def cli(ctx, path, **kwds): """Source output to activate a conda environment for this tool. % . <(planemo conda_env bowtie2.xml) % which bowtie2 TODO_PLACE_PATH_HERE """ conda_context = build_conda_context(use_planemo_shell_exec=False, **kwds) conda_targets = collect_conda_targets( path, conda_context=conda_context ) installed_conda_targets = conda_util.filter_installed_targets( conda_targets, conda_context=conda_context ) env_name, exit_code = conda_util.build_isolated_environment( installed_conda_targets, conda_context=conda_context ) if exit_code: error("Failed to build environmnt for request.") return 1 ps1 = ps1_for_path(path, base="PRE_CONDA_PS1") remove_env = "%s env remove -y --name '%s'" % ( conda_context.conda_exec, env_name ) deactivate = conda_context.deactivate activate = conda_context.activate command = SOURCE_COMMAND % ( activate, env_name, ps1, deactivate, remove_env ) print(command)
def cli(ctx, paths, **kwds): """Install conda packages for tool requirements.""" conda_context = build_conda_context(ctx, **kwds) if not conda_context.is_conda_installed(): auto_init = kwds.get("conda_auto_init", False) failed = True if auto_init: if conda_context.can_install_conda(): if conda_util.install_conda(conda_context): error("Attempted to install conda and failed.") else: failed = False else: error("Cannot install conda, failing conda_install.") else: error( "Conda not configured - run planemo conda_init' or pass --conda_auto_init to continue." ) if failed: raise ExitCodeException(EXIT_CODE_FAILED_DEPENDENCIES) return_codes = [] for conda_target in collect_conda_targets(ctx, paths): ctx.log("Install conda target %s" % conda_target) return_code = conda_util.install_conda_target( conda_target, conda_context=conda_context) return_codes.append(return_code) return coalesce_return_codes(return_codes, assert_at_least_one=True)
def cli(ctx, paths, **kwds): """Install conda packages for tool requirements.""" conda_context = build_conda_context(ctx, **kwds) if not conda_context.is_conda_installed(): auto_init = kwds.get("conda_auto_init", False) failed = True if auto_init: if conda_context.can_install_conda(): if conda_util.install_conda(conda_context): error("Attempted to install conda and failed.") else: failed = False else: error("Cannot install conda, failing conda_install.") else: error("Conda not configured - run planemo conda_init' or pass --conda_auto_init to continue.") if failed: raise ExitCodeException(EXIT_CODE_FAILED_DEPENDENCIES) return_codes = [] for conda_target in collect_conda_targets(ctx, paths): ctx.log("Install conda target %s" % conda_target) return_code = conda_util.install_conda_target( conda_target, conda_context=conda_context ) return_codes.append(return_code) return coalesce_return_codes(return_codes, assert_at_least_one=True)
def cli(ctx, path, **kwds): """Activate a conda environment for tool. Source the output of this command to activate a conda environment for this tool. \b $ . <(planemo conda_env seqtk_seq.xml) Deactivate environment with conda_env_deactivate (seqtk_seq_v6) $ which seqtk /home/planemo/miniconda2/envs/jobdepsDkzcjjfecc6d406196737781ff4456ec60975c137e04884e4f4b05dc68192f7cec4656/bin/seqtk (seqtk_seq_v6) $ conda_env_deactivate $ """ conda_context = build_conda_context(ctx, use_planemo_shell_exec=False, **kwds) conda_targets = collect_conda_targets(ctx, [path]) installed_conda_targets = conda_util.filter_installed_targets( conda_targets, conda_context=conda_context) env_name, exit_code = conda_util.build_isolated_environment( installed_conda_targets, conda_context=conda_context, quiet=True) if exit_code: error("Failed to build environment for request.") return 1 ps1 = ps1_for_path(path, base="PRE_CONDA_PS1") remove_env = "%s env remove -y --name '%s'" % (conda_context.conda_exec, env_name) deactivate = conda_context.deactivate activate = conda_context.activate command = SOURCE_COMMAND % (activate, env_name, ps1, deactivate, remove_env) print(command)
def cli(ctx, path, **kwds): """Install conda packages for tool requirements.""" conda_context = build_conda_context(**kwds) return_codes = [] for conda_target in collect_conda_targets(path): ctx.log("Install conda target %s" % conda_target) return_code = conda_util.install_conda_target( conda_target, conda_context=conda_context) return_codes.append(return_code) return coalesce_return_codes(return_codes, assert_at_least_one=True)
def cli(ctx, paths, **kwds): """Install conda packages for tool requirements.""" conda_context = build_conda_context(ctx, handle_auto_init=True, **kwds) return_codes = [] for conda_target in collect_conda_targets(ctx, paths, recursive=kwds["recursive"]): ctx.log("Install conda target %s" % conda_target) return_code = conda_util.install_conda_target( conda_target, conda_context=conda_context, skip_environment=kwds.get("global", False) ) return_codes.append(return_code) return coalesce_return_codes(return_codes, assert_at_least_one=True)
def cli(ctx, path, **kwds): """Install conda packages for tool requirements.""" conda_context = build_conda_context(**kwds) return_codes = [] for conda_target in collect_conda_targets(path): ctx.log("Install conda target %s" % conda_target) return_code = conda_util.install_conda_target( conda_target, conda_context=conda_context ) return_codes.append(return_code) return coalesce_return_codes(return_codes, assert_at_least_one=True)
def cli(ctx, paths, **kwds): """Install conda packages for tool requirements.""" conda_context = build_conda_context(ctx, handle_auto_init=True, **kwds) return_codes = [] for conda_target in collect_conda_targets(ctx, paths, recursive=kwds["recursive"]): ctx.log("Install conda target %s" % conda_target) return_code = conda_util.install_conda_target( conda_target, conda_context=conda_context, skip_environment=kwds.get("global", False)) return_codes.append(return_code) return coalesce_return_codes(return_codes, assert_at_least_one=True)
def cli(ctx, path, **kwds): """Activate a conda environment for tool. Source the output of this command to activate a conda environment for this tool. \b $ . <(planemo conda_env seqtk_seq.xml) Deactivate environment with conda_env_deactivate (seqtk_seq_v6) $ which seqtk /home/planemo/miniconda2/envs/jobdepsDkzcjjfecc6d406196737781ff4456ec60975c137e04884e4f4b05dc68192f7cec4656/bin/seqtk (seqtk_seq_v6) $ conda_env_deactivate $ """ conda_context = build_conda_context(ctx, use_planemo_shell_exec=False, **kwds) conda_targets = collect_conda_targets( ctx, [path], conda_context=conda_context ) installed_conda_targets = conda_util.filter_installed_targets( conda_targets, conda_context=conda_context ) env_name, exit_code = conda_util.build_isolated_environment( installed_conda_targets, conda_context=conda_context, quiet=True ) if exit_code: error("Failed to build environmnt for request.") return 1 ps1 = ps1_for_path(path, base="PRE_CONDA_PS1") remove_env = "%s env remove -y --name '%s'" % ( conda_context.conda_exec, env_name ) deactivate = conda_context.deactivate activate = conda_context.activate command = SOURCE_COMMAND % ( activate, env_name, ps1, deactivate, remove_env ) print(command)