comparison jbrowse2.py @ 3:2de9f585505b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b30d2e277cc360437a02fa812c577c0c8d997cff-dirty

2:37b2c26c7b9b

logging.basicConfig(level=logging.INFO)
log = logging.getLogger("jbrowse")
TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
GALAXY_INFRASTRUCTURE_URL = None
mapped_chars = {
    ">": "__gt__",
    "<": "__lt__",
    "'": "__sq__",
    '"': "__dq__",

            fapath = genome_node["path"]
            assem = self.make_assembly(fapath, genome_name)
            assemblies.append(assem)
            self.genome_names.append(genome_name)
            if self.genome_name is None:
                self.genome_name = genome_name  # first one for all tracks - other than paf
            if self.config_json.get("assemblies", None):
                self.config_json["assemblies"] += assemblies
            else:
                self.config_json["assemblies"] = assemblies

            "--target",
            self.config_json_file,
            "-v",
            " LinearGenomeView",
        ]
        if self.debug:
            log.info("### calling set-default-session with cmd=%s" % "  ".join(cmd))
        self.subprocess_check_call(cmd)

    def write_config(self):
        with open(self.config_json_file, "w") as fp:
            json.dump(self.config_json, fp)

        """
        mafPlugin = {
            "plugins": [
                {
                    "name": "MafViewer",
                    "url": "https://unpkg.com/jbrowse-plugin-mafviewer/dist/jbrowse-plugin-mafviewer.umd.production.min.js",
                }
            ]
        }
        tId = trackData["label"]
        fname = "%s.bed" % tId

    def add_paf(self, data, trackData, pafOpts, **kwargs):
        tname = trackData["name"]
        tId = trackData["label"]
        pgname = pafOpts["genome_label"]
        if len(pgname.split() > 1):
            pgname = pgname.split()[0]  # trouble from spacey names in command lines avoidance
        asstrack, gname = self.make_assembly(pafOpts["genome"], pgname)
        self.genome_names.append(pgname)
        if self.config_json.get("assemblies", None):
            self.config_json["assemblies"].append(asstrack)
        else:
            self.config_json["assemblies"] = [asstrack,]

        style_json = self._prepare_track_style(trackData)
        url = "%s.paf" % (trackData["label"])
        dest = "%s/%s" % (self.outdir, url)
        self.symlink_or_copy(os.path.realpath(data), dest)

            json.dump(config_json, config_file, indent=2)

    def clone_jbrowse(self):
        """Clone a JBrowse directory into a destination directory."""
        dest = self.outdir
        cmd = ["jbrowse", "create", "-f", dest]
        self.subprocess_check_call(cmd)
        for fn in [
            "asset-manifest.json",
            "favicon.ico",
            "robots.txt",

            "version.txt",
            "test_data",
        ]:
            cmd = ["rm", "-rf", os.path.join(self.outdir, fn)]
            self.subprocess_check_call(cmd)
        cmd = ["cp", os.path.join(INSTALLED_TO, "servejb2.py"), self.outdir]
        self.subprocess_check_call(cmd)


def parse_style_conf(item):
    if "type" in item.attrib and item.attrib["type"] in ["boolean", "integer"]:

3:2de9f585505b

logging.basicConfig(level=logging.INFO)
log = logging.getLogger("jbrowse")
TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
GALAXY_INFRASTRUCTURE_URL = None
JB2REL="v2.10.0"
# version pinned for cloning

mapped_chars = {
    ">": "__gt__",
    "<": "__lt__",
    "'": "__sq__",
    '"': "__dq__",

            fapath = genome_node["path"]
            assem = self.make_assembly(fapath, genome_name)
            assemblies.append(assem)
            self.genome_names.append(genome_name)
            if self.genome_name is None:
                self.genome_name = (
                    genome_name  # first one for all tracks - other than paf
                )
            if self.config_json.get("assemblies", None):
                self.config_json["assemblies"] += assemblies
            else:
                self.config_json["assemblies"] = assemblies

            "--target",
            self.config_json_file,
            "-v",
            " LinearGenomeView",
        ]
        self.subprocess_check_call(cmd)

    def write_config(self):
        with open(self.config_json_file, "w") as fp:
            json.dump(self.config_json, fp)

        """
        mafPlugin = {
            "plugins": [
                {
                    "name": "MafViewer",
                    "url": "https://unpkg.com/browse/jbrowse-plugin-mafviewer@1.0.6/dist/jbrowse-plugin-mafviewer.umd.production.min.js",
                }
            ]
        }
        tId = trackData["label"]
        fname = "%s.bed" % tId

    def add_paf(self, data, trackData, pafOpts, **kwargs):
        tname = trackData["name"]
        tId = trackData["label"]
        pgname = pafOpts["genome_label"]
        if len(pgname.split() > 1):
            pgname = pgname.split()[
                0
            ]  # trouble from spacey names in command lines avoidance
        asstrack, gname = self.make_assembly(pafOpts["genome"], pgname)
        self.genome_names.append(pgname)
        if self.config_json.get("assemblies", None):
            self.config_json["assemblies"].append(asstrack)
        else:
            self.config_json["assemblies"] = [
                asstrack,
            ]

        style_json = self._prepare_track_style(trackData)
        url = "%s.paf" % (trackData["label"])
        dest = "%s/%s" % (self.outdir, url)
        self.symlink_or_copy(os.path.realpath(data), dest)

            json.dump(config_json, config_file, indent=2)

    def clone_jbrowse(self):
        """Clone a JBrowse directory into a destination directory."""
        dest = self.outdir
        cmd = ["jbrowse", "create", "-t",JB2REL, "-f", dest]
        self.subprocess_check_call(cmd)
        for fn in [
            "asset-manifest.json",
            "favicon.ico",
            "robots.txt",

            "version.txt",
            "test_data",
        ]:
            cmd = ["rm", "-rf", os.path.join(self.outdir, fn)]
            self.subprocess_check_call(cmd)
        cmd = ["cp", os.path.join(INSTALLED_TO, "webserver.py"), self.outdir]
        self.subprocess_check_call(cmd)


def parse_style_conf(item):
    if "type" in item.attrib and item.attrib["type"] in ["boolean", "integer"]: