Comments (7)
Hi, can you try running
python3 asgal.py -h
?
from galig.
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'
from galig.
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?
from galig.
Sorry, my fault, the script is asgal
:
python3 asgal -h
(this from the root of this repo).
from galig.
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...)
from galig.
Great. I suspect it is due to the shebang
Line 1 in 8808115
Can you try to change it to
#!/usr/bin/env python
and try again with
./asgal -h
?
from galig.
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
from galig.
Related Issues (16)
- Asgal (from run in your provided docker): doesn't find Transcript file, looks for gtf instead. HOT 1
- Docker permissions issue HOT 15
- .mem and sam files generated as empty HOT 45
- logs files HOT 2
- Salmon installation not found after pip installation in Asgal HOT 3
- Another permissions question HOT 6
- Adds tmp directory to asgal script
- Novel intron retention events in genome-wide mode HOT 2
- ALK ATI event HOT 9
- Error: Reference genome not found Halting... HOT 1
- Computation of PSI (percent spliced in) HOT 1
- Need help to run the tool, no result for sample.mem HOT 13
- FAILED dependencies of target libtbb; tbb-2018_U3.tgz HOT 15
- Issues with Dockerfile HOT 6
- Error when testing with example files HOT 3
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