Hi all! Thanks a lot for your feedback! I am not sure how can I close this topic so I edited my post here. I have managed to fix the problem now. Apparently I have to reconfigure it to where my RSeQC files were placed and I found it in my local Python directory in Python/bin/. RSeQC is working now! Thanks again for all your feedback!
Hi all,
I am new to RNA-Seq and I recently found this interesting software that I would like to try - RSeQC.
The thing is after installation I have trouble getting it to run as every time I input the commands, the returning message was command not found.
Let me describe my problem in more detail:
I am using a shared server installed with Python 2.6.6 but RSeQC requires Python 2.7 or higher to run; so I installed Python 2.7.13 locally. Then to enable Python 2.7.13 locally when I log in, I insert these lines into my bash_profile.
export PATH=/mnt/SeaGate_HDD1/ben/Python/Python-2.7.13/:$PATH
export PYTHONPATH=/mnt/SeaGate_HDD1/ben/Python/Python-2.7.13
export PATH=$PATH:$HOME/.local/bin
Then after I installed RSeQC using pip, I thought it should run with no problems at all but it doesn't work. So I thought that because I am using a local Python, I should reconfigure the path for RSeQC as well. This is the instructions I got from the manual, but I am not really sure how should I reconfigure it.
export PYTHONPATH=/home/user/lib/python2.7/site-packages:$PYTHONPATH
export PATH=/home/user/bin:$PATH
My current configuration is as below but it doesn't work.
export PYTHONPATH=/mnt/SeaGate_HDD1/ben/Python/lib/python2.7/site-packages:$PYTHONPATH
export PATH=$PATH:$HOME/bin
Can anyone advice how I should configure RSeQC properly here? Thank you very much!
Do you see RSeQC in
$HOME/.local/bin
? What is the output ofls -l $HOME/.local/bin
?Nope. The output is shown below:
Should the PATH=$PATH:$HOME/bin be the location of the RSeQC files?
What is in
ls -l $HOME/bin
? Since you did not specify a directory when doing pip install I would have thought that RSeQC would have gone into$HOME/.local/bin
?I don't have the $HOME/bin directory.
Please use sensible tags, rseqc would be logical here. I have updated your post.
Which command did you use with pip? Are you sure the correct pip was used?
Try
python2.7 -m pip install RSeQC
Thanks! I am sorry for the trouble. I have removed the RNA-Seq tag.
Yes, I used the pip command as instructed on the RSeQC website which is:
pip install RSeQC
It might be that you then used the pip from your python2.6.6.
Not likely as the python 2.6.6 in the shared server doesn't even have pip.