Mercurial > repos > hammock > hammock
comparison Hammock/settings/settings.prop @ 0:b1ac138f0287 draft
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| author | hammock |
|---|---|
| date | Mon, 26 Jan 2015 06:24:21 -0500 |
| parents | |
| children | d90f4809ccc6 |
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| -1:000000000000 | 0:b1ac138f0287 |
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| 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 #hhalignOutDirectory= | |
| 18 #hhsearchOutDirectory= | |
| 19 #fastaDatabaseFile= | |
| 20 #Tool parameters. Generally, it is not recommended to change this section. | |
| 21 clustalOmegaParameters= | |
| 22 hmmbuildParameters=--enone --fragthresh 1.0 --hand --wnone --amino | |
| 23 hmmsearchParameters=--nobias --F1 0.5 --F2 0.05 --F3 1e-2 --nonull2 | |
| 24 hmmalignParameters=--outformat selex --amino | |
| 25 hhmakeParameters=-M a2m -id 100 -diff inf -pcm 3 -nocontxt -v 0 | |
| 26 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 |