Mercurial > repos > hammock > hammock
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Hammock/settings/settings.prop Mon Jan 26 06:24:21 2015 -0500 @@ -0,0 +1,26 @@ +#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