Question: Problem running RSeQC
0
gravatar for heir_of_isildur88
2.4 years ago by
heir_of_isildur8810 wrote:

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!

rseqc • 1.4k views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by heir_of_isildur8810

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

ADD REPLYlink written 2.4 years ago by genomax70k

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?

ADD REPLYlink modified 2.4 years ago by WouterDeCoster40k • written 2.4 years ago by heir_of_isildur8810

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?

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by genomax70k

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

ADD REPLYlink written 2.4 years ago by heir_of_isildur8810

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

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by WouterDeCoster40k

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

ADD REPLYlink written 2.4 years ago by heir_of_isildur8810

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

ADD REPLYlink written 2.4 years ago by WouterDeCoster40k

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

ADD REPLYlink written 2.4 years ago by heir_of_isildur8810
1
gravatar for h.mon
2.4 years ago by
h.mon27k
Brazil
h.mon27k wrote:

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.

ADD COMMENTlink written 2.4 years ago by h.mon27k

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.

ADD REPLYlink written 2.4 years ago by heir_of_isildur8810
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