comparison jbrowse2.py @ 38:07849bf248e3 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a74e469a81b38c7142f63de510ae31d3754d1767

37:7adde511daa1

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

TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
GALAXY_INFRASTRUCTURE_URL = None
JB2REL = "v2.10.1"
# version pinned for cloning

mapped_chars = {
    ">": "__gt__",
    "<": "__lt__",

        )
    return metadata


class JbrowseConnector(object):
    def __init__(self, outdir, genomes):
        self.giURL = GALAXY_INFRASTRUCTURE_URL
        self.outdir = outdir
        os.makedirs(self.outdir, exist_ok=True)
        self.genome_paths = genomes
        self.genome_name = None
        self.genome_names = []
        self.trackIdlist = []

        self.config_json.update(config_json)
        with open(config_path, "w") as config_file:
            json.dump(self.config_json, config_file, indent=2)

    def clone_jbrowse(self):
        """Clone a JBrowse directory into a destination directory."""
        # dest = os.path.realpath(self.outdir)
        dest = self.outdir
        cmd = ["rm", "-rf", dest + "/*"]
        self.subprocess_check_call(cmd)
        cmd = ["jbrowse", "create", dest, "-t", JB2VER, "-f"]
        self.subprocess_check_call(cmd)
        for fn in [
            "asset-manifest.json",
            "favicon.ico",
            "robots.txt",
            "umd_plugin.js",
            "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, "jb2_webserver.py"),
            self.outdir,
        ]
        self.subprocess_check_call(cmd)


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

if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="", epilog="")
    parser.add_argument("--xml", help="Track Configuration")
    parser.add_argument("--outdir", help="Output directory", default="out")
    parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.0.1")
    args = parser.parse_args()
    tree = ET.parse(args.xml)
    root = tree.getroot()

        # so we'll prepend `http://` and hope for the best. Requests *should*
        # be GET and not POST so it should redirect OK
        GALAXY_INFRASTRUCTURE_URL = "http://" + GALAXY_INFRASTRUCTURE_URL
    jc = JbrowseConnector(
        outdir=args.outdir,
        genomes=[
            {
                "path": os.path.realpath(x.attrib["path"]),
                "meta": metadata_from_node(x.find("metadata")),
            }

38:07849bf248e3

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

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

# version pinned for cloning

mapped_chars = {
    ">": "__gt__",
    "<": "__lt__",

        )
    return metadata


class JbrowseConnector(object):
    def __init__(self, outdir, jbrowse2path, genomes):
        self.giURL = GALAXY_INFRASTRUCTURE_URL
        self.outdir = outdir
        self.jbrowse2path = jbrowse2path
        os.makedirs(self.outdir, exist_ok=True)
        self.genome_paths = genomes
        self.genome_name = None
        self.genome_names = []
        self.trackIdlist = []

        self.config_json.update(config_json)
        with open(config_path, "w") as config_file:
            json.dump(self.config_json, config_file, indent=2)

    def clone_jbrowse(self):
        """Clone a JBrowse directory into a destination directory. This also works in Biocontainer testing now """
        dest = self.outdir
        #self.subprocess_check_call(['jbrowse', 'create', dest, '--tag', f"{JB_VER}"])
        shutil.copytree(self.jbrowse2path, dest, dirs_exist_ok=True)
        for fn in [
            "asset-manifest.json",
            "favicon.ico",
            "robots.txt",
            "umd_plugin.js",
            "version.txt",
            "test_data",
        ]:
            cmd = ["rm", "-rf", os.path.join(dest, fn)]
            self.subprocess_check_call(cmd)
        cmd = ["cp", os.path.join(INSTALLED_TO, "jb2_webserver.py"), dest]
        self.subprocess_check_call(cmd)


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

if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="", epilog="")
    parser.add_argument("--xml", help="Track Configuration")
    parser.add_argument("--jbrowse2path", help="Path to JBrowse2 directory in biocontainer or Conda")
    parser.add_argument("--outdir", help="Output directory", default="out")
    parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.0.1")
    args = parser.parse_args()
    tree = ET.parse(args.xml)
    root = tree.getroot()

        # so we'll prepend `http://` and hope for the best. Requests *should*
        # be GET and not POST so it should redirect OK
        GALAXY_INFRASTRUCTURE_URL = "http://" + GALAXY_INFRASTRUCTURE_URL
    jc = JbrowseConnector(
        outdir=args.outdir,
        jbrowse2path=args.jbrowse2path,
        genomes=[
            {
                "path": os.path.realpath(x.attrib["path"]),
                "meta": metadata_from_node(x.find("metadata")),
            }