Mercurial > repos > mvdbeek > igv_take_screenshots

changeset 31:474837e086cc draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit cfa400e89cb4bb8de9ca2ca75ee2e50b77c9a610
author mvdbeek
date Sun, 20 Jan 2019 13:30:21 -0500
parents 9d6b4d2ca187
children 9382c8499e73
files Dockerfile igv_make_screenshots.xml test-data/igv_session.xml
diffstat 3 files changed, 31 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Dockerfile	Sun Jan 20 13:30:21 2019 -0500
@@ -0,0 +1,4 @@
+FROM continuumio/miniconda3:4.5.11
+
+RUN apt-get update && apt-get install -y xvfb libxrender1 libxtst6 && apt-get clean
+RUN conda create -p /usr/local --copy -y -c conda-forge -c bioconda xvfbwrapper samtools igv openjdk=8 freetype font-ttf-dejavu-sans-mono fontconfig coreutils && rm -Rf /opt
--- a/igv_make_screenshots.xml	Fri Jun 15 14:01:18 2018 -0400
+++ b/igv_make_screenshots.xml	Sun Jan 20 13:30:21 2019 -0500
@@ -15,10 +15,19 @@
 ]]></token>
     </macros>
     <requirements>
+        <!-- Conda can't give us a fully functioning xvfb at this time,
+             need to use custom built container
         <requirement type="package" version="0.2.9">xvfbwrapper</requirement>
-        <!-- TODO: uncomment when igv in conda
-        <requirement type="package" version="2.3.93">igv</requirement>
+        <requirement type="package" version="2.4.9">igv</requirement>
+        <requirement type="package" version="1.6.6">xorg-libx11</requirement>
+        <requirement type="package" version="1.17.4">xorg-x11-server-xvfb-cos6-x86_64</requirement>
+        <requirement type="package" version="11.0.7">mesa-libgl-cos6-x86_64</requirement>
+        <requirement type="package" version="2.0.94">libselinux-cos6-x86_64</requirement>
+        <requirement type="package" version="1.0.2">openssl</requirement>
+        <requirement type="package" version="1.9">samtools</requirement>
+        <requirement type="package" version="8.30">coreutils</requirement>
         -->
+        <container type="docker">mvdbeek/igv_make_screenshots:0.1.2</container>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 #if $genome_source.input_type_selector == 'history':
@@ -27,24 +36,23 @@
     ln -s '$genome_source.genome.fields.path' genome.fa &&
 #end if
 samtools faidx genome.fa &&
-sed -i.bak -e "s|\"genome.fa\"|\"\$PWD/genome.fa\"|g" '$igv_session' &&
+cp '$igv_session' igv_session.xml &&
+sed -i.bak -e "s|\"genome.fa\"|\"\$PWD/genome.fa\"|g" igv_session.xml &&
 #for $i, $inputsection in enumerate($inputfiles):
     @PATH@
     ln -fs '$inputsection.input' '$path' &&
-    sed -i.bak -e "s|\"$path\"|\"\$PWD/$path\"|g" '$igv_session' &&
+    sed -i.bak -e "s|\"$path\"|\"\$PWD/$path\"|g" igv_session.xml &&
     #if $inputsection.input.is_of_type('bam')
         ln -fs $inputsection.input.metadata.bam_index '$path'.bai &&
     #end if
 #end for
-ln -fs $igv_session igv_session.xml &&
 cat '$load_session' > load_session.txt &&
 echo snapshotDirectory "\$PWD" >> load_session.txt &&
 cat load_session.txt '$script_file' '$exit_session' > igv_script.txt &&
 cp '$igv_session_remote' '$igv_session_out'
 #if not $skip_screenshots:
     && python $__tool_directory__/xvfb_igv.py igv_script.txt '$igv_preferences' $width,$height &&
-    zip screenshots.zip *.png &&
-    cp screenshots.zip '$screenshots_out'
+    mkdir screenshots && mv *.png screenshots
 #end if
     ]]></command>
     <configfiles>
@@ -162,19 +170,22 @@
         <param name="height" label="Select the screenshot height" type="integer" min="640" value="1080"/>
     </inputs>
     <outputs>
-        <data name="igv_session_out" format="xml"/>
-        <data name="screenshots_out" format="zip">
+        <data name="igv_session_out" format="xml" label="IGV session for ${on_string}"/>
+        <collection name="screenshots_out" type="list" label="IGV screenshots for ${on_string}">
             <filter>skip_screenshots == False</filter>
-        </data>
+            <discover_datasets pattern="__name_and_ext__" directory="screenshots" />
+        </collection>
     </outputs>
     <tests>
         <test>
             <param name="genome_source|input_type_selector" value="history"/>
             <param name="genome_source|genome" value="rover_reference.fa"/>
+            <param name="script_file" value="complete_batchscript.txt"/>
             <repeat name="inputfiles">
                 <param name="input" value="rover_corrected.bam"/>
             </repeat>
             <output name="igv_session_out" file="igv_session.xml" lines_diff="6"/>
+            <output_collection name="screenshots_out" type="list" count="1"/>
         </test>
     </tests>
     <help><![CDATA[
--- a/test-data/igv_session.xml	Fri Jun 15 14:01:18 2018 -0400
+++ b/test-data/igv_session.xml	Sun Jan 20 13:30:21 2019 -0500
@@ -1,13 +1,15 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<Session genome="/Users/mvandenb/src/galaxy/database/jobs_directory/000/350/working/genome.fa" hasGeneTrack="false" hasSequenceTrack="true" version="8">
+<Session genome="dm6" hasGeneTrack="true" hasSequenceTrack="true" version="8">
     <Resources>
-        <Resource path="/Users/mvandenb/src/galaxy/database/jobs_directory/000/350/working/0.rover_corrected.bam.bam"/>
+<Resource path="http://localhost:8080/display_application/d836242eec778a25/igv_bam/local_default/None/data/galaxy_d836242eec778a25.bam"/>
     </Resources>
+            
+
             <Panel height="300" name="Panelrover_corrected.bam" width="1920">
-            <Track altColor="0,0,178" autoScale="true" color="175,175,175" colorScale="ContinuousColorScale;0.0;10.0;255,255,255;175,175,175" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="0.rover_corrected.bam.bam_coverage" name="rover_corrected.bam Coverage" showReference="false" snpThreshold="0.2" sortable="true" visible="true">
+            <Track altColor="0,0,178" autoScale="true" color="175,175,175" colorScale="ContinuousColorScale;0.0;10.0;255,255,255;175,175,175" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="http://localhost:8080/display_application/d836242eec778a25/igv_bam/local_default/None/data/galaxy_d836242eec778a25.bam_coverage" name="rover_corrected.bam Coverage" showReference="false" snpThreshold="0.2" sortable="true" visible="true">
                 <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="10.0" minimum="0.0" type="LINEAR"/>
             </Track>
-            <Track altColor="0,0,178" autoScale="false" color="0,0,178" displayMode="EXPANDED" featureVisibilityWindow="-1" fontSize="10" id="/Users/mvandenb/src/galaxy/database/jobs_directory/000/350/working/0.rover_corrected.bam.bam" name="rover_corrected.bam" sortable="true" visible="true">
+            <Track altColor="0,0,178" autoScale="false" color="0,0,178" displayMode="EXPANDED" featureVisibilityWindow="-1" fontSize="10" id="http://localhost:8080/display_application/d836242eec778a25/igv_bam/local_default/None/data/galaxy_d836242eec778a25.bam" name="rover_corrected.bam" sortable="true" visible="true">
                 <RenderOptions colorByTag="CD" colorOption="TAG" flagUnmappedPairs="false" groupByOption="NONE" groupByTag="BR" linkByTag="READNAME" linkedReads="false" maxInsertSize="1000" minInsertSize="50" quickConsensusMode="false" shadeBasesOption="QUALITY" shadeCenters="true" showAllBases="false" sortByTag="" viewPairs="false"/>
             </Track>
             </Panel>