def cli(ctx, path, template=None, **kwds):
    """(Experimental) Initialize a new tool project.

    This is only a proof-of-concept demo right now.
    """
    if template is None:
        warn("Creating empty project, this function doesn't do much yet.")
    if not os.path.exists(path):
        os.makedirs(path)
    if template is None:
        return

    tempdir = tempfile.mkdtemp()
    try:
        untar_args = UNTAR_ARGS % (tempdir)
        untar_to(DOWNLOAD_URL, tempdir, untar_args)
        template_dir = os.path.join(tempdir, template)
        shell("ls '%s'" % (template_dir))
        shell("mv '%s'/* '%s'" % (template_dir, path))
        dot_files = [os.path.join(template_dir, f) for f in os.listdir(template_dir) if f.startswith(".")]
        if len(dot_files) > 0:
            dot_files_quoted = "'" + "' '".join(dot_files) + "'"
            shell("mv %s '%s'" % (dot_files_quoted, path))
    finally:
        shutil.rmtree(tempdir)
Beispiel #2
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def _install_galaxy_via_download(ctx, galaxy_root, env, kwds):
    branch = _galaxy_branch(kwds)
    untar_to("https://codeload.github.com/galaxyproject/galaxy/tar.gz/" +
             branch,
             tar_args=['-xvzf', '-', 'galaxy-' + branch],
             dest_dir=galaxy_root)
    _install_with_command(ctx, galaxy_root, env, kwds)
Beispiel #3
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def cli(ctx, path, template=None, **kwds):
    """(Experimental) Initialize a new tool project.

    This is only a proof-of-concept demo right now.
    """
    if template is None:
        warn("Creating empty project, this function doesn't do much yet.")
    if not os.path.exists(path):
        os.makedirs(path)
    if template is None:
        return

    tempdir = tempfile.mkdtemp()
    try:
        untar_args = UNTAR_ARGS % (tempdir)
        untar_to(DOWNLOAD_URL, tempdir, untar_args)
        template_dir = os.path.join(tempdir, template)
        shell("ls '%s'" % (template_dir))
        shell("mv '%s'/* '%s'" % (template_dir, path))
        dot_files = [
            os.path.join(template_dir, f) for f in os.listdir(template_dir)
            if f.startswith(".")
        ]
        if len(dot_files) > 0:
            dot_files_quoted = "'" + "' '".join(dot_files) + "'"
            shell("mv %s '%s'" % (dot_files_quoted, path))
    finally:
        shutil.rmtree(tempdir)
Beispiel #4
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def _try_download_hub(planemo_hub_path):
    link = _hub_link()
    # Strip URL base and .tgz at the end.
    basename = link.split("/")[-1].rsplit(".", 1)[0]
    untar_to(link,
             tar_args="-zxvf - %s/bin/hub -O > '%s'" %
             (basename, planemo_hub_path))
    communicate(["chmod", "+x", planemo_hub_path])
Beispiel #5
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def download_tar(tsi, repo_id, destination, to_directory):
    base_url = tsi.base_url
    if not base_url.endswith("/"):
        base_url += "/"
    download_url = REPOSITORY_DOWNLOAD_TEMPLATE % (base_url, repo_id)
    if to_directory:
        untar_args = "-xzf - -C %s --strip-components 1" % destination
    else:
        untar_args = None
    untar_to(download_url, destination, untar_args)
Beispiel #6
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def download_tar(tsi, repo_id, destination, to_directory):
    base_url = tsi.base_url
    if not base_url.endswith("/"):
        base_url += "/"
    download_url = REPOSITORY_DOWNLOAD_TEMPLATE % (base_url, repo_id)
    if to_directory:
        untar_args = "-xzf - -C %s --strip-components 1" % destination
    else:
        untar_args = None
    untar_to(download_url, destination, untar_args)
def download_tar(tsi, repo_id, destination, to_directory):
    base_url = tsi.base_url
    if not base_url.endswith("/"):
        base_url += "/"
    download_url = REPOSITORY_DOWNLOAD_TEMPLATE % (base_url, repo_id)
    if to_directory:
        tar_args = ['-xzf', '-', '--strip-components=1']
        untar_to(download_url, tar_args=tar_args, dest_dir=destination)
    else:
        untar_to(download_url, path=destination)
def cli(ctx, path, template=None, **kwds):
    """Initialize a new tool project (demo only right now).
    """
    if template is None:
        warn("Creating empty project, this function doesn't do much yet.")
    if not os.path.exists(path):
        os.makedirs(path)
    if template is None:
        return

    tempdir = tempfile.mkdtemp()
    try:
        untar_args = UNTAR_ARGS % (tempdir)
        untar_to(DOWNLOAD_URL, tempdir, untar_args)
        shell("ls '%s'" % (tempdir))
        shell("mv '%s/%s'/* '%s'" % (tempdir, template, path))
    finally:
        shutil.rmtree(tempdir)
def cli(ctx, path, template=None, **kwds):
    """Initialize a new tool project (demo only right now).
    """
    if template is None:
        warn("Creating empty project, this function doesn't do much yet.")
    if not os.path.exists(path):
        os.makedirs(path)
    if template is None:
        return

    tempdir = tempfile.mkdtemp()
    try:
        untar_args = UNTAR_ARGS % (tempdir)
        untar_to(DOWNLOAD_URL, tempdir, untar_args)
        shell("ls '%s'" % (tempdir))
        shell("mv '%s/%s'/* '%s'" % (tempdir, template, path))
    finally:
        shutil.rmtree(tempdir)
Beispiel #10
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def download_tarball(ctx, tsi, path, **kwds):
    destination = kwds.get('destination', 'shed_download.tar.gz')
    repo_id = find_repository_id(ctx, tsi, path, **kwds)
    base_url = tsi.base_url
    if not base_url.endswith("/"):
        base_url += "/"
    download_url = REPOSITORY_DOWNLOAD_TEMPLATE % (base_url, repo_id)
    to_directory = not destination.endswith("gz")
    if to_directory:
        untar_args = "-xzf - -C %s --strip-components 1" % destination
    else:
        untar_args = None
    untar_to(download_url, destination, untar_args)
    if to_directory:
        clean = kwds.get("clean", False)
        if clean:
            archival_file = os.path.join(destination, ".hg_archival.txt")
            if os.path.exists(archival_file):
                os.remove(archival_file)
Beispiel #11
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def download_tarball(ctx, tsi, path, **kwds):
    destination = kwds.get('destination', 'shed_download.tar.gz')
    repo_id = find_repository_id(ctx, tsi, path, **kwds)
    base_url = tsi.base_url
    if not base_url.endswith("/"):
        base_url += "/"
    download_url = REPOSITORY_DOWNLOAD_TEMPLATE % (base_url, repo_id)
    to_directory = not destination.endswith("gz")
    if to_directory:
        untar_args = "-xzf - -C %s --strip-components 1" % destination
    else:
        untar_args = None
    untar_to(download_url, destination, untar_args)
    if to_directory:
        clean = kwds.get("clean", False)
        if clean:
            archival_file = os.path.join(destination, ".hg_archival.txt")
            if os.path.exists(archival_file):
                os.remove(archival_file)
def cli(ctx, path, template=None, **kwds):
    """(Experimental) Initialize a new tool project.

    This is only a proof-of-concept demo right now.
    """
    if template is None:
        warn("Creating empty project, this function doesn't do much yet.")
    if not os.path.exists(path):
        os.makedirs(path)
    if template is None:
        return

    tempdir = tempfile.mkdtemp()
    try:
        untar_args = UNTAR_ARGS % (tempdir)
        untar_to(DOWNLOAD_URL, tempdir, untar_args)
        template_dir = os.path.join(tempdir, template)
        for entry in os.listdir(template_dir):
            shutil.move(os.path.join(template_dir, entry), path)
    finally:
        shutil.rmtree(tempdir)
def cli(ctx, path, template=None, **kwds):
    """(Experimental) Initialize a new tool project.

    This is only a proof-of-concept demo right now.
    """
    if template is None:
        warn("Creating empty project, this function doesn't do much yet.")
    if not os.path.exists(path):
        os.makedirs(path)
    if template is None:
        return

    tempdir = tempfile.mkdtemp()
    try:
        untar_args = UNTAR_ARGS % (tempdir)
        untar_to(DOWNLOAD_URL, tempdir, untar_args)
        template_dir = os.path.join(tempdir, template)
        for entry in os.listdir(template_dir):
            shutil.move(os.path.join(template_dir, entry), path)
    finally:
        shutil.rmtree(tempdir)
Beispiel #14
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def _try_download_hub(planemo_hub_path):
    link = _hub_link()
    # Strip URL base and .tgz at the end.
    basename = link.split("/")[-1].rsplit(".", 1)[0]
    untar_to(link, tar_args="-Ozxvf - %s/bin/hub > '%s'" % (basename, planemo_hub_path))
    communicate(["chmod", "+x", planemo_hub_path])