# HG changeset patch
# User fubar
# Date 1728014823 0
# Node ID ae07c55ab96b676bd9054e62f3a3f8182839b1fb
# Parent  478ee3e780dec4b37e396d41bb70d25fba1b4492
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a9124072bc71dd670ee58ff8e4846e14d6d603ec

diff -r 478ee3e780de -r ae07c55ab96b __pycache__/jbrowse2.cpython-312.pyc
Binary file __pycache__/jbrowse2.cpython-312.pyc has changed
diff -r 478ee3e780de -r ae07c55ab96b jbrowse2.py
--- a/jbrowse2.py	Thu Oct 03 06:07:18 2024 +0000
+++ b/jbrowse2.py	Fri Oct 04 04:07:03 2024 +0000
@@ -21,7 +21,7 @@
 logging.basicConfig(level=logging.DEBUG)
 log = logging.getLogger("jbrowse")
 
-JB2VER = "v2.12.3"
+JB2VER = "v2.15.4"
 # version pinned if cloning - but not cloning now
 logCommands = True
 # useful for seeing what's being written but not for production setups
@@ -1547,7 +1547,7 @@
 
         """
         dest = self.outdir
-        if realclone:
+        if (not os.path.exists(self.jbrowse2path)) or realclone:
             self.subprocess_check_call(
                 ["jbrowse", "create", dest, "-f", "--tag", f"{JB2VER}"]
             )
diff -r 478ee3e780de -r ae07c55ab96b jbrowse2.xml
--- a/jbrowse2.xml	Thu Oct 03 06:07:18 2024 +0000
+++ b/jbrowse2.xml	Fri Oct 04 04:07:03 2024 +0000
@@ -21,7 +21,7 @@
     <command detect_errors="aggressive"><![CDATA[
 mkdir -p '$output.files_path' &&
 cp '$trackxml' '$output.files_path/galaxy.xml' &&
-export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 &&
+export JBROWSE2_PATH=\$(realpath \$(dirname \$(which jbrowse))/../opt/jbrowse2) &&
 #if $jbgen.ucol.formcoll=="collect":
     python '$__tool_directory__/autogenJB2.py'
     #for $key in $autoCollection.keys():
diff -r 478ee3e780de -r ae07c55ab96b macros.xml
--- a/macros.xml	Thu Oct 03 06:07:18 2024 +0000
+++ b/macros.xml	Fri Oct 04 04:07:03 2024 +0000
@@ -25,7 +25,7 @@
         </requirements>
     </xml>
     <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <xml name="creators">
         <creator>
             <person givenName="Helena" familyName="Rasche" url="https://github.com/hexylena"/>