|
0
|
1 #Lines starting with hash (#) are ignored
|
|
|
2 #Tool commands. Define full paths if needed. By default (not specified) means locations relative to .jar file in Hammock/dist foltder
|
|
|
3 #clustalOmegaCommand=
|
|
|
4 #hmmbuildCommand=
|
|
|
5 #hmmsearchCommand=
|
|
|
6 #hhmakeCommand=
|
|
|
7 #hhsearchCommand=
|
|
|
8 #reformatCommand=
|
|
|
9 #Directory for all temporal files. Define full path if needed. Default (not specified): /tmp
|
|
|
10 #tempDirectory=
|
|
|
11 #Temporal files subdirectories. Define full paths if needed. Default (not specified): directories in tempDirectory/Hammock_temp/[time]/
|
|
|
12 #fastaDirectory=
|
|
|
13 #msaDirectory=
|
|
|
14 #hmmDirectory=
|
|
|
15 #hhDirectory=
|
|
|
16 #hmmsearchOutDirectory=
|
|
|
17 #hhsearchOutDirectory=
|
|
|
18 #fastaDatabaseFile=
|
|
|
19 #Tool parameters. Generally, it is not recommended to change this section.
|
|
|
20 clustalOmegaParameters=
|
|
1
|
21 hmmbuildParameters=--enone --fragthresh 1.0 --hand --wnone --amino --seed 42
|
|
|
22 hmmsearchParameters=--nobias --F1 0.5 --F2 0.05 --F3 1e-2 --nonull2 --seed 42
|
|
|
23 hmmalignParameters=--outformat selex --amino --seed 42
|
|
0
|
24 hhmakeParameters=-M a2m -id 100 -diff inf -pcm 3 -nocontxt -v 0
|
|
1
|
25 hhsearchParameters=-norealign -alt 1 -corr 0 -shift 0 -ssm 0 -tags -nocons -nopred -nodssp -sc 0 -v 0 -z 2 -Z 500000 -local -p 0.0 -vit -b 100.0 -E 100.0 -e 100.0 -z 100
|
