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Add BlobToolkit to the list of interactive tools #18630

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Sep 5, 2024
Merged

Add BlobToolkit to the list of interactive tools #18630

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0bc0f98
add blob toolkit to the list of interactive tools
Delphine-L Jul 31, 2024
8dea665
Apply suggestions from code review
Delphine-L Aug 1, 2024
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1 change: 1 addition & 0 deletions lib/galaxy/config/sample/tool_conf.xml.sample
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Original file line number Diff line number Diff line change
Expand Up @@ -134,6 +134,7 @@
<section id="interactivetools" name="Interactive tools">
<tool file="interactive/interactivetool_askomics.xml" />
<tool file="interactive/interactivetool_bam_iobio.xml" />
<tool file="interactive/interactivetool_blobtoolkit.xml" />
<tool file="interactive/interactivetool_cellxgene_0.16.2.xml" />
<tool file="interactive/interactivetool_cellxgene_1.1.1.xml" />
<tool file="interactive/interactivetool_ethercalc.xml" />
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53 changes: 53 additions & 0 deletions tools/interactive/interactivetool_blobtoolkit.xml
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@@ -0,0 +1,53 @@
<tool id="interactive_tool_blobtoolkit" tool_type="interactive" name="Interactive BlobToolKit" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
<description>genome assembly QC viewer</description>
<macros>
<token name="@TOOL_VERSION@">4.1.0</token>
<token name="@VERSION_SUFFIX@">0</token>
</macros>
<requirements>
<container type="docker">quay.io/galaxy/blobtoolkit-server:@TOOL_VERSION@</container>
</requirements>
<entry_points>
<entry_point name="Blobtoolkit View" requires_domain="True">
<port>80</port>
<url>view/all</url>
</entry_point>
</entry_points>
<command detect_errors="exit_code"><![CDATA[
## The following is a hack. Our embedded pulsar is not respecting the Galaxy jwd-tmp dir.
export TEMP=\$PWD &&
export TMP=\$PWD &&
export TMPDIR=\$PWD &&
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Is this some old copy and paste ? If there is a problem with embeded pulsar and the temp dir handling issue should be opened.

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@bgruening @kysrpex do you know where this originated from, is this still needed ?

mkdir datasets &&
cd datasets &&
mkdir './Blobdir' &&
#if $blobdir:
#if $blobdir.is_of_type("tgz")
tar -zxf '${blobdir}' -C './Blobdir' &&
#else
tar -xf '${blobdir}' -C './Blobdir' &&
#end if
cd .. &&
export BTK_FILE_PATH=\$PWD/datasets &&
startup.sh
#else:
cd .. &&
startup.sh
#end if
]]></command>
<inputs>
<param name="blobdir" type="data" format="tgz,tar" optional="true" label="Blobdir file" help="This file should be generated by the module create. The collection of JSON files should be packed in the tarbal file without directory structure." />
</inputs>
<outputs>
<data name="Interactive BlobToolKit on data ${on_string}" format="txt"/>
</outputs>
<tests>
</tests>
<help><![CDATA[
BlobToolKit is a software suite to aid researchers in identifying and isolating non-target data in draft and publicly available genome assemblies. It can be used to process assembly,
read and analysis files for fully reproducible interactive exploration in the browser-based Viewer. BlobToolKit can be used during assembly to filter non-target DNA, helping researchers produce assemblies with high biological credibility.
]]></help>
<citations>
<citation type="doi">10.1534/g3.119.400908</citation>
</citations>
</tool>
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