdist.linux-x86_64/egg/SomVarIUS_calling.py", line 7, in File "build/bdist.linux-x86_64/egg/SomVarIUS_calling.py", line 6, in bootstrap File "cfaidx.pxd", line 40, in init SomVarIUS_calling (SomVarIUS/SomVarIUS_calling.c:25100) ImportError: No module named cfaidx

kylessmith commented 7 years ago

cfaidx.pxd is from pysam. However, it looks like the newest version renamed the modules. You can download an older version of pysam, but I will update the files by tomorrow morning.

mingyi-wang commented 7 years ago

I cannot install an older version of pysam because our python shared by other users. Could you update the files? Thanks!

kylessmith commented 7 years ago

The files should be up to date now

mingyi-wang commented 7 years ago

Now, we got compile errors for installation:

pip install SomVarIUS

Downloading/unpacking SomVarIUS Downloading SomVarIUS-1.1.tar.gz (179kB): 179kB downloaded Running setup.py (path:/tmp/pip_build_root/SomVarIUS/setup.py) egg_info for package SomVarIUS Traceback (most recent call last): File "", line 17, in File "/tmp/pip_build_root/SomVarIUS/setup.py", line 42, in ext_modules=cythonize(extensions), File "/DCEG/Resources/Tools/python/2.7.8-shared/lib/python2.7/site-packages/Cython/Build/Dependencies.py", line 799, in cythonize aliases=aliases) File "/DCEG/Resources/Tools/python/2.7.8-shared/lib/python2.7/site-packages/Cython/Build/Dependencies.py", line 691, in create_extension_list for file in nonempty(sorted(extended_iglob(filepattern)), "'%s' doesn't match any files" % filepattern): File "/DCEG/Resources/Tools/python/2.7.8-shared/lib/python2.7/site-packages/Cython/Build/Dependencies.py", line 107, in nonempty raise ValueError(error_msg) ValueError: 'SomVarIUS/SomVarIUS_calling.pyx' doesn't match any files Complete output from command python setup.py egg_info: Traceback (most recent call last):

File "", line 17, in

File "/tmp/pip_build_root/SomVarIUS/setup.py", line 42, in 

ext_modules=cythonize(extensions),

File "/DCEG/Resources/Tools/python/2.7.8-shared/lib/python2.7/site-packages/Cython/Build/Dependencies.py", line 799, in cythonize

aliases=aliases)

File "/DCEG/Resources/Tools/python/2.7.8-shared/lib/python2.7/site-packages/Cython/Build/Dependencies.py", line 691, in create_extension_list

for file in nonempty(sorted(extended_iglob(filepattern)), "'%s' doesn't match any files" % filepattern):

File "/DCEG/Resources/Tools/python/2.7.8-shared/lib/python2.7/site-packages/Cython/Build/Dependencies.py", line 107, in nonempty

raise ValueError(error_msg)

ValueError: 'SomVarIUS/SomVarIUS_calling.pyx' doesn't match any files

kylessmith commented 7 years ago

I will work on updating the pypi version. Currently the github version is the most up to date.