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EBISPOT / gwas-sumstats-tools

gwas-sumstats-tools
https://ebispot.github.io/gwas-sumstats-tools-documentation/#/
Apache License 2.0
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Singularity image: gwas-ssf: command not found #2 #44

Open kauralasoo opened 2 months ago

kauralasoo commented 2 months ago

System information

RedHat Linux

Description of the Issue

I tried to install gwas sumstats tools using following the singularity instructions but was unsuccessful.

What is the path to the gwas-ssf tool within the Singularity image?

Error Message

bash: gwas-ssh: command not found

Command used and terminal output

singularity build gwas-sumstats-tools.sif docker://ebispot/gwas-sumstats-tools:latest
(base) [a72094@login2 ~]$ singularity shell gwas-sumstats-tools.sif
Singularity> gwas-ssf

First 10 Rows of the Input File

No response

Relevant files

No response

jiyue1214 commented 1 week ago

Hi @kauralasoo Thank you for using the gwas-sumstats-tools and for reporting your issue.

It seems that the problem is due to differences in how Docker and Singularity handle the working directory. To proceed, try the following steps after entering the Singularity shell:

cd /application
python3 gwas_sumstats_tools/cli.py -h
python3 gwas_sumstats_tools/cli.py format -h

This should allow you to run the tools successfully.

We will work on improving the Docker image to make it more straightforward for use with Singularity in the future.