# HG changeset patch
# User mvdbeek
# Date 1548012627 18000
# Node ID 9382c8499e7339f58fb8a06ca8b68f6d34c7c164
# Parent  474837e086cc0dac8b596fe6ff17a7c61e587e14
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit c6f25b122899a00695b5ca9e70d34e2c1d288236-dirty

diff -r 474837e086cc -r 9382c8499e73 Dockerfile
--- a/Dockerfile	Sun Jan 20 13:30:21 2019 -0500
+++ b/Dockerfile	Sun Jan 20 14:30:27 2019 -0500
@@ -1,4 +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
+RUN conda install -y -c conda-forge -c bioconda xvfbwrapper samtools igv openjdk=8 freetype font-ttf-dejavu-sans-mono fontconfig coreutils
diff -r 474837e086cc -r 9382c8499e73 igv_make_screenshots.xml
--- a/igv_make_screenshots.xml	Sun Jan 20 13:30:21 2019 -0500
+++ b/igv_make_screenshots.xml	Sun Jan 20 14:30:27 2019 -0500
@@ -51,7 +51,7 @@
 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 &&
+    && xvfb-run --server-args="-screen 0 ${width}x${height}x24" igv -g genome.fa -o '$igv_preferences' --batch igv_script.txt &&
     mkdir screenshots && mv *.png screenshots
 #end if
     ]]></command>
diff -r 474837e086cc -r 9382c8499e73 xvfb_igv.py
--- a/xvfb_igv.py	Sun Jan 20 13:30:21 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
-import os
-import subprocess
-import sys
-
-import xvfbwrapper
-
-
-def take_screenshots(igv_script, preferences_file, screensize):
-    width, height = screensize.split(',')
-    with xvfbwrapper.Xvfb(width=width, height=height) as xvfb:
-        exit_code = subprocess.call(['igv', '-g', 'genome.fa', '-o', preferences_file, '--batch', igv_script], env=os.environ.copy())
-    sys.exit(exit_code)
-
-
-if __name__ == '__main__':
-    take_screenshots(sys.argv[1], sys.argv[2], sys.argv[3])
-