[med-svn] r11114 - in trunk/packages/strap/trunk/debian: . bin2

[Christoph Gille]

Author: christophgil-guest
Date: 2012-05-30 23:22:44 +0000 (Wed, 30 May 2012)
New Revision: 11114

Added:
   trunk/packages/strap/trunk/debian/bin2/
   trunk/packages/strap/trunk/debian/bin2/strap_util_toClustal
   trunk/packages/strap/trunk/debian/bin2/strap_util_toFasta
   trunk/packages/strap/trunk/debian/bin2/strap_util_toMultipleFasta
   trunk/packages/strap/trunk/debian/bin2/toXXX.sh
Modified:
   trunk/packages/strap/trunk/debian/Sed.sh
Log:


Modified: trunk/packages/strap/trunk/debian/Sed.sh
===================================================================
--- trunk/packages/strap/trunk/debian/Sed.sh	2012-05-30 23:13:01 UTC (rev 11113)
+++ trunk/packages/strap/trunk/debian/Sed.sh	2012-05-30 23:22:44 UTC (rev 11114)
@@ -1,7 +1,7 @@
-cat bin/toXXX.sh | sed 's|-toXXX|-toFasta|1' > bin/strap_util_toFasta
-cat bin/toXXX.sh | sed 's|-toXXX|-toMultipleFasta|1' > bin/strap_util_toMultipleFasta
-cat bin/toXXX.sh | sed 's|-toXXX|-toClustal|1' > bin/strap_util_toClustal
-chmod a+x bin/*
+cat bin2/toXXX.sh | sed 's|-toXXX|-toFasta|1' > bin2/strap_util_toFasta
+cat bin2/toXXX.sh | sed 's|-toXXX|-toMultipleFasta|1' > bin2/strap_util_toMultipleFasta
+cat bin2/toXXX.sh | sed 's|-toXXX|-toClustal|1' > bin2/strap_util_toClustal
+chmod a+x bin2/*
 
 cat man/toXXX.1 | sed 's|toXXX|toClustal|1;s|FORMAT|clustal|1;s|OUTPUT|A single file in clustal format is written.|1' > man/strap_util_toClustal.1
 

Added: trunk/packages/strap/trunk/debian/bin2/strap_util_toClustal
===================================================================
--- trunk/packages/strap/trunk/debian/bin2/strap_util_toClustal	                        (rev 0)
+++ trunk/packages/strap/trunk/debian/bin2/strap_util_toClustal	2012-05-30 23:22:44 UTC (rev 11114)
@@ -0,0 +1,23 @@
+#! /bin/sh
+
+# See http://3d-alignment.eu/ 
+
+
+. /usr/lib/java-wrappers/java-wrappers.sh
+find_java_runtime java6
+
+# Java option max heap size 
+xmx=-Xmx200M
+
+for i in $*; do
+    if [ $i != ${i##-Xmx} ]; then xmx=$i; fi
+done
+
+# The maximum heap size option is $xmx.
+# To change, add a program line option like -Xmx500M 
+# which would set heap size to 500 Megabytes.
+
+
+$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toClustal
+ 
+


Property changes on: trunk/packages/strap/trunk/debian/bin2/strap_util_toClustal
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/strap/trunk/debian/bin2/strap_util_toFasta
===================================================================
--- trunk/packages/strap/trunk/debian/bin2/strap_util_toFasta	                        (rev 0)
+++ trunk/packages/strap/trunk/debian/bin2/strap_util_toFasta	2012-05-30 23:22:44 UTC (rev 11114)
@@ -0,0 +1,23 @@
+#! /bin/sh
+
+# See http://3d-alignment.eu/ 
+
+
+. /usr/lib/java-wrappers/java-wrappers.sh
+find_java_runtime java6
+
+# Java option max heap size 
+xmx=-Xmx200M
+
+for i in $*; do
+    if [ $i != ${i##-Xmx} ]; then xmx=$i; fi
+done
+
+# The maximum heap size option is $xmx.
+# To change, add a program line option like -Xmx500M 
+# which would set heap size to 500 Megabytes.
+
+
+$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toFasta
+ 
+


Property changes on: trunk/packages/strap/trunk/debian/bin2/strap_util_toFasta
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/strap/trunk/debian/bin2/strap_util_toMultipleFasta
===================================================================
--- trunk/packages/strap/trunk/debian/bin2/strap_util_toMultipleFasta	                        (rev 0)
+++ trunk/packages/strap/trunk/debian/bin2/strap_util_toMultipleFasta	2012-05-30 23:22:44 UTC (rev 11114)
@@ -0,0 +1,23 @@
+#! /bin/sh
+
+# See http://3d-alignment.eu/ 
+
+
+. /usr/lib/java-wrappers/java-wrappers.sh
+find_java_runtime java6
+
+# Java option max heap size 
+xmx=-Xmx200M
+
+for i in $*; do
+    if [ $i != ${i##-Xmx} ]; then xmx=$i; fi
+done
+
+# The maximum heap size option is $xmx.
+# To change, add a program line option like -Xmx500M 
+# which would set heap size to 500 Megabytes.
+
+
+$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toMultipleFasta
+ 
+


Property changes on: trunk/packages/strap/trunk/debian/bin2/strap_util_toMultipleFasta
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/strap/trunk/debian/bin2/toXXX.sh
===================================================================
--- trunk/packages/strap/trunk/debian/bin2/toXXX.sh	                        (rev 0)
+++ trunk/packages/strap/trunk/debian/bin2/toXXX.sh	2012-05-30 23:22:44 UTC (rev 11114)
@@ -0,0 +1,23 @@
+#! /bin/sh
+
+# See http://3d-alignment.eu/ 
+
+
+. /usr/lib/java-wrappers/java-wrappers.sh
+find_java_runtime java6
+
+# Java option max heap size 
+xmx=-Xmx200M
+
+for i in $*; do
+    if [ $i != ${i##-Xmx} ]; then xmx=$i; fi
+done
+
+# The maximum heap size option is $xmx.
+# To change, add a program line option like -Xmx500M 
+# which would set heap size to 500 Megabytes.
+
+
+$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toXXX
+ 
+


Property changes on: trunk/packages/strap/trunk/debian/bin2/toXXX.sh
___________________________________________________________________
Added: svn:executable
   + *