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view Hammock/settings/settings.prop @ 0:b1ac138f0287 draft
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author | hammock |
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date | Mon, 26 Jan 2015 06:24:21 -0500 |
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children | d90f4809ccc6 |
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#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= #hhalignOutDirectory= #hhsearchOutDirectory= #fastaDatabaseFile= #Tool parameters. Generally, it is not recommended to change this section. clustalOmegaParameters= hmmbuildParameters=--enone --fragthresh 1.0 --hand --wnone --amino hmmsearchParameters=--nobias --F1 0.5 --F2 0.05 --F3 1e-2 --nonull2 hmmalignParameters=--outformat selex --amino 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 -BLOSUM65