# HG changeset patch
# User fubar
# Date 1709254989 0
# Node ID bc57164eb270468704c7bc7c47ff098ba16acfac
# Parent  07849bf248e3d6da29016c38e8f90a554fafd805
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit ace841acd53be99494ed9bba8bb9e2ae212d3661

diff -r 07849bf248e3 -r bc57164eb270 __pycache__/jbrowse2.cpython-310.pyc
Binary file __pycache__/jbrowse2.cpython-310.pyc has changed
diff -r 07849bf248e3 -r bc57164eb270 autogenJB2.py
--- a/autogenJB2.py	Fri Mar 01 00:40:38 2024 +0000
+++ b/autogenJB2.py	Fri Mar 01 01:03:09 2024 +0000
@@ -43,9 +43,9 @@
         default=[],
         action="append",
     )
-
+    parser.add_argument("--jbrowse2path", help="Path to JBrowse2 directory in biocontainer or Conda")
+    parser.add_argument("--outdir", help="Output directory", required=True)
     parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.10.2")
-    parser.add_argument("--outdir", help="Output directory", required=True)
     args = parser.parse_args()
     sessName = args.sessName
     # --trackmeta $jbrowseme[$key],$jbrowseme[$key].ext,'$key'
@@ -63,6 +63,7 @@
             genome_names = [x[2] for x in listgenomes]
             jc = jbC(
                 outdir=args.outdir,
+                jbrowse2path=args.jbrowse2path,
                 genomes=[
                     {
                         "path": x,
diff -r 07849bf248e3 -r bc57164eb270 autogenJB2.xml
--- a/autogenJB2.xml	Fri Mar 01 00:40:38 2024 +0000
+++ b/autogenJB2.xml	Fri Mar 01 01:03:09 2024 +0000
@@ -10,6 +10,7 @@
     <expand macro="requirements"/>
     <version_command>python '${__tool_directory__}/autogenJB2.py' --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
+export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2  &&
 python '$__tool_directory__/autogenJB2.py'
 #for $key in $autoCollection.keys():
     #if $autoCollection[$key].ext == 'fasta':
@@ -23,6 +24,7 @@
     #end if
 #end for
 --outdir '$output.files_path'
+--jbrowse2path \${JBROWSE2_PATH}
 --sessName "Autogen JBrowse" &&
 
   cp '$output.files_path/index.html' '$output'