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
+ *
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