From: Fábio Madeira <fmmarquesmadeira@dundee.ac.uk>
Date: Thu, 18 May 2017 11:00:56 +0000 (+0100)
Subject: JWS-112 Hotfix the last t-coffee version 11. The -mode quickaln preset breaks if... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e8d7803afda8d4346a66f44cc7d5bd1cfd3fd81d;p=jabaws.git

JWS-112 Hotfix the last t-coffee version 11. The -mode quickaln preset breaks if ’t_coffee’ is not found in $PATH. By calling t_coffee.sh instead, the problem is fixed by updating the $PATH on the flight and passing the original arguments to t_coffee.
---

diff --git a/binaries/src/compilebin.sh b/binaries/src/compilebin.sh
index b0e478b..39562e8 100644
--- a/binaries/src/compilebin.sh
+++ b/binaries/src/compilebin.sh
@@ -51,8 +51,9 @@ cd tcoffee
 chmod +x install
 ./install clean
 ./install t_coffee -force
+echo -e '#!/usr/bin/env bash\nPDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"\nexport PATH=$PATH:$PDIR\nt_coffee "$@"' > t_coffee_source/t_coffee.sh
 chmod +x t_coffee_source/t_coffee
-export PATH=$PATH:$PWD/t_coffee_source
+chmod +x t_coffee_source/t_coffee.sh
 cd ..
 
 echo "Compiling DisEMBL..."
diff --git a/binaries/src/tcoffee/t_coffee_source/t_coffee.sh b/binaries/src/tcoffee/t_coffee_source/t_coffee.sh
new file mode 100644
index 0000000..8e7ec9c
--- /dev/null
+++ b/binaries/src/tcoffee/t_coffee_source/t_coffee.sh
@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+PDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+export PATH=$PATH:$PDIR
+t_coffee "$@"
\ No newline at end of file
diff --git a/conf/Executable.properties b/conf/Executable.properties
index 40cdf72..9a4089e 100644
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -119,8 +119,8 @@ mafft.cluster.settings  = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu
 ###########################################################################################
 #                                  TCOFFEE CONFIGURATION                                  #
 ###########################################################################################
-local.tcoffee.bin         = binaries/src/tcoffee/t_coffee_source/t_coffee
-cluster.tcoffee.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/tcoffee/t_coffee_source/t_coffee
+local.tcoffee.bin         = binaries/src/tcoffee/t_coffee_source/t_coffee.sh
+cluster.tcoffee.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/tcoffee/t_coffee_source/t_coffee.sh
 # This variable is required by tcoffee
 tcoffee.bin.env           = HOME_4_TCOFFEE#jobsout;
 tcoffee.presets.file      = conf/settings/TcoffeePresets.xml
diff --git a/conf/Executable.properties.dundee b/conf/Executable.properties.dundee
index 2e422ff..ee909fc 100644
--- a/conf/Executable.properties.dundee
+++ b/conf/Executable.properties.dundee
@@ -119,8 +119,8 @@ mafft.cluster.settings  = -P webservices -R y -q 64bit-pri.q -q c6100.q -l h_cpu
 ###########################################################################################
 #                                  TCOFFEE CONFIGURATION                                  #
 ###########################################################################################
-local.tcoffee.bin         = binaries/src/tcoffee/t_coffee_source/t_coffee
-cluster.tcoffee.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/tcoffee/t_coffee_source/t_coffee
+local.tcoffee.bin         = binaries/src/tcoffee/t_coffee_source/t_coffee.sh
+cluster.tcoffee.bin       = /homes/www-jws2/servers/tomcat-8.5.11_jaba-2.2/webapps/jabaws/binaries/src/tcoffee/t_coffee_source/t_coffee.sh
 # This variable is required by tcoffee
 tcoffee.bin.env           = HOME_4_TCOFFEE#jobsout;
 tcoffee.presets.file      = conf/settings/TcoffeePresets.xml