Revert multithreading support for mafft as it does not seem to work

[jabaws.git] / conf / Executable.properties

diff --git a/conf/Executable.properties b/conf/Executable.properties
index b9bdac3..7ee672f 100644 (file)
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -28,8 +28,9 @@ muscle.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
 \r
 ### Mafft configuration ###\r
 #local.mafft.bin.windows=\r
-local.mafft.bin=binaries/src/mafft/binaries/mafft\r
-cluster.mafft.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/mafft/core/mafft\r
+local.mafft.bin=binaries/src/mafft/scripts/mafft\r
+cluster.mafft.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/mafft/scripts/mafft\r
+# These paths will be converted to absolute if relative.\r
 mafft.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;\r
 mafft.--aamatrix.path=binaries/matrices\r
 mafft.presets.file=conf/settings/MafftPresets.xml\r
@@ -37,6 +38,7 @@ mafft.parameters.file=conf/settings/MafftParameters.xml
 mafft.limits.file=conf/settings/MafftLimits.xml\r
 mafft.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
 \r
+\r
 ### Tcoffee configuration ###\r
 local.tcoffee.bin=binaries/src/tcoffee/t_coffee_source/t_coffee\r
 cluster.tcoffee.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/tcoffee/t_coffee_source/t_coffee\r
@@ -92,7 +94,9 @@ globplot.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
 local.iupred.bin.windows=binaries/windows/iupred/iupred.exe \r
 local.iupred.bin=binaries/src/iupred/iupred\r
 # This must point to the directory where iupred binary is, with other files it depends on\r
-iupred.bin.env=IUPred_PATH#/homes/pvtroshin/workspace/jaba2/binaries/src/iupred\r
+#iupred.bin.env=IUPred_PATH#/homes/pvtroshin/workspace/jaba2/binaries/src/iupred\r
+# This path will be converted to absolute if relative. \r
+iupred.bin.env=IUPred_PATH#binaries/src/iupred\r
 cluster.iupred.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/iupred/iupred\r
 iupred.parameters.file=conf/settings/IUPredParameters.xml\r
 iupred.limits.file=conf/settings/IUPredLimits.xml\r