Mercurial > repos > fubar > jbrowse2
diff jbrowse2.py @ 34:2893ef33fba9 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd
author | fubar |
---|---|
date | Sun, 25 Feb 2024 04:18:53 +0000 |
parents | fe48ed5810bd |
children | 15da358c3108 |
line wrap: on
line diff
--- a/jbrowse2.py Sat Feb 24 10:44:01 2024 +0000 +++ b/jbrowse2.py Sun Feb 25 04:18:53 2024 +0000 @@ -17,7 +17,7 @@ logging.basicConfig(level=logging.INFO) log = logging.getLogger("jbrowse") -JB2VER = "v2.10.1" +JB2VER = "v2.10.2" # version pinned for cloning TODAY = datetime.datetime.now().strftime("%Y-%m-%d") @@ -450,7 +450,7 @@ if len(genome_name.split()) > 1: genome_name = genome_name.split()[0] # spaces and cruft break scripts when substituted - if genome_name not in self.genome_names: + if genome_name not in self.genome_names: # ignore dupes - can have multiple pafs with same references? fapath = genome_node["path"] assem = self.make_assembly(fapath, genome_name) @@ -1015,16 +1015,16 @@ def add_paf(self, data, trackData, pafOpts, **kwargs): tname = trackData["name"] tId = trackData["label"] - pgnames = [x.strip() for x in pafOpts["genome_label"].split(',')] - pgpaths = [x.strip() for x in pafOpts["genome"].split(',')] - passnames = [self.genome_name] # always first + pgnames = [x.strip() for x in pafOpts["genome_label"].split(",")] + pgpaths = [x.strip() for x in pafOpts["genome"].split(",")] + passnames = [self.genome_name] # always first for i, gname in enumerate(pgnames): if len(gname.split()) > 1: gname = gname.split()[0] # 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. + # ignore if already there - eg for duplicates among pafs. asstrack = self.make_assembly(pgpaths[i], gname) self.genome_names.append(gname) if self.config_json.get("assemblies", None): @@ -1126,7 +1126,7 @@ # Unsanitize labels (element_identifiers are always sanitized by Galaxy) for key, value in mapped_chars.items(): track_human_label = track_human_label.replace(value, key) - track_human_label = track_human_label.replace(" ","_") + track_human_label = track_human_label.replace(" ", "_") outputTrackConfig = { "category": category, "style": {}, @@ -1149,7 +1149,7 @@ dataset_ext, outputTrackConfig, ) - elif dataset_ext in ("hic","juicebox_hic"): + elif dataset_ext in ("hic", "juicebox_hic"): self.add_hic( dataset_path, outputTrackConfig, @@ -1540,9 +1540,7 @@ default_session_data["session_name"] = root.find( "metadata/general/session_name" ).text - jc.zipOut = root.find( - "metadata/general/zipOut" - ).text == "true" + jc.zipOut = root.find("metadata/general/zipOut").text == "true" general_data = { "analytics": root.find("metadata/general/analytics").text, "primary_color": root.find("metadata/general/primary_color").text,