Hi,
I installed snakepipes through conda and saw that all dependencies were installed (star, hisat...). However, when I run the pipeline (for instance) createIndices, it throws an error "/bin/bash/ command not found" for several instances.
snakemake --snakefile /home/nagaraap/Downloads/Softwares/Anaconda/yes/envs/snakePipes/lib/python3.7/site-packages/snakePipes/workflows/createIndices/Snakefile --configfile Indices_defaults.yaml --cores 10
What is the solution for this ?
Thanks in advance.
•
written
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arunprasanna83 •
3 answers
As RamRS says, the real path is likely to be /bin/bash so drop the trailing slash in your script. Let us know if that works
Apologies - I will edit
Snakemake runs in bash strict mode, so there are #!/bin/bash at the beginning of some of the scripts. Maybe you can use grep to find which script contains #!/bin/bash.
https://snakemake.readthedocs.io/en/stable/project_info/faq.html#id27
Please try ll /bin/bash
Please also try exec bash before running your command to see if it helps.
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If you type
which bash, what do you get? Perhaps your system has bash installed outside of /bin/.I got /bin/bash only.
Okay. I assumed the /bin/bash/ extra '/' was a typo, but check out RamRS' suggestion below.
Does it say
/bin/bash/or/bin/bash?/bin/bashis not a directory and so should not have a/at the end. Please copy-paste the exact error messages you get.Are you directly running snakemake? We don't ever change away from the default shell (
/bin/bash) inside snakePipes.The defaults.yaml file instructs to run snakemake directly after editing it !
That was meant more as a possibility of "you can directly use it". I'll have the wording changed. As an aside, basically everything in that file can be changed with command line options to the various wrapper scripts.