From c9f7971449a47c55a05742cfcb93157e30dd385a Mon Sep 17 00:00:00 2001 From: =?utf8?q?F=C3=A1bio=20Madeira?= Date: Wed, 8 Feb 2017 10:17:06 +0000 Subject: [PATCH] JWS-113 Commented Jpred entries in various configuration files. --- WEB-INF/sun-jaxws.xml | 6 +++--- WEB-INF/web.xml | 18 +++++++++--------- binaries/src/setexecflag.sh | 4 ++-- conf/Executable.properties | 32 ++++++++++++++++---------------- wsbuild.xml | 26 +++++++++++++------------- 5 files changed, 43 insertions(+), 43 deletions(-) diff --git a/WEB-INF/sun-jaxws.xml b/WEB-INF/sun-jaxws.xml index 13d6fac..eff3279 100644 --- a/WEB-INF/sun-jaxws.xml +++ b/WEB-INF/sun-jaxws.xml @@ -42,9 +42,9 @@ - + + + diff --git a/WEB-INF/web.xml b/WEB-INF/web.xml index cec1884..6ec75a1 100644 --- a/WEB-INF/web.xml +++ b/WEB-INF/web.xml @@ -174,11 +174,11 @@ 1 - - JpredWS - com.sun.xml.ws.transport.http.servlet.WSServlet - 1 - + + + + + RNAalifoldWS com.sun.xml.ws.transport.http.servlet.WSServlet @@ -296,10 +296,10 @@ /IUPredWS - - JpredWS - /JpredWS - + + + + RNAalifoldWS diff --git a/binaries/src/setexecflag.sh b/binaries/src/setexecflag.sh index 38ad0fa..7e300ed 100644 --- a/binaries/src/setexecflag.sh +++ b/binaries/src/setexecflag.sh @@ -32,8 +32,8 @@ chmod +x globplot/GlobPlot.py globplot/sav_gol echo "Setting executable flag for IUPred..." chmod +x iupred/iupred -echo "Setting executable flag for Jpred..." -chmod +x jpred/i686/* jpred/x86_64/* +#echo "Setting executable flag for Jpred..." +#chmod +x jpred/i686/* jpred/x86_64/* echo "Setting executable flag for ViennaRNA..." chmod +x ViennaRNA/Progs/RNAalifold diff --git a/conf/Executable.properties b/conf/Executable.properties index cbc8474..cfacc2f 100644 --- a/conf/Executable.properties +++ b/conf/Executable.properties @@ -215,22 +215,22 @@ aacon.limits.file = conf/settings/AAConLimits.xml ########################################################################################### # JPRED CONFIGURATION # ########################################################################################### -local.jpred.bin = binaries/src/jpred/jpred.pl -#cluster.jpred.bin = /home/jabaws/binaries/src/jpred/jpred.pl -# These paths will be converted to absolute if relative. -jpred.bin.env = BLASTMAT#binaries/src/jpred/data/blast -# The varible jpred.data.uniref.path define a path to Uniref90 files used by Jpred. If -# you install the database to a different path chenge the variable here -jpred.data.uniref.path = /data/UNIREFdb -# WARNING!!! -# Redefine jpred.data.uniref.name if you do undestand what the variable means -jpred.data.uniref.name = cluster -### This parameters specifies the directory where the matrices files are stored -jpred.presets.file = conf/settings/JpredPresets.xml -jpred.parameters.file = conf/settings/JpredParameters.xml -jpred.limits.file = conf/settings/JpredLimits.xml -jpred.cluster.cpunum = 4 -#jpred.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M +#local.jpred.bin = binaries/src/jpred/jpred.pl +##cluster.jpred.bin = /home/jabaws/binaries/src/jpred/jpred.pl +## These paths will be converted to absolute if relative. +#jpred.bin.env = BLASTMAT#binaries/src/jpred/data/blast +## The varible jpred.data.uniref.path define a path to Uniref90 files used by Jpred. If +## you install the database to a different path chenge the variable here +#jpred.data.uniref.path = /data/UNIREFdb +## WARNING!!! +## Redefine jpred.data.uniref.name if you do undestand what the variable means +#jpred.data.uniref.name = cluster +#### This parameters specifies the directory where the matrices files are stored +#jpred.presets.file = conf/settings/JpredPresets.xml +#jpred.parameters.file = conf/settings/JpredParameters.xml +#jpred.limits.file = conf/settings/JpredLimits.xml +#jpred.cluster.cpunum = 4 +##jpred.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M ########################################################################################### # RNAALIFOLD CONFIGURATION # diff --git a/wsbuild.xml b/wsbuild.xml index c8aa0e5..c6966f6 100644 --- a/wsbuild.xml +++ b/wsbuild.xml @@ -18,7 +18,7 @@ - + @@ -56,18 +56,18 @@ - - - - + + + + + + + + + + + +