Closed tAndreani closed 4 years ago
This version is for Python 2. I used version 2.7.14 and it worked. We are working to release a version for Python 3. It will be available soon here: https://github.com/Mangul-Lab-USC/imrep.
Thank you for the reply, I was able to install it by upgrading anaconda. best
I have another question, which annotation is used by imrep? I have mapped the reads to hg38, can i use the command provided below?
python imrep.py --bam my_bam_mapped_hg38.bam annotated.cdr3
From what I am understanding is it possible that you do not need annotation because all the potential genes are in fasta sequence (in the folder db/mouse or db/human).. But how does it knows that is human or mouse if I do not provide this info?
thank you for your reply.
For hg38, you can use option "--hg38". To differentiate human and mouse, you can use the option "--species human" or "--species mouse".
Hello,
I am trying to install imrep following the tutorial:
1) git clone https://github.com/mandricigor/imrep.git 2) cd imrep 3) ./install.sh
It seems that most of the things are installed (i did several run of installation):
at the end I got an error:
error: command '/site/ne/home/i0439277/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc' failed with exit status 1
Before the error I got this intermediate errors:
It seems to be related with the python version maybe from https://github.com/openai/mujoco-py/issues/500. I am using python 3.7.4. Do you know which python version is required to install imrep?