comparison jbrowse2.py @ 34:2893ef33fba9 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd

33:9aedb7f1cc77

from collections import defaultdict

logging.basicConfig(level=logging.INFO)
log = logging.getLogger("jbrowse")

JB2VER = "v2.10.1"
# version pinned for cloning

TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
GALAXY_INFRASTRUCTURE_URL = None
JB2REL = "v2.10.1"

        for i, genome_node in enumerate(self.genome_paths):
            genome_name = genome_node["meta"]["dataset_dname"].strip()
            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:
                # ignore dupes - can have multiple pafs with same references?
                fapath = genome_node["path"]
                assem = self.make_assembly(fapath, genome_name)
                assemblies.append(assem)
                self.genome_names.append(genome_name)

        self.trackIdlist.append(tId)

    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
        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.
                    asstrack = self.make_assembly(pgpaths[i], gname)
                    self.genome_names.append(gname)
                    if self.config_json.get("assemblies", None):
                        self.config_json["assemblies"].append(asstrack)
                    else:

            extra_metadata,
        ) in enumerate(track["trackfiles"]):
            # 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(" ","_")
            outputTrackConfig = {
                "category": category,
                "style": {},
            }

                self.add_gff(
                    dataset_path,
                    dataset_ext,
                    outputTrackConfig,
                )
            elif dataset_ext in ("hic","juicebox_hic"):
                self.add_hic(
                    dataset_path,
                    outputTrackConfig,
                )
            elif dataset_ext in ("cool", "mcool", "scool"):

        "metadata/general/defaultLocation"
    ).text
    default_session_data["session_name"] = root.find(
        "metadata/general/session_name"
    ).text
    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,
        "secondary_color": root.find("metadata/general/secondary_color").text,
        "tertiary_color": root.find("metadata/general/tertiary_color").text,

34:2893ef33fba9

from collections import defaultdict

logging.basicConfig(level=logging.INFO)
log = logging.getLogger("jbrowse")

JB2VER = "v2.10.2"
# version pinned for cloning

TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
GALAXY_INFRASTRUCTURE_URL = None
JB2REL = "v2.10.1"

        for i, genome_node in enumerate(self.genome_paths):
            genome_name = genome_node["meta"]["dataset_dname"].strip()
            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:
                # ignore dupes - can have multiple pafs with same references?
                fapath = genome_node["path"]
                assem = self.make_assembly(fapath, genome_name)
                assemblies.append(assem)
                self.genome_names.append(genome_name)

        self.trackIdlist.append(tId)

    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
        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.
                    asstrack = self.make_assembly(pgpaths[i], gname)
                    self.genome_names.append(gname)
                    if self.config_json.get("assemblies", None):
                        self.config_json["assemblies"].append(asstrack)
                    else:

            extra_metadata,
        ) in enumerate(track["trackfiles"]):
            # 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(" ", "_")
            outputTrackConfig = {
                "category": category,
                "style": {},
            }

                self.add_gff(
                    dataset_path,
                    dataset_ext,
                    outputTrackConfig,
                )
            elif dataset_ext in ("hic", "juicebox_hic"):
                self.add_hic(
                    dataset_path,
                    outputTrackConfig,
                )
            elif dataset_ext in ("cool", "mcool", "scool"):

        "metadata/general/defaultLocation"
    ).text
    default_session_data["session_name"] = root.find(
        "metadata/general/session_name"
    ).text
    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,
        "secondary_color": root.find("metadata/general/secondary_color").text,
        "tertiary_color": root.find("metadata/general/tertiary_color").text,