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)
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)
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)
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])
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:
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)
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 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)
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])