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Logan Proteins minor fix #1860

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Logan Proteins minor fix #1860

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37120a3
Update version suffix in macros.xml and adjust query_sequences path i…
SaimMomin12 May 6, 2026
cc5eec9
Fix remote repository URL in logan_proteins .shed.yml
SaimMomin12 May 6, 2026
be8377b
Update logan_proteins tool version to 1.2.2
SaimMomin12 May 7, 2026
bec89de
Merge branch 'master' into tools/fix-search-proteins
SaimMomin12 May 7, 2026
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2 changes: 1 addition & 1 deletion tools/logan_proteins/.shed.yml
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Expand Up @@ -13,7 +13,7 @@ long_description: |
are validated and aligned with MMseqs2. The approach scales sub-linearly
with the number of queries, making it practical for large-scale metagenomic
and comparative-proteomics workflows.
remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/search_proteins
remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/logan_proteins
type: unrestricted
auto_tool_repositories:
name_template: "{{ tool_id }}"
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2 changes: 1 addition & 1 deletion tools/logan_proteins/macros.xml
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@@ -1,6 +1,6 @@
<macros>
<token name="@TOOL_VERSION@">1.2.0</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@PROFILE@">25.0</token>
<xml name="requirements">
<requirements>
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3 changes: 2 additions & 1 deletion tools/logan_proteins/search_database.xml
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Expand Up @@ -9,10 +9,11 @@
mkdir -p results/intermediate_files &&
ln -s '$query_embeddings_npy' results/intermediate_files/query_embeddings.npy &&
ln -s '$query_embeddings_names' results/intermediate_files/query_embeddings.names.txt &&
ln -s '$query_sequences' query_sequences.fasta &&
python /app/search_database.py
--database '$database.fields.path'
--output results/
--query_sequences '$query_sequences'
--query_sequences query_sequences.fasta
--num_threads \${GALAXY_SLOTS:-8}
#if $outfmt:
--outfmt '$outfmt'
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