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biostars / biostar-handbook

Issue tracker for the Biostar Handbook
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Stuck at Doctor.py step for installation process #264

Closed nush320 closed 1 year ago

nush320 commented 1 year ago

Hi,

I am getting the following statements when I run the doctor.py program in the step-by-step installation process. I have tried deactivating conda, uninstalling and reinstalling it, doing the same with python according to the troubleshooting guide but I am getting the same error. Please help! 

$ doctor.py
# Doctor! Doctor! Give me the news.
# Checking symptoms ...
# bwa           --> ERROR
# datamash      --> ERROR
# fastqc -h     --> ERROR
# hisat2        --> ERROR
# seqret -h     --> ERROR
# featureCounts --> ERROR
# efetch        ... OK
# esearch       ... OK
# samtools      --> ERROR
# fastq-dump    ... OK
# bowtie2       --> ERROR
# bcftools      --> ERROR
# seqtk         --> ERROR
# seqkit        --> ERROR
# bio           --> ERROR
# fastq-dump -X 1 -Z SRR1553591 ... OK
ialbert commented 1 year ago

first do a 

conda activate bioinfor

did it work? and if so then what does the

conda list

print?

In general, your errors look as if conda is not properly activated when the doctor.py is run

nush320 commented 1 year ago

Hi, it says - command not found.

ialbert commented 1 year ago

sounds like conda is not installed quite right

what happens at steps 3,4,5 in the step-by-step instructions:

https://www.biostarhandbook.com/step-by-step.html

nush320 commented 1 year ago

Hi, @ialbert I did not notice anything out of the ordinary in those steps. They seemed to execute without a hitch.

nush320 commented 1 year ago

So I just tried troubleshooting and I uninstalled everything and was trying again. Unfortunately the Ubuntu 22.04 version I was using before did not work at all. It said "System cannot find file". I downloaded just the app titled "Ubuntu" and I could at least get through the username steps. I also realized there's an automatic installation and the step-by-step is the manual one? While doing the automatic one its stopped with the following errors. Please let me know if this tells you anything and what I could try? @ialbert

7/10 Installing bioinformatics software

# Traceback (most recent call last): File "/home/bstarnush/miniconda3/condabin/mamba", line 7, in from mamba.mamba import main File "/home/bstarnush/miniconda3/lib/python3.10/site-packages/mamba/mamba.py", line 49, in import libmambapy as api File "/home/bstarnush/miniconda3/lib/python3.10/site-packages/libmambapy/init.py", line 7, in raise e File "/home/bstarnush/miniconda3/lib/python3.10/site-packages/libmambapy/init.py", line 4, in from libmambapy.bindings import * # noqa: F401,F403 ImportError: libarchive.so.13: cannot open shared object file: No such file or directory

nush320 commented 1 year ago

Was able to figure out that my bioinfo environment was not activated.