umi_tools not found

[GerardoZA]

When trying to remove UMIs and adapters at the second step, I get the following error:

/bin/sh: 1: umi_tools: not found

My command:

apptainer exec --bind $(pwd):/data --bind $(pwd):/rnadb trax_latest.sif bash
trimadapters.py --runname=adapters --runfile=AdaptSamp_data.txt --cores=2 --umilength 18

[andrewdholmes]

OK I'll need to check if it's in the dependencies but to get it working you just need to get the umi_tools package and put it in your $PATH, should be able to with conda easily if you have that set up

…

On Mon, Nov 25, 2024 at 10:09 AM GerardoZA ***@***.***> wrote: When trying to remove UMIs and adapters at the second step, I get the following error: /bin/sh: 1: umi_tools: not found My command: apptainer exec --bind $(pwd):/data --bind $(pwd):/rnadb trax_latest.sif bash trimadapters.py --runname=adapters --runfile=AdaptSamp_data.txt --cores=2 --umilength 18 — Reply to this email directly, view it on GitHub <#28>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEHEMLRB56HRHTMVOIXPRVL2CNRVFAVCNFSM6AAAAABSOS5IJCVHI2DSMVQWIX3LMV43ASLTON2WKOZSGY4TCNZUGIYTCNQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>