VOG database install fails

[linsalrob]

Installing the VOG database fails

mkdir: cannot create directory ‘/tmp/10353939/mamba-build/opt/mamba/envs/reneo/lib/python3.10/site-packages/reneo/workflow/../../databases/VOG’: File exists
[Sat Mar 30 17:51:49 2024]
Error in rule vog_db_download:
    jobid: 2
    output: /tmp/10353939/mamba-build/opt/mamba/envs/reneo/lib/python3.10/site-packages/reneo/workflow/../../databases/AllVOG.hmm
    conda-env: /tmp/10353939/mamba-build/opt/mamba/envs/reneo/lib/python3.10/site-packages/reneo/workflow/conda/233e73b39830a98b818f43b5ca8b38d3_
    shell:
        
            curl -Lo /tmp/10353939/mamba-build/opt/mamba/envs/reneo/lib/python3.10/site-packages/reneo/workflow/../../databases/vog.hmm.tar.gz http://fileshare.csb.univie.ac.at/vog/latest/vog.hmm.tar.gz
            mkdir /tmp/10353939/mamba-build/opt/mamba/envs/reneo/lib/python3.10/site-packages/reneo/workflow/../../databases/VOG
            tar -xf /tmp/10353939/mamba-build/opt/mamba/envs/reneo/lib/python3.10/site-packages/reneo/workflow/../../databases/vog.hmm.tar.gz -C /tmp/10353939/mamba-build/opt/mamba/envs/reneo/lib/python3.10/site-packages/reneo/workflow/../../databases/VOG
            cat /tmp/10353939/mamba-build/opt/mamba/envs/reneo/lib/python3.10/site-packages/reneo/workflow/../../databases/VOG/* > /tmp/10353939/mamba-build/opt/mamba/envs/reneo/lib/python3.10/site-packages/reneo/workflow/../../databases/AllVOG.hmm
            rm -rf /tmp/10353939/mamba-build/opt/mamba/envs/reneo/lib/python3.10/site-packages/reneo/workflow/../../databases/vog.hmm.tar.gz
            rm -rf /tmp/10353939/mamba-build/opt/mamba/envs/reneo/lib/python3.10/site-packages/reneo/workflow/../../databases/VOG
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message


ERROR: Databases were not setup.

(Note, I have a funky install location, so I've truncated it to start at python3.10)

The HMMs are downloaded and extracted to python3.10/site-packages/databases/VOG/hmm/:

$ ls python3.10/site-packages/databases/VOG/hmm/ | wc -l
59207

The cat command is failing:

first, the extraction puts everything into VOG/hmm and then, you can't cat VOG/hmm/* as there are too many files:

This is what reneo is trying to do:

cat python3.10/site-packages/reneo/workflow/../../databases/VOG/* > python3.10/site-packages/reneo/workflow/../../databases/AllVOG.hmm
cat: python3.10/site-packages/reneo/workflow/../../databases/VOG/hmm: Is a directory

This doesn't work

cat python3.10/site-packages/reneo/workflow/../../databases/VOG/hmm/* > python3.10/site-packages/reneo/workflow/../../databases/AllVOG.hmm
bash: /usr/bin/cat: Argument list too long

but this does:

find python3.10/site-packages/reneo/workflow/../../databases/VOG/ -type f -exec cat {} + > python3.10/site-packages/reneo/workflow/../../databases/AllVOG.hmm

[Vini2]

Hi @linsalrob,

The version 0.2.0 had the cat command to combine the VOGDB HMM files. I've released a new version to fix this issue.

[Vini2]

Hi @linsalrob,

The new version of Reneo is now live on Bioconda.

[linsalrob]

Thanks, This closes #3

…

On Thu, 6 Jun 2024 at 14:49, Vijini Mallawaarachchi < ***@***.***> wrote: Hi @linsalrob <https://github.com/linsalrob>, The new version of Reneo is now live on Bioconda. — Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGMFBZJFDHEPIPPCATN733ZF7WNDAVCNFSM6AAAAABFPNYSQOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNJRGQZTCNZXGQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>