Question: bowtie2: ImportError: No module named argparse
0
gravatar for BioBaby
10 weeks ago by
BioBaby0
BioBaby0 wrote:

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

ADD COMMENTlink modified 10 weeks ago by WouterDeCoster36k • written 10 weeks ago by BioBaby0

How did you install bowtie? Which is your python version?

ADD REPLYlink written 10 weeks ago by WouterDeCoster36k

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

ADD REPLYlink written 10 weeks ago by BioBaby0

That's a really old python version. I agree with colindaven, just use bioconda for all your bioinformatics software.

ADD REPLYlink written 10 weeks ago by WouterDeCoster36k

i updated python version still I got same error.

ADD REPLYlink written 10 weeks ago by BioBaby0

How did you update python? Which version do you have now? Look, just use bioconda okay?

ADD REPLYlink written 10 weeks ago by WouterDeCoster36k

solved...I copy argparse.py script and paste into bowtie2 folder. Thanks WouterDeCoster and colindaven

ADD REPLYlink written 10 weeks ago by BioBaby0
1

You temporarily patched the problem, but all of this is suggestive of far more problems you will encounter later. Anyway, good luck.

ADD REPLYlink written 10 weeks ago by WouterDeCoster36k

I'd go for bioconda and follow their tutorial. It'll save you a world of pain ....

ADD REPLYlink written 10 weeks ago by colindaven1.0k
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