From 3445a95085025faa5afa88c4d3b276fa74134156 Mon Sep 17 00:00:00 2001
From: Luke Sargent <luke.c.sargent@gmail.com>
Date: Wed, 3 Mar 2021 12:09:39 -0800
Subject: [PATCH 1/3] updating bam.iobio interactive tool wrapper for new
 docker image

---
 .../interactive/interactivetool_bam_iobio.xml | 59 +++++++++----------
 1 file changed, 28 insertions(+), 31 deletions(-)

diff --git a/tools/interactive/interactivetool_bam_iobio.xml b/tools/interactive/interactivetool_bam_iobio.xml
index 67b844210db..e6662db0660 100644
--- a/tools/interactive/interactivetool_bam_iobio.xml
+++ b/tools/interactive/interactivetool_bam_iobio.xml
@@ -1,46 +1,43 @@
-<tool id="interactive_tool_bam_iobio" tool_type="interactive" name="BAM (iobio) Visualisation" version="0.1">
+<tool id="interactive_tool_bam_iobio" tool_type="interactive" name="bam.iobio visualisation" version="0.2">
     <requirements>
-        <container type="docker">qiaoy/iobio-bundle.bam-iobio:1.0-ondemand</container>
+        <container type="docker">anderspitman/bam.iobio.io:latest</container>
     </requirements>
     <entry_points>
-        <entry_point name="BAM io.bio visualisation of $infile.display_name" requires_domain="True">
-            <port>80</port>
-            <url><![CDATA[/?bam=http://localhost/tmp/bamfile.bam&region=1]]></url>
+        <entry_point name="BAM io.bio visualisation of $baminfile.display_name" requires_domain="True">
+            <port>9001</port>
+            <url>/</url>
         </entry_point>
     </entry_points>
     <command><![CDATA[
-    ## ToDo: websocket could not be found
-    ## WebSocket connection to 'ws://localhost/bamreaddepther/' failed: Error in connection establishment: net::ERR_CONNECTION_REFUSED
-
-    #set $PUB_HOSTNAME = 'localhost'
-    #set $PUB_HTTP_PORT = '80'
-
-    cd /var/www/html &&
-    sed -i "s@\"wss://services.iobio.io/samtools/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/samtools/\"@" js/bam.iobio.js/bam.iobio.js &&
-    sed -i "s@\"wss://services.iobio.io/bamreaddepther/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/bamreaddepther/\"@" js/bam.iobio.js/bam.iobio.js &&
-    sed -i "s@\"wss://services.iobio.io/bamstatsalive/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/bamstatsalive/\"@" js/bam.iobio.js/bam.iobio.js &&
-    sed -i "s@\"wss://services.iobio.io/samheader/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/samheader/\"@" js/bam.iobio.js/bam.iobio.js &&
-
-    sed -i 's/deny all;//g' /etc/nginx/nginx.conf &&
-
-        cp '${infile}' /input/bamfile.bam &&
-        cp '${infile.metadata.bam_index}' /input/bamfile.bam.bai &&
-        mkdir /var/log/supervisor/ &&
-        head -n -2  /etc/supervisor.d/app.conf > /tmp/app.conf &&
-        mv /tmp/app.conf /etc/supervisor.d/app.conf &&
-
-        /usr/bin/supervisord -c /etc/supervisord.conf
+        #import re
+        mkdir -p /bam/input_files;
+        #set $bam_cleaned_name = re.sub('[^\w\-\.]', '_', str($baminfile.element_identifier))
+        #set $bai_cleaned_name = re.sub('[^\w\-\.]', '_', str($baiinfile.element_identifier))
+        ln -sf '$baminfile' '/bam/input_files/${bam_cleaned_name}' &&
+        ln -sf '$baiinfile' '/bam/input_files/${bai_cleaned_name}' &&
+        echo '{ "bam": "http://localhost:9999/${bam_cleaned_name}", "bai":"http://localhost:9999/${bai_cleaned_name}"}' >> /bam/config/config.json &&
+        cd /bam/input_files &&
+        node /iobio-gru-backend/src/static_server.js 9999 &
+        node /iobio-gru-backend/src/index.js --tools-dir=/iobio-gru-backend/tool_bin --app-dir=/bam;
     ]]>
     </command>
     <inputs>
-        <param name="infile" type="data" format="bam" label="BAM file"/>
+        <param name="baminfile" type="data" format="bam" label="BAM file"/>
+        <param name="baiinfile" type="data" format="bai" label="BAI file"/>
     </inputs>
-    <outputs>
-        <data name="outfile" format="txt" />
-    </outputs>
     <tests>
     </tests>
     <help>
-        BAM iobio visualisation.
+        Required inputs:
+
+        1. BAM file: binary alignment map file
+
+        2. BAI file: corresponding index file
+
+        The `iobio project`_ is developed by the `Marth lab`_ at the `University of Utah Center for Genetic Discovery`_.
+
+        .. _iobio project: https://iobio.io
+        .. _Marth lab: https://marthlab.org/
+        .. _University of Utah Center for Genetic Discovery: https://ucgd.genetics.utah.edu/
     </help>
 </tool>

From de3092483dbd630a9209a7c3eccd5ef246e054d3 Mon Sep 17 00:00:00 2001
From: Luke Sargent <luke.c.sargent@gmail.com>
Date: Thu, 4 Mar 2021 14:54:00 -0800
Subject: [PATCH 2/3] implementing requested changes -- dockerhub->quay,
 versioning image, adding output, suppressing stderr for green history item

---
 tools/interactive/interactivetool_bam_iobio.xml | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/tools/interactive/interactivetool_bam_iobio.xml b/tools/interactive/interactivetool_bam_iobio.xml
index e6662db0660..892073e8ce2 100644
--- a/tools/interactive/interactivetool_bam_iobio.xml
+++ b/tools/interactive/interactivetool_bam_iobio.xml
@@ -1,6 +1,6 @@
 <tool id="interactive_tool_bam_iobio" tool_type="interactive" name="bam.iobio visualisation" version="0.2">
     <requirements>
-        <container type="docker">anderspitman/bam.iobio.io:latest</container>
+        <container type="docker">quay.io/iobio/bam.iobio.io:0.3.0</container>
     </requirements>
     <entry_points>
         <entry_point name="BAM io.bio visualisation of $baminfile.display_name" requires_domain="True">
@@ -12,19 +12,20 @@
         #import re
         mkdir -p /bam/input_files;
         #set $bam_cleaned_name = re.sub('[^\w\-\.]', '_', str($baminfile.element_identifier))
-        #set $bai_cleaned_name = re.sub('[^\w\-\.]', '_', str($baiinfile.element_identifier))
         ln -sf '$baminfile' '/bam/input_files/${bam_cleaned_name}' &&
-        ln -sf '$baiinfile' '/bam/input_files/${bai_cleaned_name}' &&
-        echo '{ "bam": "http://localhost:9999/${bam_cleaned_name}", "bai":"http://localhost:9999/${bai_cleaned_name}"}' >> /bam/config/config.json &&
+        ln -sf '$baminfile.metadata.bam_index' '/bam/input_files/${bam_cleaned_name}.bai' &&
+        echo '{ "bam": "http://localhost:9999/${bam_cleaned_name}", "bai":"http://localhost:9999/${bam_cleaned_name}.bai"}' >> /bam/config/config.json &&
         cd /bam/input_files &&
-        node /iobio-gru-backend/src/static_server.js 9999 &
-        node /iobio-gru-backend/src/index.js --tools-dir=/iobio-gru-backend/tool_bin --app-dir=/bam;
+        node /iobio-gru-backend/src/static_server.js 9999 > /dev/null 2>&1 &
+        node /iobio-gru-backend/src/index.js --tools-dir=/iobio-gru-backend/tool_bin --app-dir=/bam > /dev/null 2>&1;
     ]]>
     </command>
     <inputs>
         <param name="baminfile" type="data" format="bam" label="BAM file"/>
-        <param name="baiinfile" type="data" format="bai" label="BAI file"/>
     </inputs>
+    <outputs>
+        <data name="outfile" format="txt" />
+    </outputs>
     <tests>
     </tests>
     <help>
@@ -32,8 +33,6 @@
 
         1. BAM file: binary alignment map file
 
-        2. BAI file: corresponding index file
-
         The `iobio project`_ is developed by the `Marth lab`_ at the `University of Utah Center for Genetic Discovery`_.
 
         .. _iobio project: https://iobio.io

From 66c7508186d382197f9af9ed26fb73cc44af8722 Mon Sep 17 00:00:00 2001
From: Luke Sargent <luke.c.sargent@gmail.com>
Date: Wed, 12 May 2021 12:25:51 -0700
Subject: [PATCH 3/3] suggested changes

---
 tools/interactive/interactivetool_bam_iobio.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/interactive/interactivetool_bam_iobio.xml b/tools/interactive/interactivetool_bam_iobio.xml
index 892073e8ce2..5afcd03534d 100644
--- a/tools/interactive/interactivetool_bam_iobio.xml
+++ b/tools/interactive/interactivetool_bam_iobio.xml
@@ -1,9 +1,9 @@
-<tool id="interactive_tool_bam_iobio" tool_type="interactive" name="bam.iobio visualisation" version="0.2">
+<tool id="interactive_tool_bam_iobio" tool_type="interactive" name="bam.iobio visualisation" version="0.4.0">
     <requirements>
-        <container type="docker">quay.io/iobio/bam.iobio.io:0.3.0</container>
+        <container type="docker">quay.io/iobio/bam.iobio.io:0.4.0</container>
     </requirements>
     <entry_points>
-        <entry_point name="BAM io.bio visualisation of $baminfile.display_name" requires_domain="True">
+        <entry_point name="BAM io.bio visualisation of $baminfile.element_identifier" requires_domain="True">
             <port>9001</port>
             <url>/</url>
         </entry_point>