Mercurial > repos > fubar > jbrowse2
diff jbrowse2.py @ 98:b1260bca5fdc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
| author | bgruening |
|---|---|
| date | Wed, 05 Jun 2024 10:00:07 +0000 |
| parents | 74074746ccd8 |
| children | 990291e918c7 |
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--- a/jbrowse2.py Sat Jun 01 05:37:13 2024 +0000 +++ b/jbrowse2.py Wed Jun 05 10:00:07 2024 +0000 @@ -3,6 +3,7 @@ import argparse import binascii import datetime +# import hashlib import json import logging import os @@ -20,9 +21,9 @@ log = logging.getLogger("jbrowse") JB2VER = "v2.11.0" -# version pinned if cloning - but not cloning now +# version pinned if cloning - but not used until now logCommands = True -# useful for seeing what's being written but NOT for production setups +# useful for seeing what's being written but not for production setups TODAY = datetime.datetime.now().strftime("%Y-%m-%d") SELF_LOCATION = os.path.dirname(os.path.realpath(__file__)) GALAXY_INFRASTRUCTURE_URL = None @@ -41,6 +42,32 @@ } +INDEX_TEMPLATE = """<!doctype html> +<html lang="en" style="height:100%"> +<head> +<meta charset="utf-8"/> +<link rel="shortcut icon" href="./favicon.ico"/> +<meta name="viewport" content="width=device-width,initial-scale=1"/> +<meta name="theme-color" content="#000000"/> +<meta name="description" content="A fast and flexible genome browser"/> +<link rel="manifest" href="./manifest.json"/> +<title>JBrowse</title> +</script> +</head> +<body style="overscroll-behavior:none; height:100%; margin: 0;"> +<iframe + id="jbframe" + title="JBrowse2" + frameborder="0" + width="100%" + height="100%" + src='index_noview.html?config=config.json__SESSION_SPEC__'> +</iframe> +</body> +</html> +""" + + class ColorScaling(object): COLOR_FUNCTION_TEMPLATE = """ @@ -398,7 +425,6 @@ return self.outdir else: return subprocess.check_output(["pwd"]).decode("utf-8").strip() - # return None def subprocess_check_call(self, command, output=None, cwd=True): if output: @@ -429,7 +455,7 @@ log.error(command) log.error(output) log.error(err) - raise RuntimeError("Command failed with exit code %s" % (retcode)) + raise RuntimeError(f"Command ( {command} ) failed with exit code {retcode}") def subprocess_check_output(self, command): if logCommands: @@ -473,7 +499,7 @@ nrow = len(fl) except Exception: nrow = 0 - logging.debug("### getNrow %s returning %d" % (url, nrow)) + logging.debug("getNrow %s returning %d" % (url, nrow)) return nrow def process_genomes(self, genomes): @@ -514,9 +540,6 @@ return primaryGenome def make_assembly(self, fapath, gname, useuri): - """added code to grab the first contig name and length for broken default session from Anthony and Helena's code - that poor Bjoern is trying to figure out. - """ if useuri: faname = fapath scontext = ssl.SSLContext(ssl.PROTOCOL_TLS_CLIENT) @@ -675,8 +698,8 @@ ] } categ = trackData["category"] - fname = tId - dest = "%s/%s" % (self.outdir, fname) + fname = f"{tId}" + dest = os.path.join(self.outdir, fname) gname = trackData["assemblyNames"] cmd = [ @@ -931,10 +954,6 @@ def add_vcf(self, data, trackData): tId = trackData["label"] - # url = "%s/api/datasets/%s/display" % ( - # self.giURL, - # trackData["metadata"]["dataset_id"], - # ) categ = trackData["category"] useuri = trackData["useuri"].lower() == "yes" if useuri: @@ -1195,14 +1214,29 @@ "category": category, "style": {}, } + + # hashData = [ + # str(dataset_path), + # track_human_label, + # track["category"], + # ] + # hashData = "|".join(hashData).encode("utf-8") + # hash_string = hashlib.md5(hashData).hexdigest() + outputTrackConfig["assemblyNames"] = track["assemblyNames"] outputTrackConfig["key"] = track_human_label outputTrackConfig["useuri"] = useuri outputTrackConfig["path"] = dataset_path outputTrackConfig["ext"] = dataset_ext - outputTrackConfig["trackset"] = track.get("trackset", {}) outputTrackConfig["label"] = track["label"] + # outputTrackConfig["label"] = "%s_%i_%s_%s" % ( + # dataset_ext, + # trackIndex, + # track_human_label, + # hash_string, + # ) + outputTrackConfig["metadata"] = extra_metadata outputTrackConfig["name"] = track_human_label if track["label"] in self.trackIdlist: @@ -1237,10 +1271,6 @@ hic_path, ] ) - logging.debug( - "### ext=cool: wasCool=%s, hic_path=%s" - % (outputTrackConfig["wasCool"], hic_path) - ) self.add_hic( hic_path, outputTrackConfig, @@ -1263,7 +1293,6 @@ ) elif dataset_ext == "bam": real_indexes = track["conf"]["options"]["bam"]["bam_index"] - logging.debug("**** add bam got %s for indexes" % real_indexes) self.add_bam( dataset_path, outputTrackConfig, @@ -1271,7 +1300,6 @@ ) elif dataset_ext == "cram": real_indexes = track["conf"]["options"]["cram"]["cram_index"] - logging.debug("**** add cram got %s for indexes" % real_indexes) self.add_cram( dataset_path, outputTrackConfig, @@ -1292,7 +1320,7 @@ track["conf"]["options"]["paf"], ) else: - logging.warn("Do not know how to handle %s", dataset_ext) + logging.warning("Do not know how to handle %s", dataset_ext) # Return non-human label for use in other fields yield outputTrackConfig["label"] @@ -1303,7 +1331,6 @@ https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py """ # TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708 - bpPerPx = 50 # this is tricky since browser window width is unknown - this seems a compromise that sort of works.... track_types = {} with open(self.config_json_file, "r") as config_file: config_json = json.load(config_file) @@ -1342,17 +1369,24 @@ "displays": [style_data], } ) + view_json = { + "type": "LinearGenomeView", + "offsetPx": 0, + "minimized": False, + "tracks": tracks_data, + } first = [x for x in self.ass_first_contigs if x[0] == gnome] - drdict = { + if len(first) > 0: + [gnome, refName, end] = first[0] + start = 0 + end = int(end) + drdict = { + "refName": refName, + "start": start, + "end": end, "reversed": False, "assemblyName": gnome, } - if len(first) > 0: - [gnome, refName, end] = first[0] - drdict["refName"] = refName - drdict["start"] = 0 - end = int(end) - drdict["end"] = end else: ddl = default_data.get("defaultLocation", None) if ddl: @@ -1370,13 +1404,6 @@ "@@@ regexp could not match contig:start..end in the supplied location %s - please fix" % ddl ) - view_json = { - "type": "LinearGenomeView", - "offsetPx": 0, - "bpPerPx" : bpPerPx, - "minimized": False, - "tracks": tracks_data - } if drdict.get("refName", None): # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome view_json["displayedRegions"] = [ @@ -1392,10 +1419,12 @@ for key, value in mapped_chars.items(): session_name = session_name.replace(value, key) session_json["name"] = session_name + if "views" not in session_json: session_json["views"] = session_views else: session_json["views"] += session_views + pp = json.dumps(session_views, indent=2) config_json["defaultSession"] = session_json self.config_json.update(config_json) @@ -1430,33 +1459,6 @@ https://github.com/GMOD/jbrowse-components/discussions/3568 https://github.com/GMOD/jbrowse-components/pull/4148 """ - - - INDEX_TEMPLATE = """<!doctype html> - <html lang="en" style="height:100%"> - <head> - <meta charset="utf-8"/> - <link rel="shortcut icon" href="./favicon.ico"/> - <meta name="viewport" content="width=device-width,initial-scale=1"/> - <meta name="theme-color" content="#000000"/> - <meta name="description" content="A fast and flexible genome browser"/> - <link rel="manifest" href="./manifest.json"/> - <title>JBrowse</title> - </script> - </head> - <body style="overscroll-behavior:none; height:100%; margin: 0;"> - <iframe - id="jbframe" - title="JBrowse2" - frameborder="0" - width="100%" - height="100%" - src='index_noview.html?config=config.json__SESSION_SPEC__'> - </iframe> - </body> - </html> - """ - new_index = "Nothing written" session_spec = {"views": []} logging.debug("def ass_first=%s\ndata=%s" % (self.ass_first_contigs, data)) @@ -1522,8 +1524,13 @@ json.dump(self.config_json, config_file, indent=2) def clone_jbrowse(self, realclone=False): - """Clone a JBrowse directory into a destination directory. This also works in Biocontainer testing now - Leave as True between version updates on temporary tools - requires manual conda trigger :( + """ + Clone a JBrowse directory into a destination directory. + + `realclone=true` will use the `jbrowse create` command. + To allow running on internet-less compute and for reproducibility + use frozen code with `realclone=false + """ dest = self.outdir if realclone: