Mercurial > repos > hammock > hammock
view Hammock/settings/settings.prop @ 1:d90f4809ccc6 draft
Uploaded
author | hammock |
---|---|
date | Fri, 28 Aug 2015 07:38:12 -0400 |
parents | b1ac138f0287 |
children |
line wrap: on
line source
#Lines starting with hash (#) are ignored #Tool commands. Define full paths if needed. By default (not specified) means locations relative to .jar file in Hammock/dist foltder #clustalOmegaCommand= #hmmbuildCommand= #hmmsearchCommand= #hhmakeCommand= #hhsearchCommand= #reformatCommand= #Directory for all temporal files. Define full path if needed. Default (not specified): /tmp #tempDirectory= #Temporal files subdirectories. Define full paths if needed. Default (not specified): directories in tempDirectory/Hammock_temp/[time]/ #fastaDirectory= #msaDirectory= #hmmDirectory= #hhDirectory= #hmmsearchOutDirectory= #hhsearchOutDirectory= #fastaDatabaseFile= #Tool parameters. Generally, it is not recommended to change this section. clustalOmegaParameters= hmmbuildParameters=--enone --fragthresh 1.0 --hand --wnone --amino --seed 42 hmmsearchParameters=--nobias --F1 0.5 --F2 0.05 --F3 1e-2 --nonull2 --seed 42 hmmalignParameters=--outformat selex --amino --seed 42 hhmakeParameters=-M a2m -id 100 -diff inf -pcm 3 -nocontxt -v 0 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