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  • 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.

  • #2
    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.

    Comment


    • #3
      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, 07:21 AM.

      Comment


      • #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.

        Comment


        • #5
          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?

          Comment

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