help with HTSeq installation

madhuk11 · 12-06-2011, 07:28 AM

Hi,
I am trying to install HTSeq-0.5.3p3 from the source package (as I failed to use available HTSeq-0.3.7 binary package with python 2.6). Downloaded into a Downloads folder and tried as advised for Windows (at http://www-huber.embl.de/users/ander...c/install.html). Ended up with cc1.exe error with options -mno-cygwin (I have both mingw and cygwin on the system, but removed cygwin later!).
Buidling and Installation were successful without specifying the compiler (python setup.py build; python setup.py install) in the commandline shell. However, I did not detect any HTSeq packages added to site-packages folder. Below is the output on the screen.

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.win32\egg
running install_lib
running build_py
running build_ext
building 'HTSeq._HTSeq' extension
error: None

Do I need to transfer any files/folder manually into python?
Thanks.

Simon Anders · 12-06-2011, 08:23 AM

After running "python setup.py build", have you also run "python setup.py install"? The latter moves the files to were they will be found by Python.

madhuk11 · 12-07-2011, 03:54 AM

Yes. After install command, I saw the screen telling me successful installation (and pasted the log in my last posting, setupTools installed). I did not see any files moved to Lib\site-packages. When I say,
>>>import numpy
>>> (successful)
>>>import HTSeq
Not found!
I had earlier tried using HTSeq-0.3.7 (binary package) that was installed and HTSeq could be found in Lib\site-packages. However, import HTSeq gave me an error (numpy.pxd; numpy 1.6.1 wasn't proper?).

I retried (uninstalling Python 2.6, numpy and then, reinstalling); following the log below, still could not locate HTSeq in site-packages folder.

Could not import 'setuptools', falling back to 'distutils'.
running install
running build
running build_py
running build_ext
building 'HTSeq._HTSeq' extension
error: None

Yet, when I inspect HTSeq folder, nothing seem to have happened!

Binary packages seem to install o.k. However, failed to execute (numpy.pxd!). Do I really need numpy-devel? I don't see it at PyPI site.
Thanks.

madhuk11 · 12-08-2011, 04:30 AM

Is it possible to obtain a binary version of HTSeq 0.5.3p3 as available 0.3.7 does not work with numpy 1.6.1. I have been managing counting with a java code; I can not use annotation files (gff; that would make better sense) with my code; so, it is now restricted to using cDNA index for alignments. If you are willing to send it, I can give you my email id. Thanks.

wangli · 06-07-2012, 11:04 AM

I tried to install HTseq 0.5.3 source package, but Xcode is not installed on my computer, and I cannot get it installed now. Do anyone know where i can get the binary package of HTseq, which doesnot require Xcode installed?

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12-06-2011, 07:28 AM	#1
madhuk11 Junior Member Location: London Join Date: Aug 2011 Posts: 4	help with HTSeq installation Hi, I am trying to install HTSeq-0.5.3p3 from the source package (as I failed to use available HTSeq-0.3.7 binary package with python 2.6). Downloaded into a Downloads folder and tried as advised for Windows (at http://www-huber.embl.de/users/ander...c/install.html). Ended up with cc1.exe error with options -mno-cygwin (I have both mingw and cygwin on the system, but removed cygwin later!). Buidling and Installation were successful without specifying the compiler (python setup.py build; python setup.py install) in the commandline shell. However, I did not detect any HTSeq packages added to site-packages folder. Below is the output on the screen. 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.win32\egg running install_lib running build_py running build_ext building 'HTSeq._HTSeq' extension error: None Do I need to transfer any files/folder manually into python? Thanks.

12-07-2011, 03:54 AM	#3
madhuk11 Junior Member Location: London Join Date: Aug 2011 Posts: 4	Yes. After install command, I saw the screen telling me successful installation (and pasted the log in my last posting, setupTools installed). I did not see any files moved to Lib\site-packages. When I say, >>>import numpy >>> (successful) >>>import HTSeq Not found! I had earlier tried using HTSeq-0.3.7 (binary package) that was installed and HTSeq could be found in Lib\site-packages. However, import HTSeq gave me an error (numpy.pxd; numpy 1.6.1 wasn't proper?). I retried (uninstalling Python 2.6, numpy and then, reinstalling); following the log below, still could not locate HTSeq in site-packages folder. Could not import 'setuptools', falling back to 'distutils'. running install running build running build_py running build_ext building 'HTSeq._HTSeq' extension error: None Yet, when I inspect HTSeq folder, nothing seem to have happened! Binary packages seem to install o.k. However, failed to execute (numpy.pxd!). Do I really need numpy-devel? I don't see it at PyPI site. Thanks. Last edited by madhuk11; 12-07-2011 at 07:21 AM.

12-08-2011, 04:30 AM	#4
madhuk11 Junior Member Location: London Join Date: Aug 2011 Posts: 4	HTSeq 0.5.3p3 binary Is it possible to obtain a binary version of HTSeq 0.5.3p3 as available 0.3.7 does not work with numpy 1.6.1. I have been managing counting with a java code; I can not use annotation files (gff; that would make better sense) with my code; so, it is now restricted to using cDNA index for alignments. If you are willing to send it, I can give you my email id. Thanks.

12-06-2011, 08:23 AM	#2
Simon Anders Senior Member Location: Heidelberg, Germany Join Date: Feb 2010 Posts: 994	After running "python setup.py build", have you also run "python setup.py install"? The latter moves the files to were they will be found by Python.

06-07-2012, 11:04 AM	#5
wangli Member Location: Texas Join Date: Apr 2012 Posts: 48	I tried to install HTseq 0.5.3 source package, but Xcode is not installed on my computer, and I cannot get it installed now. Do anyone know where i can get the binary package of HTseq, which doesnot require Xcode installed?