# HG changeset patch
# User fubar
# Date 1710571817 0
# Node ID 469c0f6d87d77cdb8dd5f9f951f8f5ea14607d2d
# Parent  d6b0feb22584c713ff5c35dba78908683fb43ab5
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 0553bb75a96ae401623face516c1cf6e1cfe743f

diff -r d6b0feb22584 -r 469c0f6d87d7 jbrowse2.py
--- a/jbrowse2.py	Thu Mar 14 00:59:36 2024 +0000
+++ b/jbrowse2.py	Sat Mar 16 06:50:17 2024 +0000
@@ -481,10 +481,10 @@
                                 self.genome_firstcontig = fl.split()[0].strip()
                             else:
                                 self.genome_firstcontig = fl
-                        else:
-                            fl = urrlib.request.urlopen(faname+".fai").readline()
-                            if fl: # is first row of the text fai so the first contig name
-                                self.genome_firstcontig = fl.decode('utf8').strip().split()[0]
+                    else:
+                        fl = urllib.request.urlopen(fapath+".fai").readline()
+                        if fl: # is first row of the text fai so the first contig name
+                            self.genome_firstcontig = fl.decode('utf8').strip().split()[0]
         if self.config_json.get("assemblies", None):
             self.config_json["assemblies"] += assemblies
         else:
@@ -870,16 +870,14 @@
     def add_cram(self, data, trackData, cram_index=None, **kwargs):
         tId = trackData["label"]
         useuri = trackData["useuri"].lower() == "yes"
-        bindex = cram_index
         if useuri:
             url = data
         else:
             fname = "%s.cram" % trackData["label"]
             dest = "%s/%s" % (self.outdir, fname)
-            bindex = fname + '.crai'
             url = fname
             self.subprocess_check_call(["cp", data, dest])
-            if bindex is not None and os.path.exists(bindex):
+            if cram_index is not None and os.path.exists(cram_index):
                 if not os.path.exists(dest+'.crai'):
                     # most probably made by galaxy and stored in galaxy dirs, need to copy it to dest
                     self.subprocess_check_call(
@@ -899,7 +897,7 @@
                 "type": "CramAdapter",
                 "cramLocation": {"uri": url},
                 "craiLocation": {
-                    "uri": bindex,
+                    "uri": url + '.crai',
                 },
                 "sequenceAdapter": self.genome_sequence_adapter,
             },
@@ -1277,7 +1275,7 @@
             "reversed": False,
             "assemblyName": self.genome_name,
             "start": 2000,
-            "end": 0,
+            "end": 200000,
             "refName": "x",
         }