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Update DBs URLs and Dockerfiles #156

Merged
merged 15 commits into from
May 31, 2024
Merged

Update DBs URLs and Dockerfiles #156

merged 15 commits into from
May 31, 2024

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JoseEspinosa
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@JoseEspinosa JoseEspinosa commented May 30, 2024 •
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  • Update colabfold DBs to the last version:

    • uniref30_2202 to uniref30_2302.
    • update colabfold dockerfile accordingly

  • Update alphafold DBs to the last version:

    • change ftp to https protocol for some of the URLs, when available.
    • mgnify_link, from https://storage.googleapis.com/alphafold-databases/casp14_versions/mgy_clusters_2018_12.fa.gz to https://storage.googleapis.com/alphafold-databases/v2.3/mgy_clusters_2022_05.fa.gz
    • pdb_obsolote from ftp://ftp.wwpdb.org/pub/pdb/data/status/obsolete.dat to https://files.wwpdb.org/pub/pdb/data/status/obsolete.dat.
    • uniref_90, from https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz to https://ftp.ebi.ac.uk/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz.
    • pdb_seqres from ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt to https://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt.

  • Fix LD_LIBRARY_PATH for Alphafold2 dockerfiles (match version with base cuda image version)

Closes #148

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

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github-actions bot commented May 30, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d979d3f

+| ✅ 195 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-30 14:46:23

@JoseEspinosa JoseEspinosa changed the title Update colabfold DBs URLs, other URL and Dockerfiles Update DBs URLs and Dockerfiles May 30, 2024
ggabernet
ggabernet approved these changes May 30, 2024
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LGTM

@JoseEspinosa JoseEspinosa merged commit 8126d0e into nf-core:dev May 31, 2024
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@JoseEspinosa JoseEspinosa mentioned this pull request May 31, 2024
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@ggabernet ggabernet ggabernet approved these changes

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