""" Some commands to install common databases like mirbase and some human/mouse annotation """ from __future__ import print_function import os.path as op import os import sys from argparse import ArgumentParser import subprocess import contextlib import yaml from seqcluster.libs import do, utils try: import bcbio except: print ("Probably this will fail, you need bcbio-nextgen for many installation functions.") pass REMOTES = { "requirements": "https://raw.github.com/lpantano/seqcluster/master/requirements.txt", "gitrepo": "https://github.com/lpantano/seqcluster.git", "gitrepo-bcbio": "https://github.com/chapmanb/bcbio-nextgen.git" } def _mkdir(path): try: os.makedirs(path) except OSError: if not os.path.isdir(path): raise @contextlib.contextmanager def chdir(new_dir): """ stolen from bcbio. Context manager to temporarily change to a new directory. http://lucentbeing.com/blog/context-managers-and-the-with-statement-in-python/ """ cur_dir = os.getcwd() _mkdir(new_dir) os.chdir(new_dir) try: yield finally: os.chdir(cur_dir) def _get_miraligner(): opts = "-Xms750m -Xmx4g" try: tool = "miraligner" ret = os.system(tool) if ret != 0: raise SystemExit("%s not installed." % tool) except SystemExit: tool = None print("miraligner not found. I'll try to download it.") pass if not tool: if not utils.file_exists(op.abspath("miraligner.jar")): url = "https://raw.githubusercontent.com/lpantano/seqbuster/miraligner/modules/miraligner/miraligner.jar" cmd = ["wget", "-O miraligner.jar", "--no-check-certificate", url] do.run(" ".join(cmd), "Download miraligner.") tool = "java -jar {opts} %s" % op.abspath("miraligner.jar") else: tool = "%s {opts}" % tool return tool.format(**locals()) def _get_flavor(): """ Download flavor from github """ target = op.join("seqcluster", "flavor") url = "https://github.com/lpantano/seqcluster.git" if not os.path.exists(target): # shutil.rmtree("seqcluster") subprocess.check_call(["git", "clone","-b", "flavor", "--single-branch", url]) return op.abspath(target) def _install(path, args): """ small helper for installation in case outside bcbio """ try: from bcbio import install as bcb except: raise ImportError("It needs bcbio to do the quick installation.") path_flavor = _get_flavor() s = {"fabricrc_overrides": {"system_install": path, "local_install": os.path.join(path, "local_install"), "use_sudo": "false", "edition": "minimal"}} s = {"flavor": path_flavor, # "target": "[brew, conda]", "vm_provider": "novm", "hostname": "localhost", "fabricrc_overrides": {"edition": "minimal", "use_sudo": "false", "keep_isolated": "true", "conda_cmd": bcb._get_conda_bin(), "distribution": "__auto__", "dist_name": "__auto__"}} s["actions"] = ["install_biolinux"] s["fabricrc_overrides"]["system_install"] = path s["fabricrc_overrides"]["local_install"] = os.path.join(path, "local_install") cbl = bcb.get_cloudbiolinux(bcb.REMOTES) sys.path.insert(0, cbl["dir"]) cbl_deploy = __import__("cloudbio.deploy", fromlist=["deploy"]) cbl_deploy.deploy(s) def _install_data(data_dir, path_flavor, args): """Upgrade required genome data files in place. """ try: from bcbio import install as bcb except: raise ImportError("It needs bcbio to do the quick installation.") bio_data = op.join(path_flavor, "../biodata.yaml") s = {"flavor": path_flavor, # "target": "[brew, conda]", "vm_provider": "novm", "hostname": "localhost", "fabricrc_overrides": {"edition": "minimal", "use_sudo": "false", "keep_isolated": "true", "conda_cmd": bcb._get_conda_bin(), "distribution": "__auto__", "dist_name": "__auto__"}} s["actions"] = ["setup_biodata"] s["fabricrc_overrides"]["data_files"] = data_dir s["fabricrc_overrides"]["galaxy_home"] = os.path.join(data_dir, "galaxy") cbl = bcb.get_cloudbiolinux(bcb.REMOTES) s["genomes"] = _get_biodata(bio_data, args) sys.path.insert(0, cbl["dir"]) cbl_deploy = __import__("cloudbio.deploy", fromlist=["deploy"]) cbl_deploy.deploy(s) def _get_biodata(base_file, args): with open(base_file) as in_handle: config = yaml.load(in_handle) config["install_liftover"] = False config["genome_indexes"] = args.aligners config["genomes"] = [g for g in config["genomes"] if g["dbkey"] in args.genomes] return config def _install_mirbase(): for fn in ["hairpin.fa.gz", "miRNA.str.gz"]: out_file = op.join("mirbase", fn) _mkdir("mirbase") url = "ftp://mirbase.org/pub/mirbase/CURRENT/%s" % fn cmd = ["wget", "-O", out_file, "--no-check-certificate", url] subprocess.check_call(cmd) subprocess.check_call(["gunzip", "-f", out_file]) return "mirbase/hairpin.fa", "mirbase/miRNA.str" def _upgrade(): conda_dir = os.path.join(os.path.dirname(os.path.realpath(sys.executable))) try: import bcbio.install as install install._set_pip_ssl(conda_dir) except ImportError: print("bcbio was not found, this may error.") pass pip_bin = os.path.join(conda_dir, "pip") cmd = [pip_bin, "install", "--upgrade", "--no-deps", "git+%s#egg=seqcluster" % REMOTES["gitrepo"]] print(" ".join(cmd)) subprocess.check_call(cmd) #subprocess.check_call([pip_bin, "install", "--upgrade", "--no-deps", # "git+%s#egg=bcbio-nextgen" % REMOTES["gitrepo-bcbio"]]) def actions(args): if args.upgrade: _upgrade() if False: db = set(args.data) if isinstance(args.data, list) else [args.data] if "mirbase" in db: _install_mirbase() if "hg19" in db: with chdir("hg19"): subprocess.check_call(["wget", "--no-check-certificate", "-p", "https://raw.githubusercontent.com/lpantano/seqcluster/master/scripts/hg19.sh", "-O", "hg19.sh", ]) subprocess.check_call(["bash", "hg19.sh"]) if "mm10" in db: with chdir("mm10"): subprocess.check_call(["wget", "--no-check-certificate", "-p", "https://raw.githubusercontent.com/lpantano/seqcluster/master/scripts/mm10.sh", "-O", "mm10.sh", ]) subprocess.check_call(["bash", "mm10.sh"]) if args.tools: _install(op.abspath(args.tools), args) if args.data: path_flavor = _get_flavor() _install_data(args.data, path_flavor, args) def main(**kwargs): parser = ArgumentParser(description="small RNA analysis installer") parser.add_argument("--tools", help="install tools") parser.add_argument("--data", help="path install data") parser.add_argument("--upgrade", action="store_true", help="upgrade seqcluster", default=[]) parser.add_argument("--genomes", default=[], action="append") parser.add_argument("--aligners", default=[], action="append") args = parser.parse_args() actions(args)