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] 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