def _ensure_galaxy_repository_available(ctx):
workspace = ctx.workspace
gx_repo = os.path.join(workspace, "gx_repo")
if os.path.exists(gx_repo):
# Attempt fetch - but don't fail if not interweb, etc...
shell("git --git-dir %s fetch >/dev/null 2>&1" % gx_repo)
else:
remote_repo = "https://github.com/galaxyproject/galaxy"
command = git.command_clone(ctx, remote_repo, gx_repo, bare=True)
shell(command)
def _ensure_galaxy_repository_available(ctx, kwds):
workspace = ctx.workspace
cwl = kwds.get("cwl", False)
gx_repo = os.path.join(workspace, "gx_repo")
if cwl:
gx_repo += "_cwl"
if os.path.exists(gx_repo):
# Attempt fetch - but don't fail if not interweb, etc...
shell("git --git-dir %s fetch >/dev/null 2>&1" % gx_repo)
else:
remote_repo = _galaxy_source(kwds)
command = git.command_clone(ctx, remote_repo, gx_repo, bare=True)
shell(command)
return gx_repo
def _ensure_galaxy_repository_available(ctx, kwds):
workspace = ctx.workspace
cwl = kwds.get("cwl", False)
gx_repo = os.path.join(workspace, "gx_repo")
if cwl:
gx_repo += "_cwl"
if os.path.exists(gx_repo):
# Attempt fetch - but don't fail if not interweb, etc...
shell("git --git-dir %s fetch >/dev/null 2>&1" % gx_repo)
else:
if cwl:
remote_repo = "https://github.com/common-workflow-language/galaxy"
else:
remote_repo = "https://github.com/galaxyproject/galaxy"
command = git.command_clone(ctx, remote_repo, gx_repo, bare=True)
shell(command)
return gx_repo
def _ensure_galaxy_repository_available(ctx, kwds):
workspace = ctx.workspace
cwl = kwds.get("cwl", False)
galaxy_source = kwds.get('galaxy_source')
if galaxy_source and galaxy_source != DEFAULT_GALAXY_SOURCE:
sanitized_repo_name = "".join(c if c.isalnum() else '_' for c in kwds['galaxy_source']).rstrip()[:255]
gx_repo = os.path.join(workspace, "gx_repo_%s" % sanitized_repo_name)
else:
gx_repo = os.path.join(workspace, "gx_repo")
if cwl:
gx_repo += "_cwl"
if os.path.exists(gx_repo):
# Attempt fetch - but don't fail if not interweb, etc...
shell("git --git-dir %s remote update >/dev/null 2>&1" % gx_repo)
else:
remote_repo = _galaxy_source(kwds)
command = git.command_clone(ctx, remote_repo, gx_repo, mirror=True)
shell(command)
return gx_repo
def _install_galaxy_via_git(ctx, config_directory, env, kwds):
gx_repo = _ensure_galaxy_repository_available(ctx, kwds)
branch = _galaxy_branch(kwds)
command = git.command_clone(ctx, gx_repo, "galaxy-dev", branch=branch)
_install_with_command(ctx, config_directory, command, env, kwds)
def _install_galaxy_via_git(ctx, config_directory, kwds):
_ensure_galaxy_repository_available(ctx)
workspace = ctx.workspace
gx_repo = os.path.join(workspace, "gx_repo")
command = git.command_clone(ctx, gx_repo, "galaxy-dev")
_install_with_command(config_directory, command)
def _install_galaxy_via_git(ctx, galaxy_root, env, kwds):
gx_repo = _ensure_galaxy_repository_available(ctx, kwds)
branch = _galaxy_branch(kwds)
command = git.command_clone(ctx, gx_repo, galaxy_root, branch=branch)
_install_with_command(ctx, command, galaxy_root, env, kwds)
def _install_galaxy_via_git(ctx, galaxy_root, env, kwds):
gx_repo = _ensure_galaxy_repository_available(ctx, kwds)
branch = _galaxy_branch(kwds)
command = git.command_clone(ctx, gx_repo, galaxy_root, branch=branch)
_install_with_command(ctx, command, galaxy_root, env, kwds)
def _install_galaxy_via_git(ctx, config_directory, env, kwds):
gx_repo = _ensure_galaxy_repository_available(ctx, kwds)
branch = _galaxy_branch(kwds)
command = git.command_clone(ctx, gx_repo, "galaxy-dev", branch=branch)
_install_with_command(ctx, config_directory, command, env, kwds)
def _install_galaxy_via_git(ctx, config_directory, kwds):
_ensure_galaxy_repository_available(ctx)
workspace = ctx.workspace
gx_repo = os.path.join(workspace, "gx_repo")
command = git.command_clone(ctx, gx_repo, "galaxy-dev")
_install_with_command(config_directory, command)