-
Notifications
You must be signed in to change notification settings - Fork 7
/
default.yaml
96 lines (83 loc) · 2.37 KB
/
default.yaml
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
gen_feature_with_jackhmmer: No # if Yes, jackhmmer_result will be used to generate feature
path:
output_base: /data/work/qing/DeepContact/test
# run hhblits and reformat output to aln file
# see hhblits_runner.py
hhblits:
command: hhblits
uniprot_db: /data/work/yang/Qing/databases/data/uniprot20_2016_02/uniprot20_2016_02
n_threads: 20
n_iters: 3
e_value: 0.001
maxfilt: 500000
diff: inf
id: 99
cov: 50
# run jackhmmer
# see jackhmmer_runner.py
jackhmmer:
command: /data/work/yang/Qing/software/hmmer-3.1b2/bin/jackhmmer
uniref_db: /data/work/yang/Qing/databases/data/new_uniref/uniref100.fasta
n_threads: 20
inc_E: 10.0
n_iter: 3
# run hhfilter after jackhmmer
# see jackhmmer_runner.py
hhfilter:
command: hhfilter
# run ccmpred
# see ccmpred_runner.py
ccmpred:
command: /data/work/yang/Qing/software/CCMpred/bin/ccmpred
n_threads: 0
# optional:
cuda_dev: 6 # (do not include if use default cuda device)
# run freecontact in evfold mode
# see freecontact_runner.py
freecontact:
command: freecontact
n_threads: 20
# run alnstats
# see alnstats_runner.py
alnstats:
command: /data/work/yang/Qing/software/metapsicov/bin/alnstats
n_processes: 20
# run blastpgp
# see ss_runner.py
blast:
command: /data/work/yang/Qing/software/blast-2.2.26/bin/blastpgp
n_processes: 4
n_threads: 6
n_iters: 3
e_value: 0.001
database: nr
# run makemat
# see ss_runner.py
makemat:
command: /data/work/yang/Qing/software/blast-2.2.26/bin/makemat
n_processes: 24
# run psipred
# see ss_runner.py
psipred:
command: /data/work/yang/Qing/software/psipred/bin/psipred
data: /data/work/yang/Qing/software/psipred/data
n_processes: 24
# run psipred_pass2
# see ss_runner.py
psipred_pass2:
command: /data/work/yang/Qing/software/psipred/bin/psipass2
n_processes: 24
n_iters: 1
DCA: 1.0
DCB: 1.0
# run solvpred
# see ss_runner.py
solvpred:
command: /data/work/yang/Qing/software/metapsicov/bin/solvpred
data: /data/work/yang/Qing/software/metapsicov/data/weights_solv.dat
n_processes: 24
# run hhmake (includes neff)
# see hhmake_runner
hhmake:
command: hhmake
n_processes: 20