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isugifNF / polishCLR

A nextflow pipeline for polishing CLR assemblies
https://isugifnf.github.io/polishCLR/
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Rebuild new image for DockerHub and test on singularity (HPC) #36

Closed j23414 closed 2 years ago

j23414 commented 2 years ago

@Sivanandan Tag, you're it :)

Thanks for bringing up the singularity issue

Sivanandan commented 2 years ago

I rebuilt the docker image but looks like I am having the same problem with singularity. I'll have to check again though.

j23414 commented 2 years ago

Darn, I was hoping the new micromamba image would auto load "base" env. Kay, I added:

ENV PATH "$PATH:$MAMBA_ROOT_PREFIX/envs/polishCLR_env/bin"

Could you try again? I'm happy to jump on a zoom call if it's still hitting any errors.

Sivanandan commented 2 years ago

:( still doesn't work..

singularity inspect polish-clr.sif 
org.label-schema.build-arch: amd64
org.label-schema.build-date: Saturday_28_May_2022_13:28:36_CDT
org.label-schema.schema-version: 1.0
org.label-schema.usage.singularity.deffile.bootstrap: docker
org.label-schema.usage.singularity.deffile.from: csiva2022/polishclr:latest
org.label-schema.usage.singularity.version: 3.8.5-2.el7
(base) [sivanandan.chudalayandi@ceres-login Siva_2022]$ singularity shell polish-clr.sif
Singularity> echo $PATH
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/conda/envs/polishCLR_env/bin
Singularity> echo $SHELL
/bin/bash
Singularity> samtools
bash: samtools: command not found
Singularity> micromamba

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

Version: 0.23.3
j23414 commented 2 years ago

We fixed it for singularity via:

ENV PATH "$PATH:$MAMBA_ROOT_PREFIX/bin"

@Sivanandan , thanks for meeting and co-troubleshooting!