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Compleasm: use symlink instead of copying busco data #6679

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Jan 20, 2025
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Compleasm: use symlink instead of copying busco data #6679

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Compleasm: use symlink instead of copying busco data
abretaud Jan 16, 2025
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abretaud Jan 17, 2025
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40 changes: 25 additions & 15 deletions tools/compleasm/compleasm.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,17 +11,18 @@
</requirements>
<version_command>compleasm --version</version_command>
<command><![CDATA[

mkdir -p galaxy_db &&
cp -r '${busco_database.fields.path}/lineages/${lineage_dataset}/' 'galaxy_db/' &&
mkdir -p 'galaxy_db/' &&
ln -s '${busco_database.fields.path}/lineages/${lineage_dataset}/' 'galaxy_db/${lineage_dataset}' &&
## Create a compleasm-specific empty file to avoid redownloading the lineage data (https://github.com/huangnengCSU/compleasm/blob/0.2.6/compleasm.py#L165)
touch 'galaxy_db/${lineage_dataset}.done' &&
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Is this an empty file also existing in the DB folder? Then I would prefer a symlink.

Anyway a small explaining comment would be great.

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It's just an empty file specific to compleasm, to make it understand that it should not redownload it, I'm gonna add a comment


compleasm run
-a '$input'
-o galaxy_output
--mode $mode
-L 'galaxy_db'
-l '$lineage_dataset'
-t "\${GALAXY_SLOTS:-1}"
-t "\${GALAXY_SLOTS:-1}"

#if str($specified_contigs) != '':
--specified_contigs '$specified_contigs'
Expand All @@ -43,7 +44,7 @@
</sanitizer>
<validator type="regex">[0-9a-zA-Z_ ]+</validator>
</param>

<param name="outputs" type="select" multiple="true" label="Which outputs should be generated">
<option value="full_table_busco" selected="true">full busco table</option>
<option value="full_table">full table</option>
Expand Down Expand Up @@ -72,26 +73,32 @@
</data>
<data name='translated_protein' format='fasta' label="${tool.name} on ${on_string}: Translated protein" from_work_dir="galaxy_output/*_odb10/translated_protein.fasta">
<filter>outputs and 'translated_protein' in outputs</filter>
</data>
</data>
</outputs>

<tests>
<test expect_num_outputs="4">
<param name="input" value="small_genome.fasta"/>
<param name="mode" value="busco"/>
<param name="outputs" value="full_table_busco,full_table,miniprot,translated_protein"/>
<param name="busco_database" value="eukaryota_odb10"/>
<param name="lineage_dataset" value="eukaryota_odb10"/>
<param name="busco_database" value="entomoplasmatales_odb10"/>
<param name="lineage_dataset" value="entomoplasmatales_odb10"/>
<output name="full_table_busco">
<assert_contents>
<has_text text="Busco id"/>
<has_text text="Missing"/>
<has_text text="496at186328&#009;Missing"/>
<has_text text="165at186328&#009;Complete"/>
<has_text text="421at186328&#009;Complete"/>
<has_text text="90at186328&#009;Complete"/>
</assert_contents>
</output>
<output name="full_table">
<assert_contents>
<has_text text="Gene"/>
<has_text text="Missing"/>
<has_text text="Gene&#009;Status"/>
<has_text text="496at186328&#009;Missing"/>
<has_text text="165at186328&#009;Single"/>
<has_text text="421at186328&#009;Single"/>
<has_text text="90at186328&#009;Single"/>
</assert_contents>
</output>
<output name="miniprot">
Expand All @@ -101,19 +108,22 @@
</output>
<output name="translated_protein">
<assert_contents>
<has_text text="GGWLIGNGGAGGSGAAGVNGGAGGNGGAGGNGGAGG"/>
<has_text text="AAVFADRGAHVVLAVRNLEKGNAARARIMAARPGAHVTLQQLDLCSLDSVRAAADALRTAYPRIDVLINNAGVMW"/>
<has_text text="EKDFYQELGVSSDASPEEIKRAYRKLARDLHPDANPGNPAA"/>
<has_text text="AASITILEGLEAVRKRPGMYIGSTGERGLHHLIWEVVD"/>
</assert_contents>
</output>
<assert_stdout>
<has_text text="S:1.20%, 4"/>
</assert_stdout>
</test>
</tests>
<help><![CDATA[

compleasm_ assesses genome completeness based on genome assembly.
compleasm_ assesses genome completeness based on genome assembly.

.. _compleasm: https://github.com/huangnengCSU/compleasm

]]>
]]>
</help>
<expand macro="citation"/>
</tool>
4 changes: 2 additions & 2 deletions tools/compleasm/macros.xml
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@@ -1,10 +1,10 @@
<macros>
<token name="@TOOL_VERSION@">0.2.6</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@VERSION_SUFFIX@">2</token>

<xml name="citation">
<citations>
<citation type="doi">10.1101/2023.06.03.543588</citation>
<citation type="doi">10.1101/2023.06.03.543588</citation>
</citations>
</xml>

Expand Down
4 changes: 2 additions & 2 deletions tools/compleasm/test-data/busco_database.loc
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Expand Up @@ -2,5 +2,5 @@
# - value
# - name
# - version
# - /path/to/data
eukaryota_odb10 eukaryota 5.4.6 ${__HERE__}/test-db/busco_downloads
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May I ask why you updated the test (data)?

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to keep the test-data dir as small as possible as entomoplasmatales_odb10 is a much smaller lineage than eukaryota_odb10

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True, but changing it will increase the size of the repo. The "problem" with git repos is that everything that is in in will be there forever.

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But changing it might still be a good idea if the runtime is reduced significantly.

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the previous dataset was non-functional and not really used, so I see no other way than adding this new minimal one

# - /path/to/data
entomoplasmatales_odb10 entomoplasmatales 5.4.6 ${__HERE__}/test-db/busco_downloads
199 changes: 0 additions & 199 deletions tools/compleasm/test-data/test-db/busco_downloads/information/lineages_list.2021-12-14.txt
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