# HG changeset patch
# User fubar
# Date 1709268292 0
# Node ID bea0916e1080e4d658a1a5916afd9d15c585b5f5
# Parent  7e14b3f1f8e1e36ad6440e13803cb9194f89e4f1
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 015c77d802595a85f78739ee2316b452c519c796-dirty

diff -r 7e14b3f1f8e1 -r bea0916e1080 jbrowse2.py
--- a/jbrowse2.py	Fri Mar 01 02:44:25 2024 +0000
+++ b/jbrowse2.py	Fri Mar 01 04:44:52 2024 +0000
@@ -477,7 +477,7 @@
     def make_assembly(self, fapath, gname):
 
         faname = gname + ".fa.gz"
-        fadest = os.path.join(self.outdir, faname)
+        fadest = os.path.realpath(os.path.join(self.outdir, faname))
         cmd = "bgzip -i -c %s -I %s.gzi > %s && samtools faidx %s" % (
             fapath,
             fadest,