X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=conf%2FExecutable.properties;h=f0b72c850042a1e4d57b92efb654a87a72554275;hb=603a6be6b9459625f535bf42c6d8ec5462e218e2;hp=b9bdac3bf7acb43fe584a1847c2d03baf9e69fa3;hpb=0c18a9f74394c551d5192b37cf6ff1ba64feb21c;p=jabaws.git

diff --git a/conf/Executable.properties b/conf/Executable.properties
index b9bdac3..f0b72c8 100644
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -30,6 +30,7 @@ muscle.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M
 #local.mafft.bin.windows=
 local.mafft.bin=binaries/src/mafft/binaries/mafft
 cluster.mafft.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/mafft/core/mafft
+# These paths will be converted to absolute if relative.
 mafft.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34;
 mafft.--aamatrix.path=binaries/matrices
 mafft.presets.file=conf/settings/MafftPresets.xml
@@ -92,7 +93,9 @@ 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 
 local.iupred.bin=binaries/src/iupred/iupred
 # This must point to the directory where iupred binary is, with other files it depends on
-iupred.bin.env=IUPred_PATH#/homes/pvtroshin/workspace/jaba2/binaries/src/iupred
+#iupred.bin.env=IUPred_PATH#/homes/pvtroshin/workspace/jaba2/binaries/src/iupred
+# This path will be converted to absolute if relative. 
+iupred.bin.env=IUPred_PATH#binaries/src/iupred
 cluster.iupred.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/iupred/iupred
 iupred.parameters.file=conf/settings/IUPredParameters.xml
 iupred.limits.file=conf/settings/IUPredLimits.xml