[24.2] Fix mulled-search --destination quay, add index reuse
#20107
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jdavcs
approved these changes
Jun 11, 2025
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Hmm, weirdly, I get search results even on vanilla 24.2 without these changes: % mulled-search -d quay -s samtools bwa (.venv)
The query returned the following result(s).
LOCATION NAME VERSION COMMAND
quay samtools 1.22--h96c455f_0 docker pull quay.io/biocontainers/samtools:1.22--h96c455f_0
quay samtools 1.6--h5fe306e_12 docker pull quay.io/biocontainers/samtools:1.6--h5fe306e_12
quay samtools 1.3.1--h60f3df9_12 docker pull quay.io/biocontainers/samtools:1.3.1--h60f3df9_12
quay samtools 1.21--h96c455f_1 docker pull quay.io/biocontainers/samtools:1.21--h96c455f_1
quay samtools 1.1--h96c455f_9 docker pull quay.io/biocontainers/samtools:1.1--h96c455f_9
quay samtools 1.6--h5fe306e_11 docker pull quay.io/biocontainers/samtools:1.6--h5fe306e_11
quay samtools 1.3--h60f3df9_9 docker pull quay.io/biocontainers/samtools:1.3--h60f3df9_9
quay samtools 0.1.19--h96c455f_13 docker pull quay.io/biocontainers/samtools:0.1.19--h96c455f_13
quay samtools 0.1.19--h96c455f_12 docker pull quay.io/biocontainers/samtools:0.1.19--h96c455f_12
quay samtools 0.1.18--h96c455f_14 docker pull quay.io/biocontainers/samtools:0.1.18--h96c455f_14
quay samtools 1.21--h50ea8bc_0 docker pull quay.io/biocontainers/samtools:1.21--h50ea8bc_0
quay samtools 1.20--h50ea8bc_1 docker pull quay.io/biocontainers/samtools:1.20--h50ea8bc_1
...
quay samtools 0.1.19--hf89b575_7 docker pull quay.io/biocontainers/samtools:0.1.19--hf89b575_7
quay samtools 1.3.1--h80b0bb3_7 docker pull quay.io/biocontainers/samtools:1.3.1--h80b0bb3_7
quay samtools 1.3--h80b0bb3_4 docker pull quay.io/biocontainers/samtools:1.3--h80b0bb3_4
quay samtools 1.3--h0592bc0_3 docker pull quay.io/biocontainers/samtools:1.3--h0592bc0_3
quay samtools 1.2 docker pull quay.io/biocontainers/samtools:1.2 |
nsoranzo
reviewed
Jun 11, 2025
Co-authored-by: Nicola Soranzo <[email protected]>
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Author
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@ahmedhamidawan it works for things that are on the first page, which includes samtools, but not bwa (which is why your results only include samtools, and not bwa or the mulled containers with samtools + bwa). |
6176b00
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galaxyproject:release_24.2
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This was broken because the API is paginated. Because fetching the full list of biocontainers repos takes some time, I also added index reuse.
Mentioned here: https://lpembleton.rbind.io/posts/mulled-biocontainers/
How to test the changes?
(Select all options that apply)
cd packages/tool_util && pip install -e '.[mulled]'mulled-search -d quay -s samtools bwaLicense