| Previous changeset 23:39b717d934a8 (2024-02-03) Next changeset 25:172acf9c7a53 (2024-02-03) |
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Commit message:
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit cde4b8a574ded34a0ff8df3ecafc1a057787dcfb-dirty |
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modified:
jbrowse2.py readme.rst |
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added:
cool_in_jb2.jpg dm4_in_jb2.png |
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| diff -r 39b717d934a8 -r fb6cc7bc24df cool_in_jb2.jpg |
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| Binary file cool_in_jb2.jpg has changed |
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| diff -r 39b717d934a8 -r fb6cc7bc24df dm4_in_jb2.png |
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| Binary file dm4_in_jb2.png has changed |
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| 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 |
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| @@ -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" |
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| 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 |
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| @@ -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 |
