Trouble installing htseq-count

feralBiologist

Member

Join Date: Jun 2011
Posts: 61

Trouble installing htseq-count

08-28-2013, 09:00 AM

I tried to install htseq-count on CentOS 5.9. I am getting errors:

Code:

[root@cltnfs HTSeq-0.5.4p3]# python setup.py build
/usr/lib64/python2.4/distutils/dist.py:236: UserWarning: Unknown distribution option: 'requires'
  warnings.warn(msg)
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.4
creating build/lib.linux-x86_64-2.4/HTSeq
copying HTSeq/__init__.py -> build/lib.linux-x86_64-2.4/HTSeq
copying HTSeq/_HTSeq_internal.py -> build/lib.linux-x86_64-2.4/HTSeq
copying HTSeq/StepVector.py -> build/lib.linux-x86_64-2.4/HTSeq
copying HTSeq/_version.py -> build/lib.linux-x86_64-2.4/HTSeq
creating build/lib.linux-x86_64-2.4/HTSeq/scripts
copying HTSeq/scripts/__init__.py -> build/lib.linux-x86_64-2.4/HTSeq/scripts
copying HTSeq/scripts/qa.py -> build/lib.linux-x86_64-2.4/HTSeq/scripts
copying HTSeq/scripts/count.py -> build/lib.linux-x86_64-2.4/HTSeq/scripts
running build_ext
building 'HTSeq._HTSeq' extension
creating build/temp.linux-x86_64-2.4
creating build/temp.linux-x86_64-2.4/src
gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fPIC -I/usr/lib64/python2.4/site-packages/numpy/core/include -I/usr/include/python2.4 -c src/_HTSeq.c -o build/temp.linux-x86_64-2.4/src/_HTSeq.o -w
gcc -pthread -shared build/temp.linux-x86_64-2.4/src/_HTSeq.o -o build/lib.linux-x86_64-2.4/HTSeq/_HTSeq.so
building 'HTSeq._StepVector' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fPIC -I/usr/include/python2.4 -c src/StepVector_wrap.cxx -o build/temp.linux-x86_64-2.4/src/StepVector_wrap.o -w
c++ -pthread -shared build/temp.linux-x86_64-2.4/src/StepVector_wrap.o -o build/lib.linux-x86_64-2.4/HTSeq/_StepVector.so
running build_scripts
creating build/scripts-2.4
copying and adjusting scripts/htseq-qa -> build/scripts-2.4
copying and adjusting scripts/htseq-count -> build/scripts-2.4
changing mode of build/scripts-2.4/htseq-qa from 644 to 755
changing mode of build/scripts-2.4/htseq-count from 644 to 755
[root@cltnfs HTSeq-0.5.4p3]# sudo python setup.py install
/usr/lib64/python2.4/distutils/dist.py:236: UserWarning: Unknown distribution option: 'requires'
  warnings.warn(msg)
running install
running bdist_egg
running egg_info
writing HTSeq.egg-info/PKG-INFO
writing top-level names to HTSeq.egg-info/top_level.txt
writing dependency_links to HTSeq.egg-info/dependency_links.txt
reading manifest file 'HTSeq.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
no previously-included directories found matching 'example_data'
no previously-included directories found matching 'test'
warning: no previously-included files found matching 'todo.txt'
writing manifest file 'HTSeq.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
running build_ext
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/HTSeq
copying build/lib.linux-x86_64-2.4/HTSeq/__init__.py -> build/bdist.linux-x86_64/egg/HTSeq
copying build/lib.linux-x86_64-2.4/HTSeq/_HTSeq_internal.py -> build/bdist.linux-x86_64/egg/HTSeq
copying build/lib.linux-x86_64-2.4/HTSeq/StepVector.py -> build/bdist.linux-x86_64/egg/HTSeq
copying build/lib.linux-x86_64-2.4/HTSeq/_version.py -> build/bdist.linux-x86_64/egg/HTSeq
creating build/bdist.linux-x86_64/egg/HTSeq/scripts
copying build/lib.linux-x86_64-2.4/HTSeq/scripts/__init__.py -> build/bdist.linux-x86_64/egg/HTSeq/scripts
copying build/lib.linux-x86_64-2.4/HTSeq/scripts/qa.py -> build/bdist.linux-x86_64/egg/HTSeq/scripts
copying build/lib.linux-x86_64-2.4/HTSeq/scripts/count.py -> build/bdist.linux-x86_64/egg/HTSeq/scripts
copying build/lib.linux-x86_64-2.4/HTSeq/_HTSeq.so -> build/bdist.linux-x86_64/egg/HTSeq
copying build/lib.linux-x86_64-2.4/HTSeq/_StepVector.so -> build/bdist.linux-x86_64/egg/HTSeq
byte-compiling build/bdist.linux-x86_64/egg/HTSeq/__init__.py to __init__.pyc
  File "build/bdist.linux-x86_64/egg/HTSeq/__init__.py", line 842
    except ValueError as e:
                       ^
SyntaxError: invalid syntax
byte-compiling build/bdist.linux-x86_64/egg/HTSeq/_HTSeq_internal.py to _HTSeq_internal.pyc
byte-compiling build/bdist.linux-x86_64/egg/HTSeq/StepVector.py to StepVector.pyc
byte-compiling build/bdist.linux-x86_64/egg/HTSeq/_version.py to _version.pyc
byte-compiling build/bdist.linux-x86_64/egg/HTSeq/scripts/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/HTSeq/scripts/qa.py to qa.pyc
byte-compiling build/bdist.linux-x86_64/egg/HTSeq/scripts/count.py to count.pyc
  File "build/bdist.linux-x86_64/egg/HTSeq/scripts/count.py", line 187
    rr = r[0] if r[0] is not None else r[1]
               ^
SyntaxError: invalid syntax
creating stub loader for HTSeq/_HTSeq.so
creating stub loader for HTSeq/_StepVector.so
byte-compiling build/bdist.linux-x86_64/egg/HTSeq/_HTSeq.py to _HTSeq.pyc
byte-compiling build/bdist.linux-x86_64/egg/HTSeq/_StepVector.py to _StepVector.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.4/htseq-qa -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.4/htseq-count -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/htseq-qa to 755
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/htseq-count to 755
writing HTSeq.egg-info/native_libs.txt
copying HTSeq.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying HTSeq.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying HTSeq.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying HTSeq.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
HTSeq.StepVector: module references __file__
creating dist
creating 'dist/HTSeq-0.5.4p3-py2.4-linux-x86_64.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing HTSeq-0.5.4p3-py2.4-linux-x86_64.egg
creating /usr/lib64/python2.4/site-packages/HTSeq-0.5.4p3-py2.4-linux-x86_64.egg
Extracting HTSeq-0.5.4p3-py2.4-linux-x86_64.egg to /usr/lib64/python2.4/site-packages
  File "/usr/lib64/python2.4/site-packages/HTSeq-0.5.4p3-py2.4-linux-x86_64.egg/HTSeq/__init__.py", line 842
    except ValueError as e:
                       ^
SyntaxError: invalid syntax
  File "/usr/lib64/python2.4/site-packages/HTSeq-0.5.4p3-py2.4-linux-x86_64.egg/HTSeq/scripts/count.py", line 187
    rr = r[0] if r[0] is not None else r[1]
               ^
SyntaxError: invalid syntax
Adding HTSeq 0.5.4p3 to easy-install.pth file
Installing htseq-count script to /usr/bin
Installing htseq-qa script to /usr/bin

Installed /usr/lib64/python2.4/site-packages/HTSeq-0.5.4p3-py2.4-linux-x86_64.egg
Processing dependencies for HTSeq==0.5.4p3


[root@cltnfs HTSeq-0.5.4p3]# cd ..
[root@cltnfs software]# python
Python 2.4.3 (#1, Jan  9 2013, 06:47:03)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-54)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import HTSeq
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/lib64/python2.4/site-packages/HTSeq-0.5.4p3-py2.4-linux-x86_64.egg/HTSeq/__init__.py", line 842
    except ValueError as e:
                       ^

Can anyone help?

Tags: htseq-count, installation

dpryan

Devon Ryan

Join Date: Jul 2011

Posts: 3478
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#2

08-28-2013, 09:31 AM

As someone on biostars mentioned, try a more recent version of python.
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feralBiologist

Member

Join Date: Jun 2011

Posts: 61
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#3

08-29-2013, 03:56 AM

Originally posted by dpryan View Post

As someone on biostars mentioned, try a more recent version of python.

Thanks. It was a good advice but, unfortunately, I can't upgrade the system-wide python as I risk losing yum and other essential packages. I installed python26 via easyinstall but I encountered other difficulties: http://www.biostars.org/p/80019/#80080
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sphil

Senior Member

Join Date: Apr 2010

Posts: 192
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#4

08-29-2013, 05:32 AM

here is a way to install python not using the system python: http://toomuchdata.com/2012/06/25/ho...on-centos-6-2/ linking the recourses correct should do the job
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feralBiologist

Member

Join Date: Jun 2011

Posts: 61
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#5

09-09-2013, 06:02 AM

Thanks a lot to @sphil and @dpryan - the issue was resolved by the system admin by updating python and enabling internet access.
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Trouble installing htseq-count

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