Page Comparison

...

 Image from:http://www-huber.embl.de/users/anders/HTSeq/

Htseq is NOT a module on lonestar6, but not part of biocontainers. Module spider htseq shows us the other modules  (intel/17.0.4) we need in order to load htseqdoesn't find anything, so we have to install it.

module spider htseq
module load intel/17.0.4
module load htseq

htseq-count -h

Installing HTseq

Generally, installing tools to a cluster is a pain, so avoid it if you can. However, if you have to install something, remember that you cannot install things on TACC globally, so you'll have to use options to install the tool locally to a directory that is accessible to you. Detour to how to install tools locally

1.Download HTseq source code (tar archive)  from https://pypi.org/project/HTSeq/ using wget. 

cd ~
mkdir htseq
wget https://files.pythonhosted.org/packages/9b/a5/d3259656283caa0046e8d4a7e8fb1429a69a39da5c550cb259e50aafdb71/htseq-2.0.7.tar.gz
tar -xvzf htseq-2.0.7.tar.gz 

2. Build and install the tool

cd htseq-2.0.7/
python3.9 setup.py build
python3.9 setup.py install --help

python3.9 setup.py install --user

3.  Add the location to your PATH variable

echo $HOME
#replace <yourhomedir> with YOUR HOME DIRECTORY
export PATH=<yourhomedir>/.local/bin:$PATH 

IMPORTANT NOTE:  By default, htseq assumes your reads are stranded and will only count the reads that map in the same direction as the feature. If you have unstranded data or if you want to count reads mapping in all directions (maybe to detect antisense genes), use --stranded no option. If you have truseq data which uses dUTP method for creating stranded libraries, your reads will actually be in reverse direction when compared to the feature. So, use --stranded reverse.

...