Trouble with HTSeq install

[austinpa]

I am looking for any advice on troubles with installing HTSeq on windows from a source package. Here is the code I get from the install

$ python setup.py build --compiler=mingw32
Could not import 'setuptools', falling back to 'distutils'.
running build
running build_py
creating build
creating build\lib.win32-2.6
creating build\lib.win32-2.6\HTSeq
copying HTSeq\__init__.py -> build\lib.win32-2.6\HTSeq
copying HTSeq\_HTSeq_internal.py -> build\lib.win32-2.6\HTSeq
copying HTSeq\StepVector.py -> build\lib.win32-2.6\HTSeq
copying HTSeq\_version.py -> build\lib.win32-2.6\HTSeq
creating build\lib.win32-2.6\HTSeq\scripts
copying HTSeq\scripts\__init__.py -> build\lib.win32-2.6\HTSeq\scripts
copying HTSeq\scripts\qa.py -> build\lib.win32-2.6\HTSeq\scripts
copying HTSeq\scripts\count.py -> build\lib.win32-2.6\HTSeq\scripts
running build_ext
building 'HTSeq._HTSeq' extension
creating build\temp.win32-2.6
creating build\temp.win32-2.6\Release
creating build\temp.win32-2.6\Release\src
C:\MinGW\bin\gcc.exe -mno-cygwin -mdll -O -Wall -IC:\Python26\lib\site-packages\
numpy\core\include -IC:\Python26\include -IC:\Python26\PC -c src/_HTSeq.c -o bui
ld\temp.win32-2.6\Release\src\_htseq.o -w
writing build\temp.win32-2.6\Release\src\_HTSeq.def
C:\MinGW\bin\gcc.exe -mno-cygwin -shared -s build\temp.win32-2.6\Release\src\_ht
seq.o build\temp.win32-2.6\Release\src\_HTSeq.def -LC:\Python26\libs -LC:\Python
26\PCbuild -lpython26 -lmsvcr90 -o build\lib.win32-2.6\HTSeq\_HTSeq.pyd
building 'HTSeq._StepVector' extension
C:\MinGW\bin\gcc.exe -mno-cygwin -mdll -O -Wall -IC:\Python26\include -IC:\Pytho
n26\PC -c src/StepVector_wrap.cxx -o build\temp.win32-2.6\Release\src\stepvector
_wrap.o -w
gcc: CreateProcess: No such file or directory
error: command 'gcc' failed with exit status 1

$ python setup.py install
Could not import 'setuptools', falling back to 'distutils'.
running install
running build
running build_py
running build_ext
building 'HTSeq._StepVector' extension
error: None

Thanks.

[Simon Anders]

I try to avoid having to work on Windows as fas as possible, and so don't have too much experience, but some googling for your error message, "CreateProcess: No such file or directory", leads me to believe that GCC cannot find its own binaries. The problem seems common. Maybe this guy's solution works for you, too.

On my Windows installation, this doesn't seem to be necessary, though. I'll upload a new Windows binary package to PyPI beginning of next week.

[austinpa]

HTSeq install

Hi Simon,

The other solution did not work. But thank you for posting a windows binary install. I am currently working through the tutorial and look forward to using the software to obtain raw counts from tophat mapping.

Cheers,
Austin

[frewise]

cent os 5.2 install HTSeq

I try to avoid having to work on Windows as fas as possible, and so don't have too much experience, but some googling for your error message, "CreateProcess: No such file or directory", leads me to believe that GCC cannot find its own binaries. The problem seems common. Maybe this guy's solution works for you, too.

On my Windows installation, this doesn't seem to be necessary, though. I'll upload a new Windows binary package to PyPI beginning of next week.

Hi Simon, when I installing HTSeq on cent os 5.2, there are similar problem and I don't know how this come about. Is there any advice? Thanks!

Could not import 'setuptools', falling back to 'distutils'.
running build
running build_py
running build_ext
building 'HTSeq._StepVector' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/share/biosoft/software/python/Python-2.6.4/Include -I/share/biosoft/software/python/Python-2.6.4 -c src/StepVector_wrap.cxx -o build/temp.linux-x86_64-2.6/src/StepVector_wrap.o -w
gcc: error trying to exec 'cc1plus': execvp: No such file or directory
error: command 'gcc' failed with exit status 1

[Simon Anders]

I guess it means that your GCC installation is incomplete. It seems that CentOS has separate packages for C and C++. Try 'sudo yum install gcc44-c++'.

By the way: You can debug such problems with the help of an RPM search engine such as http://rpm.pbone.net . What I just did was to cklick there on "advanced search", enter the file name that could not be found according to your error message ("cc1plus"), checked "CentOS 5", clicked "search", and learned that, in CentOS 5, this file is provided by the package "gcc44-c++".

[frewise]

I guess it means that your GCC installation is incomplete. It seems that CentOS has separate packages for C and C++. Try 'sudo yum install gcc44-c++'.

By the way: You can debug such problems with the help of an RPM search engine such as http://rpm.pbone.net . What I just did was to cklick there on "advanced search", enter the file name that could not be found according to your error message ("cc1plus"), checked "CentOS 5", clicked "search", and learned that, in CentOS 5, this file is provided by the package "gcc44-c++".

Thank you Simon! I will try it.

[thanhhoang]

HELP with Htseq install in Linux

Hi Simon,
I want to test for DE genes using TopHat>Htseq-count> DEseq workflow. I got BAM files from TopHat converted to SAM files. Now I am trying to install Htseq-count in Linux but I got following error:

python setup.py install --user [ 7:31AM]
Could not import 'setuptools', falling back to 'distutils'.
running install
running build
running build_py
running build_ext
running build_scripts
running install_lib
running install_scripts
changing mode of /home/robinson_lab/.local/bin/htseq-count to 775
changing mode of /home/robinson_lab/.local/bin/htseq-qa to 775
running install_egg_info

I try to run Htseq-count on my SAM file:htseq-count -m intersection-nonempty -t gene -i ID - E1.sam annotation.gtf > E1_count
zsh: command not found: htseq-count
Do you know how to fix this?
Thanh

[GenoMax]

htseq-count is not installed in a directory that is in your $PATH variable, which is why you are seeing the "command not found error".

If you provide the full path to the directory where htseq-count is installed in your command it should work.

$ /path_to/htseq-count -m intersection-nonempty -t gene -i ID - E1.sam annotation.gtf > E1_count

[thanhhoang]

Hi GenoMax,
Thank you for your reply
Here is the command i ran before:
robinson_lab@cbfgws2[HTSeq-0.5.4p3] htseq-count -m intersection-nonempty -t gene -i ID - E1.sam annotation.gtf > E1_count
You mean that i should run like this:
robinson_lab@cbfgws2[HTSeq-0.5.4p3] $ /path_to/htseq-count -m intersection-nonempty -t gene -i ID - E1.sam annotation.gtf > E1_count
zsh: command not found: $
Sorry, I am just learning Bioinformatics
Thanh

[GenoMax]

Hi GenoMax,
Thank you for your reply
Here is the command i ran before:
robinson_lab@cbfgws2[HTSeq-0.5.4p3] htseq-count -m intersection-nonempty -t gene -i ID - E1.sam annotation.gtf > E1_count
You mean that i should run like this:
robinson_lab@cbfgws2[HTSeq-0.5.4p3] $ /path_to/htseq-count -m intersection-nonempty -t gene -i ID - E1.sam annotation.gtf > E1_count
zsh: command not found: $
Sorry, I am just learning Bioinformatics
Thanh

"/path_to" is a generic reference to the actual directory where you installed htseq-count. e.g. if your htseq-count program is in "/usr/bin/" directory then the command would be (this is only an example you will need to replace /usr/bin part with correct path from your machine)

/usr/bin/htseq-count -m intersection-nonempty -t gene -i ID - E1.sam annotation.gtf > E1_count

A good guide for a biologist to learn basic unix is here: http://korflab.ucdavis.edu/Unix_and_...1.1.html#part1

[thanhhoang]

"/path_to" is a generic reference to the actual directory where you installed htseq-count. e.g. if your htseq-count program is in "/usr/bin/" directory then the command would be (this is only an example you will need to replace /usr/bin part with correct path from your machine)

/usr/bin/htseq-count -m intersection-nonempty -t gene -i ID - E1.sam annotation.gtf > E1_count

A good guide for a biologist to learn basic unix is here: http://korflab.ucdavis.edu/Unix_and_...1.1.html#part1

Hi, i downloaded the HTSEq -0.5.4p3 version
robinson_lab@cbfgws2[HTSeq-0.5.4p3] Does not it means that I am already in the htseq_count directory??
Sorry if my question is silly
Thanh

[GenoMax]

Hi, i downloaded the HTSEq -0.5.4p3 version
robinson_lab@cbfgws2[HTSeq-0.5.4p3] Does not it means that I am already in the htseq_count directory??
Sorry if my question is silly
Thanh

Looks like it.
Can you run the following commands and post the file listing of the directory you are in (HTSeq-0.5.4p3)?

$ pwd
$ ls -l

[thanhhoang]

Hi,
Finnally I got Htseq-count working. Here is is the code i used:
htseq-count -m intersection-nonempty -s no F1.sam annotation.gtf > F1_count
And my result:
no_feature 5773655
ambiguous 210396
too_low_aQual 0
not_aligned 0
alignment_not_unique 24423669

ENSMUSG00000000001 2038
ENSMUSG00000000003 0
ENSMUSG00000000028 78
ENSMUSG00000000031 2780
ENSMUSG00000000037 45
ENSMUSG00000000049 0
ENSMUSG00000000056 308
ENSMUSG00000000058 70
ENSMUSG00000000078 238
ENSMUSG00000000085 460

The default setting is gene_id in GTF file. Just wondering how can i make gene name show up instead of gene_id? Also, will that affect the subsequent analysis with DESeq ?
Thank you

[thanhhoang]

Sorry, I figured it out
htseq-count -m intersection-nonempty -s no -i gene_name E1.sam annotation.gtf > E1_count