# HG changeset patch
# User fubar
# Date 1706960996 0
# Node ID fb6cc7bc24df5d92e795be3c0ee2f974afb338eb
# Parent  39b717d934a8ec8fc11000f4de6af704e977078a
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit cde4b8a574ded34a0ff8df3ecafc1a057787dcfb-dirty

diff -r 39b717d934a8 -r fb6cc7bc24df cool_in_jb2.jpg
Binary file cool_in_jb2.jpg has changed
diff -r 39b717d934a8 -r fb6cc7bc24df dm4_in_jb2.png
Binary file dm4_in_jb2.png has changed
diff -r 39b717d934a8 -r fb6cc7bc24df jbrowse2.py
--- a/jbrowse2.py	Sat Feb 03 10:17:27 2024 +0000
+++ b/jbrowse2.py	Sat Feb 03 11:49:56 2024 +0000
@@ -461,7 +461,7 @@
                 self.genome_firstcontig = None
                 fl = open(fapath, "r").readline().strip().split(">", 1)
                 if len(fl) > 1:
-                    self.genome_firstcontig = fl[1].strip()
+                    self.genome_firstcontig = fl[1].split().strip()
         if self.config_json.get("assemblies", None):
             self.config_json["assemblies"] += assemblies
         else:
@@ -1148,7 +1148,6 @@
                     outputTrackConfig,
                 )
             elif dataset_ext in ("cool", "mcool", "scool"):
-                hictempd = tempfile.mkdtemp()
                 hic_path = os.path.join(
                     self.outdir, "%s_%d_%s.hic" % (track_human_label, i, dataset_ext)
                 )
@@ -1159,8 +1158,6 @@
                         "-f",
                         "--output-fmt",
                         "hic",
-                        "--tmpdir",
-                        hictempd,
                         dataset_path,
                         hic_path,
                     ]
@@ -1169,7 +1166,6 @@
                     hic_path,
                     outputTrackConfig,
                 )
-                shutil.rmtree(hictempd)
             elif dataset_ext in ("bed",):
                 self.add_bed(
                     dataset_path,
@@ -1283,9 +1279,9 @@
                 refName = loc_match.group(1)
                 drdict["refName"] = refName
                 if loc_match.group(2) > "":
-                    drdict["start"] = int(loc_match.group(2))
+                    drdict["start"] = int(loc_match.group(2).replace(',',''))
                 if loc_match.group(3) > "":
-                    drdict["end"] = int(loc_match.group(3))
+                    drdict["end"] = int(loc_match.group(3).replace(',',''))
             else:
                 logging.info(
                     "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
diff -r 39b717d934a8 -r fb6cc7bc24df readme.rst
--- a/readme.rst	Sat Feb 03 10:17:27 2024 +0000
+++ b/readme.rst	Sat Feb 03 11:49:56 2024 +0000
@@ -1,6 +1,12 @@
 JBrowse2 in Galaxy
 ==================
 
+Added Feb 3: cool/mcool -> hic 
+
+.. image:: dm4_in_jb2.png
+
+Other tracks
+
 .. image:: jbrowse8.png
 
 JBrowse2 is a fast, embeddable genome browser built completely with