| Previous changeset 54:d6b0feb22584 (2024-03-14) Next changeset 56:c0097a584a8a (2024-03-19) |
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Commit message:
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 0553bb75a96ae401623face516c1cf6e1cfe743f |
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modified:
jbrowse2.py |
| b |
| 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", } |