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Old 05-19-2010, 07:00 AM   #1
dariober
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Default HTSeq: Problem with installation

Hi there,

I just discovered the existence of the pyhton package HTSeq (thanks to the developers!). I tried to install it but I get the error below.

I'm working on Windows XP (...sorry about that!), pyhton 2.6.4, numpy 1.4.1-win32, HTseq installed by HTSeq-0.4.0.win32-py2.6.exe

Any help much appreciated!

Dario

## ---------------------------[ Here's the problem ]-----------------------

PythonWin 2.6.4 (r264:75708, Oct 26 2009, 08:23:19) [MSC v.1500 32 bit (Intel)] on win32.
Portions Copyright 1994-2008 Mark Hammond - see 'Help/About PythonWin' for further copyright information.

>>> import numpy
>>> import HTSeq
Traceback (most recent call last):
File "<interactive input>", line 1, in <module>
File "C:\Python26\lib\site-packages\HTSeq\__init__.py", line 10, in <module>
from _HTSeq import *
File "numpy.pxd", line 43, in _HTSeq (src/_HTSeq.c:20523)
ValueError: numpy.dtype does not appear to be the correct type object
>>>
## ----------------------------------------------------------------------
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Old 05-19-2010, 07:13 AM   #2
dariober
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...Oops, problem solved: Downgrade numpy 1.4.1 to 1.3.0

Dario
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Old 05-19-2010, 08:26 AM   #3
Simon Anders
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Hi

Quote:
Originally Posted by dariober View Post
HTSeq-0.4.0.win32-py2.6.exe
I've made quite some changed since this version. Try the newest one: 0.4.4.

I've just built a Windows installer for that one, and it now takes NumPy 1.4.1.

I also added a section to the installation instructions page on how to compile from source on Windows.

Simon
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Old 05-20-2010, 12:58 AM   #4
dariober
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Many thanks for the update, Simon!

Dario
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Old 05-24-2010, 02:34 PM   #5
gen2prot
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Hi Simon,

I am having difficulty in running the htseq-qa script. I think I have installed HTSeq correctly since I get no error message for "import HTSeq" command. Then on giving the "htseq-qa -t sam accepted.sam" command, I get a Syntax error. I have given the following export command in Unix

export PYTHONPATH=$PYTHONPATH:/Library/Python/2.6/

Is this wrong? On giving the command "whereis python", I get /usr/local/python. I am confused.

Thank you
Abhijit
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Old 05-26-2010, 07:10 AM   #6
Simon Anders
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Quote:
Originally Posted by gen2prot View Post
I am having difficulty in running the htseq-qa script. I think I have installed HTSeq correctly since I get no error message for "import HTSeq" command. Then on giving the "htseq-qa -t sam accepted.sam" command, I get a Syntax error.
This sounds as if you typed "htseq-qa -t sam accepted.sam" into the Python shell. However, this is not a Python command. It is meant to be used in the operating system's shell.

You can either type it as above, but if this gives you a error that the command 'htseq-qa' cannot be found, try instead "python -m HTSeq.scripts.qa -t sam accepted.sam".

HTSeq is primarily meant as a framework for developers familiar with Python who want to develop their own scripts. htseq-count and htseq-qa are two such scripts which are provided to be used by non-developers, too, and consequently, you don't need to start Python to use them; rather, Python gets started internally on invocation of the script.

Cheers
Simon
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Old 11-15-2010, 06:15 PM   #7
James
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I'm trying to build HTseq (0.4.5p6) from source on mac OSX 10.5.8.

- Using python 2.6.6, GCC 4.01.

when I try to build the package i get this:

Code:

python setup.py build

Traceback (most recent call last):
  File "setup.py", line 3, in <module>
    from setuptools import setup, Extension
ImportError: No module named setuptools
any help is appreciated. Thanks James

Last edited by James; 11-15-2010 at 06:21 PM. Reason: add version number
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Old 11-16-2010, 01:09 AM   #8
dariober
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Hi James,

As the error message says, I think you need first to install the package setuptools (http://pypi.python.org/pypi/setuptools/0.6c11) in order to run setup.py.

Good luck!
Dario

Quote:
Originally Posted by James View Post
I'm trying to build HTseq (0.4.5p6) from source on mac OSX 10.5.8.

- Using python 2.6.6, GCC 4.01.

when I try to build the package i get this:

Code:

python setup.py build

Traceback (most recent call last):
  File "setup.py", line 3, in <module>
    from setuptools import setup, Extension
ImportError: No module named setuptools
any help is appreciated. Thanks James
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Old 11-16-2010, 07:24 AM   #9
Simon Anders
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I've just uploaded a new version, 0.4.5p7, which should install without requiring 'setuptools'. (They were unnecessary before, only the error was not properly supressed.)
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