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Improved DM #1751

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5608d12
improved DM
paulzierep Jan 13, 2026
fbd4f0d
remote test data
paulzierep Jan 13, 2026
f4b9cf0
Merge branch 'master' into update-kmetashot-DM
paulzierep Jan 13, 2026
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8 changes: 4 additions & 4 deletions data_managers/data_manager_kmetashot/data_manager/kmetashot_datamanager.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,20 +2,20 @@
<description>database builder</description>
<macros>
<token name="@TOOL_VERSION@">2.0</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@PROFILE@">24.1</token>
</macros>
<requirements>
<requirement type="package" version="@TOOL_VERSION@">kmetashot</requirement>
<requirement type="package" version="1.25.0">wget</requirement>
</requirements>
<command><![CDATA[
mkdir -p "$out_file.extra_files_path" &&
#if $test != "true":
#if $release == "1":
wget "https://zenodo.org/records/17591095/files/kMetaShot_reference.h5" &&
wget -c --tries=10 --waitretry=10 --timeout=30 "https://zenodo.org/records/17591095/files/kMetaShot_reference.h5" &&
mv "kMetaShot_reference.h5" "$out_file.extra_files_path" &&
#else:
wget "https://zenodo.org/records/17375120/files/kMetaShot_bacteria_archaea_2025-05-22.h5" &&
wget -c --tries=10 --waitretry=10 --timeout=30 "https://zenodo.org/records/17375120/files/kMetaShot_bacteria_archaea_2025-05-22.h5" &&
mv "kMetaShot_bacteria_archaea_2025-05-22.h5" "$out_file.extra_files_path" &&
#end if
#else:
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9 changes: 7 additions & 2 deletions data_managers/data_manager_kmetashot/data_manager_conf.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,11 +7,16 @@
<column name="name"/>
<column name="version"/>
<column name="path" output_ref="out_file">
<!-- we copy the .h5 file into the target -->
<move type="file">
<source>${path}</source>
<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kmetashot/${value}/${path}</target>
<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kmetashot/${value}</target>
</move>
<value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kmetashot/${value}/${path}</value_translation>
<!-- we store the path to the .h5 file -->
<value_translation>
#import os
${GALAXY_DATA_MANAGER_DATA_PATH}/kmetashot/${value}/${os.path.basename($path)}
</value_translation>
<value_translation type="function">abspath</value_translation>
</column>
</output>
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2 changes: 0 additions & 2 deletions data_managers/data_manager_kmetashot/test-data/kmetashot.loc
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