From e8d7803afda8d4346a66f44cc7d5bd1cfd3fd81d Mon Sep 17 00:00:00 2001 From: =?utf8?q?F=C3=A1bio=20Madeira?= Date: Thu, 18 May 2017 12:00:56 +0100 Subject: [PATCH] =?utf8?q?JWS-112=20Hotfix=20the=20last=20t-coffee=20version?= =?utf8?q?=2011.=20The=20-mode=20quickaln=20preset=20breaks=20if=20=E2=80=99?= =?utf8?q?t=5Fcoffee=E2=80=99=20is=20not=20found=20in=20$PATH.=20By=20callin?= =?utf8?q?g=20t=5Fcoffee.sh=20instead,=20the=20problem=20is=20fixed=20by=20u?= =?utf8?q?pdating=20the=20$PATH=20on=20the=20flight=20and=20passing=20the=20?= =?utf8?q?original=20arguments=20to=20t=5Fcoffee.?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- binaries/src/compilebin.sh | 3 ++- binaries/src/tcoffee/t_coffee_source/t_coffee.sh | 4 ++++ conf/Executable.properties | 4 ++-- conf/Executable.properties.dundee | 4 ++-- 4 files changed, 10 insertions(+), 5 deletions(-) create mode 100644 binaries/src/tcoffee/t_coffee_source/t_coffee.sh 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 -- 1.7.10.2