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yyoshiaki / VIRTUS2

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.
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Running this on an hpc with no docker installed #25

Closed SomeGuy3865 closed 1 year ago

SomeGuy3865 commented 1 year ago

Hello, I tried to run your tutorial after you redirected me here from Virtect and VIRTUS v1, but am running into an issue: my fasta files are quite large and so this necessitates me using a high performance computing cluster where I do not have installation privileges. I tried to make a conda environment with docker installed (pip install docker) but when I attempt to download the index files as you said: ./createindex.cwl https://raw.githubusercontent.com/yyoshiaki/VIRTUS2/master/workflow/createindex.job.yaml

I get the following error: INFO /data/user/kmaroney/.conda/envs/Virtus/bin/cwltool 3.1.20230624081518 INFO Resolved './workflow/createindex.cwl' to 'file:///data/user/home/kmaroney/programs/VIRTUS2/workflow/createindex.cwl' INFO [workflow ] start INFO [workflow ] starting step mkdir_virus INFO [step mkdir_virus] start ERROR Workflow or tool uses unsupported feature: Docker is required to run this tool: docker executable is not available

I don't use Docker at all - is there a workaround to this or do I have to call it from within my conda environment before running the command? (It seems to be installed from pip install docker?).

Sorry if these are very basic questions for you. Thanks for your help :)

yyoshiaki commented 1 year ago

Whether you can use docker or not in your HPC depends on your system. In most cases, for HPC, only administrators can install docker, so it would be nice to ask the administrators about that. You can use singularity instead of docker though the situation is similar.

SomeGuy3865 commented 1 year ago

I suppose what I'm wondering is if there is a simple command to download all the references without Docker? Or is everything set up through a Docker container which is called by this code and it has to be through Docker?

yyoshiaki commented 1 year ago

It is theoretically possible to download and install all tools manually, but I don't definitely recommend it. If you use docker or singularity, you don't have to set up individual tools.

SomeGuy3865 commented 1 year ago

I completely understand, but my problem is that I don’t have docker or singularity installed on the cluster where my data is stored. I’ve asked them if they can install docker as you suggested. I hope they can.

Sincerely, Kevin Maroney

M.S. Biotechnology University of California PhD student University of Alabama at Birmingham

From: Yoshiaki Yasumizu @.> Sent: Wednesday, July 5, 2023 5:18 PM To: yyoshiaki/VIRTUS2 @.> Cc: Kevin Maroney @.>; Author @.> Subject: Re: [yyoshiaki/VIRTUS2] Running this on an hpc with no docker installed (Issue #25)

It is theoretically possible to download and install all tools manually, but I don't definitely recommend it. If you use docker or singularity, you don't have to set up individual tools.

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yyoshiaki commented 1 year ago

Good luck, Docker/singularity would greatly improve your bioinformatics life!