Mercurial > repos > fubar > jbrowse2
changeset 47:3e53204c2419 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty
| author | fubar |
|---|---|
| date | Wed, 06 Mar 2024 00:23:02 +0000 |
| parents | 4181e97c70a7 |
| children | 460d5b6c5d98 |
| files | __pycache__/jbrowse2.cpython-310.pyc jb2_urlconf.py jbrowse2.py |
| diffstat | 3 files changed, 17 insertions(+), 1 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jb2_urlconf.py Wed Mar 06 00:23:02 2024 +0000 @@ -0,0 +1,16 @@ +inconf = open('config.json', 'r').readlines() +with open('config.json.local', 'w') as bak: + bak.write('\n'.join(inconf)) +urlbase = "https://galaxy.genomicsvl-students.cloud.edu.au/jbrowse/hum/" +utag = '"uri":' +for i, row in enumerate(inconf): + ispath = False + if row.strip().startswith(utag): + ispath = True + parth = row.split(utag)[1].strip() + inconf[i] = '%s%s' % (urlbase, parth) +with open('config.json', 'w') as outconf: + outconf.write('\n'.join(inconf)) + + +
--- a/jbrowse2.py Mon Mar 04 09:47:19 2024 +0000 +++ b/jbrowse2.py Wed Mar 06 00:23:02 2024 +0000 @@ -1086,9 +1086,9 @@ for i, gname in enumerate(pgnames): if len(gname.split()) > 1: gname = gname.split()[0] + passnames.append(gname) # trouble from spacey names in command lines avoidance if gname not in self.genome_names: - passnames.append(gname) # ignore if already there - eg for duplicates among pafs. asstrack = self.make_assembly(pgpaths[i], gname) self.genome_names.append(gname)