diff autogenJB2.py @ 39:bc57164eb270 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit ace841acd53be99494ed9bba8bb9e2ae212d3661

--- 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,