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!
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!