[med-svn] r11379 - in trunk/packages/strap/trunk/debian: . bin man

[Christoph Gille]

Author: christophgil-guest
Date: 2012-06-19 05:37:48 +0000 (Tue, 19 Jun 2012)
New Revision: 11379

Modified:
   trunk/packages/strap/trunk/debian/bin/strap_util_toClustal
   trunk/packages/strap/trunk/debian/bin/strap_util_toFasta
   trunk/packages/strap/trunk/debian/bin/strap_util_toMultipleFasta
   trunk/packages/strap/trunk/debian/bin/toXXX.sh
   trunk/packages/strap/trunk/debian/control
   trunk/packages/strap/trunk/debian/man/strap_util_toClustal.1
   trunk/packages/strap/trunk/debian/man/strap_util_toFasta.1
   trunk/packages/strap/trunk/debian/man/strap_util_toMultipleFasta.1
Log:
Fixed shell scripts

Modified: trunk/packages/strap/trunk/debian/bin/strap_util_toClustal
===================================================================
--- trunk/packages/strap/trunk/debian/bin/strap_util_toClustal	2012-06-19 03:55:02 UTC (rev 11378)
+++ trunk/packages/strap/trunk/debian/bin/strap_util_toClustal	2012-06-19 05:37:48 UTC (rev 11379)
@@ -18,6 +18,6 @@
 # which would set heap size to 500 Megabytes.
 
 
-$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toClustal
+$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toClustal $*
  
 

Modified: trunk/packages/strap/trunk/debian/bin/strap_util_toFasta
===================================================================
--- trunk/packages/strap/trunk/debian/bin/strap_util_toFasta	2012-06-19 03:55:02 UTC (rev 11378)
+++ trunk/packages/strap/trunk/debian/bin/strap_util_toFasta	2012-06-19 05:37:48 UTC (rev 11379)
@@ -18,6 +18,6 @@
 # which would set heap size to 500 Megabytes.
 
 
-$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toFasta
+$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toFasta $*
  
 

Modified: trunk/packages/strap/trunk/debian/bin/strap_util_toMultipleFasta
===================================================================
--- trunk/packages/strap/trunk/debian/bin/strap_util_toMultipleFasta	2012-06-19 03:55:02 UTC (rev 11378)
+++ trunk/packages/strap/trunk/debian/bin/strap_util_toMultipleFasta	2012-06-19 05:37:48 UTC (rev 11379)
@@ -18,6 +18,6 @@
 # which would set heap size to 500 Megabytes.
 
 
-$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toMultipleFasta
+$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toMultipleFasta $*
  
 

Modified: trunk/packages/strap/trunk/debian/bin/toXXX.sh
===================================================================
--- trunk/packages/strap/trunk/debian/bin/toXXX.sh	2012-06-19 03:55:02 UTC (rev 11378)
+++ trunk/packages/strap/trunk/debian/bin/toXXX.sh	2012-06-19 05:37:48 UTC (rev 11379)
@@ -18,6 +18,6 @@
 # which would set heap size to 500 Megabytes.
 
 
-$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toXXX
+$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toXXX $*
  
 

Modified: trunk/packages/strap/trunk/debian/control
===================================================================
--- trunk/packages/strap/trunk/debian/control	2012-06-19 03:55:02 UTC (rev 11378)
+++ trunk/packages/strap/trunk/debian/control	2012-06-19 05:37:48 UTC (rev 11379)
@@ -23,11 +23,12 @@
  graphical user interface which follows the paradigms of modern user
  interfaces such as drag'n drop.  The sequence alignment view and the
  Pymol 3D-visualization are tightly linked.  Information can be
- attached to residue selections such as free text notes as well as 3D
- and 1D display styles.  Figures can be created in publication
- quality. The alignment can be exported in several formats: PDF,
- MS-Word, HTML, Jalview, Multiple-Fasta, ClustalW, MSF, HSSP - see
- http://3d-alignment.eu/ for details.  Interactive alignments can be
- published in Web-pages. For this purpose, HTML code is generated
- automatically. Strap is scriptable and can be used by programs and
- web-services to display sequence alignments and 3D-superpositions.
+ attached to residue selections such as free text notes,
+ cross-references as well as 3D and 1D display style commands.
+ Figures can be created in publication quality. The alignment can be
+ exported in several formats: PDF, MS-Word, HTML, Jalview,
+ Multiple-Fasta, ClustalW, MSF, HSSP - see http://3d-alignment.eu/ for
+ details.  Interactive alignments can be published in Web-pages. For
+ this purpose, HTML code is generated automatically. Strap is
+ scriptable and can be used by programs and web-services to display
+ sequence alignments and 3D-superpositions.

Modified: trunk/packages/strap/trunk/debian/man/strap_util_toClustal.1
===================================================================
--- trunk/packages/strap/trunk/debian/man/strap_util_toClustal.1	2012-06-19 03:55:02 UTC (rev 11378)
+++ trunk/packages/strap/trunk/debian/man/strap_util_toClustal.1	2012-06-19 05:37:48 UTC (rev 11379)
@@ -42,11 +42,11 @@
 License GPL
 
 .SH "SEE ALSO"
-
-.BR jalview (1)
-.BR clustalx (1)
-.BR seaview (1)
-.BR boxshade (1)
-.BR pymol (1)
-.BR openastex (1)
-.BR strap-text-viewer (1)
+.BR strap_util_toClustal (1)
+.BR strap_util_toFasta (1)    
+.BR strap_util_toMultipleFasta (1)
+.BR strap-protein-alignment (1)
+.BR sequenceconverter (1)
+.BR bioperl (1)
+.BR cdbfasta (1)
+.BR squizz (1)

Modified: trunk/packages/strap/trunk/debian/man/strap_util_toFasta.1
===================================================================
--- trunk/packages/strap/trunk/debian/man/strap_util_toFasta.1	2012-06-19 03:55:02 UTC (rev 11378)
+++ trunk/packages/strap/trunk/debian/man/strap_util_toFasta.1	2012-06-19 05:37:48 UTC (rev 11379)
@@ -42,11 +42,11 @@
 License GPL
 
 .SH "SEE ALSO"
-
-.BR jalview (1)
-.BR clustalx (1)
-.BR seaview (1)
-.BR boxshade (1)
-.BR pymol (1)
-.BR openastex (1)
-.BR strap-text-viewer (1)
+.BR strap_util_toClustal (1)
+.BR strap_util_toFasta (1)    
+.BR strap_util_toMultipleFasta (1)
+.BR strap-protein-alignment (1)
+.BR sequenceconverter (1)
+.BR bioperl (1)
+.BR cdbfasta (1)
+.BR squizz (1)

Modified: trunk/packages/strap/trunk/debian/man/strap_util_toMultipleFasta.1
===================================================================
--- trunk/packages/strap/trunk/debian/man/strap_util_toMultipleFasta.1	2012-06-19 03:55:02 UTC (rev 11378)
+++ trunk/packages/strap/trunk/debian/man/strap_util_toMultipleFasta.1	2012-06-19 05:37:48 UTC (rev 11379)
@@ -42,11 +42,11 @@
 License GPL
 
 .SH "SEE ALSO"
-
-.BR jalview (1)
-.BR clustalx (1)
-.BR seaview (1)
-.BR boxshade (1)
-.BR pymol (1)
-.BR openastex (1)
-.BR strap-text-viewer (1)
+.BR strap_util_toClustal (1)
+.BR strap_util_toFasta (1)    
+.BR strap_util_toMultipleFasta (1)
+.BR strap-protein-alignment (1)
+.BR sequenceconverter (1)
+.BR bioperl (1)
+.BR cdbfasta (1)
+.BR squizz (1)