Entering edit mode
5.4 years ago
BioBaby
▴
20
hi all, I am beginner for NGS analysis.I installed bowtie2 and when I run bowtie2 for indexing the genome it gave this following error: ImportError: No module named argparse I tried to install this module by yum install python-argparse then it gave same error: File "/usr/local/bin/bowtie2-build", line 27, in <module> import argparse ImportError: No module named argparse. OS :centOS
How did you install bowtie? Which is your python version?
sir, I simply download from https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.3/bowtie2-2.3.4.3-linux-x86_64.zip and unzip it.Python 2.6.6
That's a really old python version. I agree with colindaven, just use bioconda for all your bioinformatics software.
i updated python version still I got same error.
How did you update python? Which version do you have now? Look, just use bioconda okay?
solved...I copy argparse.py script and paste into bowtie2 folder. Thanks WouterDeCoster and colindaven
You temporarily patched the problem, but all of this is suggestive of far more problems you will encounter later. Anyway, good luck.
I'd go for bioconda and follow their tutorial. It'll save you a world of pain ....