/bin/bash/ command not found

Question

[arunprasanna83]

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.

[Brice Sarver]

If you type which bash, what do you get? Perhaps your system has bash installed outside of /bin/.

[arunprasanna83]

I got /bin/bash only.

[Brice Sarver]

Okay. I assumed the /bin/bash/ extra '/' was a typo, but check out RamRS' suggestion below.

[Ram]

Does it say /bin/bash/ or /bin/bash? /bin/bash is not a directory and so should not have a / at the end. Please copy-paste the exact error messages you get.

[Devon Ryan]

Are you directly running snakemake? We don't ever change away from the default shell (/bin/bash) inside snakePipes.

[arunprasanna83]

The defaults.yaml file instructs to run snakemake directly after editing it !

[Devon Ryan]

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.

Answer 1

[svp]

add this path to .bashrc

EXPORT PATH=$PATH:/home/nagaraap/Downloads/Softwares/Anaconda/yes/envs/snakePipes/lib/python3.7/site-packages/snakePipes/workflows/createIndices/Snakefile

then execute

snakemake --snakefile --configfile Indices_defaults.yaml --cores 10

Answer 2

[mark.ziemann]

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

Answer 3

[Fatima]

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.

[Ram]

ll is probably an alias - it is not a builtin or a utility shipped by default in most distros (such as cat or ls). If your ll is aliased to ls -l, please suggest ls -l as that is a more reproducible command.