Mercurial > repos > fubar > jbrowse2
changeset 5:efc64d8f4b72 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
| author | fubar |
|---|---|
| date | Tue, 09 Jan 2024 05:24:48 +0000 |
| parents | 54396f0323f4 |
| children | 79f7265f90bd |
| files | jbrowse2.py jbrowse2.xml macros.xml plants.sh tstar.sh |
| diffstat | 5 files changed, 49 insertions(+), 52 deletions(-) [+] |
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--- a/jbrowse2.py Tue Jan 09 02:37:42 2024 +0000 +++ b/jbrowse2.py Tue Jan 09 05:24:48 2024 +0000 @@ -19,7 +19,7 @@ log = logging.getLogger("jbrowse") TODAY = datetime.datetime.now().strftime("%Y-%m-%d") GALAXY_INFRASTRUCTURE_URL = None -JB2REL="v2.10.0" +JB2REL = "v2.10.0" # version pinned for cloning mapped_chars = { @@ -435,16 +435,18 @@ "displayId": "%s-LinearBasicDisplay" % trackDict["trackId"], } - if trackDict.get("displays", None): - style_data["type"] = trackDict["displays"]["type"] - style_data["displayId"] = trackDict["displays"]["displayId"] - return {"displays": [style_data]} + if trackDict.get("displays", None): # use first if multiple like bed + style_data["type"] = trackDict["displays"][0]["type"] + style_data["displayId"] = trackDict["displays"][0]["displayId"] + return { + "displays": [ + style_data, + ] + } def process_genomes(self): assemblies = [] for i, genome_node in enumerate(self.genome_paths): - if self.debug: - log.info("genome_node=%s" % str(genome_node)) genome_name = genome_node["meta"]["dataset_dname"].strip() if len(genome_name.split()) > 1: genome_name = genome_name.split()[0] @@ -550,7 +552,6 @@ uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.gzi', Cool will not be likely to be a good fit - see discussion at https://github.com/GMOD/jbrowse-components/issues/2438 """ - log.info("#### trackData=%s" % trackData) tId = trackData["label"] # can be served - if public. # dsId = trackData["metadata"]["dataset_id"] @@ -579,8 +580,8 @@ }, ], } - # style_json = self._prepare_track_style(trackDict) - # trackDict["style"] = style_json + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) @@ -614,8 +615,6 @@ dest, ] self.subprocess_check_call(cmd) - if True or self.debug: - log.info("### convertMAF.sh called as %s" % " ".join(cmd)) # Construct samples list # We could get this from galaxy metadata, not sure how easily. ps = subprocess.Popen(["grep", "^s [^ ]*", "-o", data], stdout=subprocess.PIPE) @@ -625,8 +624,6 @@ soutp = outp.split("\n") samp = [x.split("s ")[1] for x in soutp if x.startswith("s ")] samples = [x.split(".")[0] for x in samp] - if self.debug: - log.info("### got samples = %s " % (samples)) trackDict = { "type": "MafTrack", "trackId": tId, @@ -644,9 +641,16 @@ }, }, "assemblyNames": [self.genome_name], + "displays": [ + { + "type": "LinearBasicDisplay", + "displayId": "%s-LinearBasicDisplay" % tId, + }, + {"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId}, + ], } - # style_json = self._prepare_track_style(trackDict) - # trackDict["style"] = style_json + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) if self.config_json.get("plugins", None): @@ -714,6 +718,8 @@ {"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId}, ], } + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) @@ -744,8 +750,8 @@ } ], } - # style_json = self._prepare_track_style(trackDict) - # trackDict["style"] = style_json + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) @@ -755,7 +761,6 @@ dest = "%s/%s" % (self.outdir, fname) url = fname self.subprocess_check_call(["cp", data, dest]) - log.info("### copied %s to %s" % (data, dest)) bloc = {"uri": url} if bam_index is not None and os.path.exists(os.path.realpath(bam_index)): # bai most probably made by galaxy and stored in galaxy dirs, need to copy it to dest @@ -792,8 +797,8 @@ }, ], } - # style_json = self._prepare_track_style(trackDict) - # trackDict["style"] = style_json + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) @@ -840,8 +845,8 @@ }, ], } - # style_json = self._prepare_track_style(trackDict) - # trackDict["style"] = style_json + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) @@ -893,8 +898,8 @@ {"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId}, ], } - # style_json = self._prepare_track_style(trackDict) - # trackDict["style"] = style_json + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) @@ -922,14 +927,18 @@ }, "displays": [ { + "type": "LinearPileupDisplay", + "displayId": "%s-LinearPileupDisplay" % tId, + }, + { "type": "LinearBasicDisplay", "displayId": "%s-LinearBasicDisplay" % tId, }, {"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId}, ], } - # style_json = self._prepare_track_style(trackDict) - # trackDict["style"] = style_json + style_json = self._prepare_track_style(trackDict) + trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) @@ -1151,17 +1160,11 @@ # We need to know the track type from the config.json generated just before track_types = {} - logging.info("### add default session has data = %s\n" % str(data)) with open(self.config_json_file, "r") as config_file: config_json = json.load(config_file) - logging.info("### config.json read \n%s\n" % (config_json)) for track_conf in self.tracksToAdd: # config_json["tracks"]: track_types[track_conf["trackId"]] = track_conf["type"] - logging.info( - "### self.tracksToAdd = %s; track_types = %s" - % (str(self.tracksToAdd), str(track_types)) - ) for on_track in data["visibility"]["default_on"]: style_data = {"type": "LinearBasicDisplay", "height": 100} @@ -1263,7 +1266,7 @@ def clone_jbrowse(self): """Clone a JBrowse directory into a destination directory.""" dest = self.outdir - cmd = ["jbrowse", "create", "-t",JB2REL, "-f", dest] + cmd = ["jbrowse", "create", "-t", JB2REL, "-f", dest] self.subprocess_check_call(cmd) for fn in [ "asset-manifest.json", @@ -1437,12 +1440,7 @@ pass track_conf["conf"] = etree_to_dict(track.find("options")) jc.add_general_configuration(general_data) - print("## processed", str(track_conf), "trackIdlist", jc.trackIdlist) x = open(args.xml, "r").read() - log.info( - "###done processing xml=%s; trackIdlist=%s, config=%s" - % (x, jc.trackIdlist, str(jc.config_json)) - ) jc.config_json["tracks"] = jc.tracksToAdd if jc.usejson: jc.write_config()
--- a/jbrowse2.xml Tue Jan 09 02:37:42 2024 +0000 +++ b/jbrowse2.xml Tue Jan 09 05:24:48 2024 +0000 @@ -997,8 +997,6 @@ can be used to let your users understand relationships between large groups of tracks. -.. image:: sections.png - Annotation Tracks ----------------- @@ -1011,6 +1009,11 @@ These are standard feature tracks. They usually highlight genes, mRNAs and other features of interest along a genomic region. +When these contain tens of millions of features, such as repeat regions from a VGP assembly, displaying one at a time leads +to extremely slow loading times when a large region is in view, unless the "LinearPileupDisplay" display option is +selected for that track in the styling options section. The default is LinearBasicDisplay, which shows all details and works +well for relatively sparse bed files. + BAM Pileups ~~~~~~~~~~~ @@ -1021,8 +1024,6 @@ BlastXML ~~~~~~~~ -.. image:: blast.png - JiG now supports both blastn and blastp datasets. JiG internally uses a blastXML to gapped GFF3 tool to convert your blastxml datasets into a format amenable to visualization in JBrowse. This tool is also @@ -1044,12 +1045,6 @@ **Protein blast search** option merely informs underlying tools that they should adjust feature locations by 3x. -Bigwig XY -~~~~~~~~~ - -.. image:: bigwig.png - - VCFs/SNPs ~~~~~~~~~
--- a/macros.xml Tue Jan 09 02:37:42 2024 +0000 +++ b/macros.xml Tue Jan 09 05:24:48 2024 +0000 @@ -280,8 +280,8 @@ </xml> <xml name="track_styling_linear"> - <param label="Show labels" name="show_labels" type="boolean" checked="true" truevalue="true" falsevalue="false" /> - <param label="Show descriptions" name="show_descriptions" type="boolean" checked="true" truevalue="true" falsevalue="false" /> + <param label="Show labels" name="show_labels" type="boolean" checked="false" truevalue="true" falsevalue="false" /> + <param label="Show descriptions" name="show_descriptions" type="boolean" checked="false" truevalue="true" falsevalue="false" /> <param name="display_mode" type="select" label="Display mode"> <option value="normal" selected="true">normal</option> <option value="compact">compact</option> @@ -296,8 +296,12 @@ <conditional name="track_style"> <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> <option value="LinearBasicDisplay" selected="true">LinearBasicDisplay</option> + <option value="LinearPileupDisplay">LinearPileupDisplay - good for dense tracks at scale</option> <option value="LinearArcDisplay">LinearArcDisplay</option> </param> + <when value="LinearPileupDisplay"> + <expand macro="track_styling_linear"/> + </when> <when value="LinearBasicDisplay"> <expand macro="track_styling_linear"/>