comparison autogenJB2.py @ 97:74074746ccd8 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99

96:5ef1ba2031f2

                        },
                    }
                    for i, x in enumerate(genome_paths)
                ],
            )
            logging.debug("@@@ paths=%s, genomes=%s" % (genome_paths, genomes))
            assref_name = jc.process_genomes(genomes[0])
            if not default_session_data.get(assref_name, None):
                default_session_data[assref_name] = {
                    "tracks": [],
                    "style": {},

                        "default_on": [],
                        "default_off": [],
                    },
                }
            listtracks = trackList
            # foo.paf must have a foo_paf.fasta or fasta.gz to match
            tnames = [x[2] for x in listtracks]
            texts = [x[1] for x in listtracks]
            for i, track in enumerate(listtracks):
                track_conf = {
                    "trackfiles": [],

                track_conf["dataset_id"] = trackname
                useuri = "no"
                if tpath.startswith("http://") or tpath.startswith("https://"):
                    useuri = "yes"
                if trext == "paf":
                    refname = trackname + "_paf.fasta"
                    refdat = [x[2] for x in listtracks if x[2] == refname]
                    if not refdat:
                        jc.logging.warn(
                            "!! No reference file %s corresponding to paf file %s found. Not building - there must be a corresponding fasta for each paf"
                            % (refname, trackname)
                        )
                        sys.exit(3)
                    else:
                        track_conf.update(
                            {
                                "conf": {
                                    "options": {
                                        "paf": {
                                            "genome": refdat,
                                            "genome_label": trackname,
                                        }
                                    }
                                }
                            }
                        )

97:74074746ccd8

                        },
                    }
                    for i, x in enumerate(genome_paths)
                ],
            )
            logging.debug("@@@autogenJB2 paths=%s, genomes=%s" % (genome_paths, genomes))
            assref_name = jc.process_genomes(genomes[0])
            if not default_session_data.get(assref_name, None):
                default_session_data[assref_name] = {
                    "tracks": [],
                    "style": {},

                        "default_on": [],
                        "default_off": [],
                    },
                }
            listtracks = trackList
            tnames = [x[2] for x in listtracks]
            texts = [x[1] for x in listtracks]
            for i, track in enumerate(listtracks):
                track_conf = {
                    "trackfiles": [],

                track_conf["dataset_id"] = trackname
                useuri = "no"
                if tpath.startswith("http://") or tpath.startswith("https://"):
                    useuri = "yes"
                if trext == "paf":
                    refdat = ["%s ~ %s" % (x[0],x[2]) for x in listtracks if x[1] in ["fasta", "fasta.gz"]]
                    if len(refdat) == 0:
                        jc.logging.warn(
                            "!! No reference file for %s found. Using main reference"
                            % (refname)
                        )
                        refdat = ["%s ~ %s" % (genomes[0].path, assref_name),]
                    else:
                        track_conf.update(
                            {
                                "conf": {
                                    "options": {
                                        "paf": {
                                            "genome": ",".join(refdat)
                                        }
                                    }
                                }
                            }
                        )