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Htseq Count Not Working

Hi all I have installed HTSeq count from the site http://pypi.python.org/pypi/HTSeq . then on my mac system, I unpacked the folder and run the command python setup.py build it goes right. I also has xcode installed on it. but when I run command htseq-count OR python -m HTSeq.scripts.count then these commands are not recongnized.

Thanks in advance Kumardeep

htseq counts
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updated by Niek De Klein Niek De Klein • written by monukmr98 monukmr98

what is the exact commandline you give and what error do you get?

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written by Niek De Klein Niek De Klein

FOR command: htseq-count error is -bash: htseq-count: command not found FOR command: python -m HTSeq.scripts.count error is /usr/bin/python: No module named _HTSeq

I have mac os lion..... while installing it showed no error. Thanks

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written by monukmr98 monukmr98

1 answer

Did you do 

python setup.py install

after the build?

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written by Niek De Klein Niek De Klein

Hi Klein I did not use the above said command. And when I used it by using like

sudo python setup.py install

It got installed and now the previous errors are not coming, means the commands are working fine. But I was wondering that official website (http://www-huber.embl.de/users/anders/HTSeq/doc/install.html#install) does not mention any such command ? Don't know why ?

They say to use install command when your folder does not contain src subfolder i.e. when you have source code downloaded. I downloaded the same source code with src as subfolder; so it was supposed to work with build command only. anyway its working Thanks again Kumardeep

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written by monukmr98 monukmr98

It says: Afterwards, proceed as with the binary package. And in the binary package install instructions it does say to do setup.py install.

Anyway, for next time you're installing a python module, the python setup.py build > python setup.py install are the two general commands to do this. If you're interested in the details look at how you can create a python package: http://guide.python-distribute.org/creation.html

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written by Niek De Klein Niek De Klein

My apologies... I overlooked that line. Thanks for suggestion and the link. :) Regards

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written by monukmr98 monukmr98

That's alright, it's not always very clear. You should accept this answer in case someone has the same problem.

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written by Niek De Klein Niek De Klein

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