From 0bc0f984f87228028e416b723dc610d782fb72a2 Mon Sep 17 00:00:00 2001
From: Delphine Lariviere <lariviere.delphine@gmail.com>
Date: Wed, 31 Jul 2024 18:57:26 -0400
Subject: [PATCH 1/2] add  blob toolkit to the list of interactive tools

---
 lib/galaxy/config/sample/tool_conf.xml.sample |  1 +
 .../interactivetool_blobtoolkit.xml           | 53 +++++++++++++++++++
 2 files changed, 54 insertions(+)
 create mode 100644 tools/interactive/interactivetool_blobtoolkit.xml

diff --git a/lib/galaxy/config/sample/tool_conf.xml.sample b/lib/galaxy/config/sample/tool_conf.xml.sample
index 153b5ae314d4..841f054b93d0 100644
--- a/lib/galaxy/config/sample/tool_conf.xml.sample
+++ b/lib/galaxy/config/sample/tool_conf.xml.sample
@@ -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" />
diff --git a/tools/interactive/interactivetool_blobtoolkit.xml b/tools/interactive/interactivetool_blobtoolkit.xml
new file mode 100644
index 000000000000..0ff46b2b817c
--- /dev/null
+++ b/tools/interactive/interactivetool_blobtoolkit.xml
@@ -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@">1</token>
+    </macros>
+    <requirements>
+        <container type="docker">quay.io/galaxy/blobtoolkit-server:4.1.0</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 &&
+    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>

From 8dea665f08a1e1ec71882a4d7082365df695ca99 Mon Sep 17 00:00:00 2001
From: Delphine Lariviere <lariviere.delphine@gmail.com>
Date: Thu, 1 Aug 2024 11:25:09 -0400
Subject: [PATCH 2/2] Apply suggestions from code review
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 tools/interactive/interactivetool_blobtoolkit.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/interactive/interactivetool_blobtoolkit.xml b/tools/interactive/interactivetool_blobtoolkit.xml
index 0ff46b2b817c..091af7f4febd 100644
--- a/tools/interactive/interactivetool_blobtoolkit.xml
+++ b/tools/interactive/interactivetool_blobtoolkit.xml
@@ -2,10 +2,10 @@
     <description>genome assembly QC viewer</description>
     <macros>
         <token name="@TOOL_VERSION@">4.1.0</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
-        <container type="docker">quay.io/galaxy/blobtoolkit-server:4.1.0</container>
+        <container type="docker">quay.io/galaxy/blobtoolkit-server:@TOOL_VERSION@</container>
     </requirements>
     <entry_points>
         <entry_point name="Blobtoolkit View" requires_domain="True">