Problem running RSeQC

Question

[heir_of_isildur88]

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!

[GenoMax]

Do you see RSeQC in $HOME/.local/bin? What is the output of ls -l $HOME/.local/bin?

[heir_of_isildur88]

Nope. The output is shown below:

rwxrwxr-x 1 bt bt 262 Mar 30 19:21 easy_install
-rwxrwxr-x 1 bt bt 262 Mar 30 19:21 easy_install-2.7
-rwxrwxr-x 1 bt bt 234 Mar 30 19:21 pip
-rwxrwxr-x 1 bt bt 234 Mar 30 19:21 pip2
-rwxrwxr-x 1 bt bt 234 Mar 30 19:21 pip2.7
-rwxrwxr-x 1 bt bt 241 Mar 30 19:21 wheel

Should the PATH=$PATH:$HOME/bin be the location of the RSeQC files?

[GenoMax]

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?

[heir_of_isildur88]

I don't have the $HOME/bin directory.

[WouterDeCoster]

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

[heir_of_isildur88]

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

[WouterDeCoster]

It might be that you then used the pip from your python2.6.6.

[heir_of_isildur88]

Not likely as the python 2.6.6 in the shared server doesn't even have pip.

Answer 1

[h.mon]

First, as others suggested, check if your locally installed Python is the one being used:

which python
which pip

Then, install virtualenv on your local Python, and use it to install and manage python packages:

virtualenv $HOME/path/to/rseqc
source $HOME/path/to/rseqc/bin/activate

RSeQC should be read to use. You can add the source $HOME/path/to/rseqc/bin/activate to your bash_profile.

[heir_of_isildur88]

Yes. The local Python and pip is being used as shown below when I execute the command above.

$ which python
/mnt/SeaGate_HDD1/benjy/Python/Python-2.7.13/python
$ which pip
~/.local/bin/pip

OK, thanks. I will try out virtualenv.