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Bump busco to 6.0.0 #7139

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Bump busco to 6.0.0 #7139

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70fdcab
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bernt-matthias Jul 14, 2025
f435956
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bernt-matthias Jul 14, 2025
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30 changes: 14 additions & 16 deletions data_managers/data_manager_fetch_busco/data_manager/busco_fetcher.xml
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Original file line number Diff line number Diff line change
@@ -1,22 +1,20 @@
<tool id="busco_fetcher" name="Busco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="23.1">
<tool id="busco_fetcher" name="Busco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="24.1">
<description>dataset dowloader</description>
<macros>
<token name="@TOOL_VERSION@">5.8.0</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@TOOL_VERSION@">6.0.0</token>
<token name="@VERSION_SUFFIX@">0</token>
</macros>
<requirements>
<requirement type="package" version="@TOOL_VERSION@">busco</requirement>
</requirements>
<command detect_errors="exit_code"><![CDATA[
busco --download_path '$out_file.extra_files_path' --download '$lineage' &&
## remove unwanted lineage folders and placement files
## https://gitlab.com/ezlab/busco/-/issues/784
if [ -d '$out_file.extra_files_path'/lineages ]; then
find '$out_file.extra_files_path'/lineages/ -mindepth 1 -maxdepth 1 ! -name '*_$datasets_version*' -exec rm -rf {} \;;
fi &&
if [ -d '$out_file.extra_files_path'/placement_files ]; then
find '$out_file.extra_files_path'/placement_files/ -mindepth 1 -maxdepth 1 ! -name '*_$datasets_version*' -delete;
fi &&
busco
--download_path '$out_file.extra_files_path'
#if $lineage == "virus"
--download virus &&
#else
--download all_'$lineage'$datasets_version &&
#end if
## unpack faa.gz files ready to use
## https://gitlab.com/ezlab/busco/-/issues/789
if [ -d '$out_file.extra_files_path'/lineages ]; then
Expand All @@ -43,9 +41,9 @@
</configfiles>
<inputs>
<param name="lineage" argument="--download" type="select" label="Select the lineage to be downloaded">
<option value="all">All</option>
<option value="prokaryota">Prokaryota</option>
<option value="eukaryota">Eukaryota</option>
<option value="">All</option>
<option value="prokaryota_">Prokaryota</option>
<option value="eukaryota_">Eukaryota</option>
<option value="virus">Virus</option>
</param>
<param argument="--datasets_version" type="select" label="OrthoDB version" help="By March 2025 OrthoDB 12 datasets were only available for Prokaryota (https://busco-data2.ezlab.org/v5/data/)">
Expand All @@ -62,7 +60,7 @@
<output name="out_file">
<assert_contents>
<has_text text="virus"/>
<has_text text="5.8.0"/>
<has_text text="@TOOL_VERSION@"/>
</assert_contents>
</output>
</test>
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4 changes: 2 additions & 2 deletions data_managers/data_manager_fetch_busco_options/data_manager/busco_options.xml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
<tool id="busco_fetcher_options" name="Busco options" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="23.1">
<tool id="busco_fetcher_options" name="Busco options" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="24.1">
<description></description>
<macros>
<token name="@TOOL_VERSION@">5.8.0</token>
<token name="@TOOL_VERSION@">6.0.0</token>
<token name="@VERSION_SUFFIX@">0</token>
</macros>
<requirements>
Expand Down
27 changes: 27 additions & 0 deletions data_managers/data_manager_fetch_busco_options/test-data/busco_database_options.loc
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Expand Up @@ -79,3 +79,30 @@ bclasvirinae_odb10 Bclasvirinae test
simplexvirus_odb10 Simplexvirus test
tequatrovirus_odb10 Tequatrovirus test
aviadenovirus_odb10 Aviadenovirus test
iridoviridae_odb10 Iridoviridae test
betabaculovirus_odb10 Betabaculovirus test
betaherpesvirinae_odb10 Betaherpesvirinae test
skunavirus_odb10 Skunavirus test
chordopoxvirinae_odb10 Chordopoxvirinae test
alphabaculovirus_odb10 Alphabaculovirus test
rudiviridae_odb10 Rudiviridae test
tevenvirinae_odb10 Tevenvirinae test
tunavirinae_odb10 Tunavirinae test
varicellovirus_odb10 Varicellovirus test
pahexavirus_odb10 Pahexavirus test
guernseyvirinae_odb10 Guernseyvirinae test
baculoviridae_odb10 Baculoviridae test
alphaherpesvirinae_odb10 Alphaherpesvirinae test
spounavirinae_odb10 Spounavirinae test
peduovirus_odb10 Peduovirus test
enquatrovirus_odb10 Enquatrovirus test
teseptimavirus_odb10 Teseptimavirus test
gammaherpesvirinae_odb10 Gammaherpesvirinae test
herpesviridae_odb10 Herpesviridae test
cheoctovirus_odb10 Cheoctovirus test
poxviridae_odb10 Poxviridae test
fromanvirus_odb10 Fromanvirus test
bclasvirinae_odb10 Bclasvirinae test
simplexvirus_odb10 Simplexvirus test
tequatrovirus_odb10 Tequatrovirus test
aviadenovirus_odb10 Aviadenovirus test
2 changes: 1 addition & 1 deletion tools/busco/busco.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="busco" name="Busco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
<tool id="busco" name="Busco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1">
<description>Assess genome assembly and annotation completeness</description>
<macros>
<import>macros.xml</import>
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4 changes: 2 additions & 2 deletions tools/busco/macros.xml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
<?xml version="1.0"?>
<macros>
<token name="@TOOL_VERSION@">5.8.0</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@TOOL_VERSION@">6.0.0</token>
<token name="@VERSION_SUFFIX@">0</token>

<xml name="citations">
<citations>
Expand Down
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