1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
|
"""
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)
|
