Mercurial > repos > iuc > data_manager_salmon_index_builder
changeset 8:ec2a1f280d67 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit 1ea9e99e1c7a7cd0f012467466e0740b6bdeb90e
| author | iuc |
|---|---|
| date | Thu, 23 Oct 2025 17:05:46 +0000 |
| parents | 9fc154508622 |
| children | |
| files | data_manager/salmon_index_builder.xml test-data/salmon_indexes_versioned.loc |
| diffstat | 2 files changed, 8 insertions(+), 3 deletions(-) [+] |
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--- a/data_manager/salmon_index_builder.xml Wed Oct 22 14:38:22 2025 +0000 +++ b/data_manager/salmon_index_builder.xml Thu Oct 23 17:05:46 2025 +0000 @@ -1,8 +1,8 @@ <tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.0"> <description>index builder</description> <macros> - <token name="@TOOL_VERSION@">1.3.0</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">1.10.1</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">24.0</token> <token name="@IDX_VERSION@">q7</token> </macros> @@ -10,6 +10,9 @@ <requirement type="package" version="@TOOL_VERSION@">salmon</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ + ## salmon uses one thread to much + SLOTS=\$(( \${GALAXY_SLOTS:-12} > 1 ? \${GALAXY_SLOTS:-12} - 1 : 1 )); + ## https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/ ## https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode @@ -27,7 +30,7 @@ -t gentrome.fa -d decoys.txt -i '$out_file.extra_files_path' - -p "\${GALAXY_SLOTS:-12}" + -p "\$SLOTS" $gencode &&
--- a/test-data/salmon_indexes_versioned.loc Wed Oct 22 14:38:22 2025 +0000 +++ b/test-data/salmon_indexes_versioned.loc Thu Oct 23 17:05:46 2025 +0000 @@ -0,0 +1,2 @@ +sequence_id phiX174 sequence_name /tmp/tmp1py4xsp5/galaxy-dev/tool-data/phiX174/salmon_index/sequence_id/q7 q7 +phiX174 phiX174 phiX174 /tmp/tmp1py4xsp5/galaxy-dev/tool-data/phiX174/salmon_index/phiX174/q7 q7