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AlgoLab
Installation Error: ModuleNotFoundError: No module named 'Bio'
I installed python3 biopython pysam gffutils pandas cmake samtools zlib in a newly created conda environment.
conda create -n asgal -y
conda activate asgal
conda install python=3.6 -y
conda install biopython
pip install pysam
pip install pandas
conda install samtools -y
conda install cmake -y
conda install gffutils -y
conda install zlib
And then execute the following commands:
git clone --recursive https://github.com/AlgoLab/galig.git
cd galig
make prerequisites
make
However when I try to run asgal (./asgal -h), there is an error:
Traceback (most recent call last):
File "./asgal", line 12, in <module>
from Bio import SeqIO
ModuleNotFoundError: No module named 'Bio'
How can I fix this problem?
Unfortunately, when I use the example data of gene CG13375 in Drosophila Melanogaster I got the same error:
This is the command I executed:
~/galig/asgal -g genome.fa -a annotation.gtf -s sample_1.fa -o asgal_out
This is the error:
Traceback (most recent call last):
File "/dat1/lisijun/galig/asgal", line 12, in <module>
from Bio import SeqIO
ModuleNotFoundError: No module named 'Bio'
Hi, can you try running
python3 asgal.py -h?
Command:
python3 asgal.py -h
Error:
python3: can't open file 'asgal.py': [Errno 2] No such file or directory
I searched though the galig directory, the bin directory and the scripts directory, but I can't find a python script named asgal.py. Where can I find asgal.py?
Sorry, my fault, the script is asgal:
python3 asgal -h
(this from the root of this repo).
Sorry, my fault, the script is
asgal:python3 asgal -h(this from the root of this repo).
It works! Now I can run the example data by asgal, thank you!
(By the way, I am wondering why there were errors like no python modules when executing asgal directly...)
Great. I suspect it is due to the shebang https://github.com/AlgoLab/galig/blob/880811546525bb9c8afff44aea5ab375d0a33651/asgal#L1
Can you try to change it to
#!/usr/bin/env python
and try again with
./asgal -h
?
Since I installed ASGAL in a conda environment, I changed
#!/usr/bin/python3
as
!/dat1/lisijun/miniconda3/envs/asgal/bin/python
And it turns out that the command works! Thank you!
./asgal -h