-
Notifications
You must be signed in to change notification settings - Fork 0
/
settings.yaml
45 lines (45 loc) · 1.37 KB
/
settings.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
trseeker:
# os: linux64
os: WIN
root_dir: /root/Dropbox/workspace/trseeker
work_dir: /home
blast_settings:
blast_location:
blast_location_NIX: legacy_blast.pl bl2seq
blast_location_WIN: c:\Program Files\NCBI\blast-2.2.26+\bin\legacy_blast.pl bl2seq.exe
repbase_db_folder: /home/rebase_blast_db/repbase
jellyfish_location_new: /home/akomissarov/libs/jellyfish-2.2.0/bin/jellyfish
jellyfish_location: /home/akomissarov/libs/jellyfish-1.1.11/bin/jellyfish
blast_e: 1e-20
blast_b: 20000000
blast_v: 20000000
trf_settings:
trf_location: /home/akomissarov/libs/trf409.linux64
trf_location_mac: /Users/akomissarov/libs/trf409.macos64
trf_location_WIN: e:/trf409.dos.exe
trf_match: 2
trf_mismatch: 5
trf_indel: 7
trf_p: 80
trf_q: 10
trf_threshold: 50
trf_length: 2000
trf_param_postfix: 2.5.7.80.10.50.2000
trf_masked_file: False
trf_flanked_data: True
trf_data_file: True
trf_nohtml: True
overlapping_cutoff: 10
overlapping_cutoff_proc: 30
overlapping_gc_diff: 0.05
jellyfish_settings:
threads: 30
hash_size: 10G
hash_bits: 10
both_strands: "--both-strands"
both_strands_new: "--canonical"
ngrams_settings:
ngram_length: 23
ngram_m: 10000000
repeatmasker:
path: /home/akomissarov/libs/RepeatMasker/RepeatMasker