[med-svn] r12695 - in trunk/packages/strap/trunk/debian: . bin

[Christoph Gille]

Author: christophgil-guest
Date: 2012-12-18 22:26:35 +0000 (Tue, 18 Dec 2012)
New Revision: 12695

Modified:
   trunk/packages/strap/trunk/debian/bin/strap_protein_alignment
   trunk/packages/strap/trunk/debian/strap_protein_alignment.1
Log:
Removed soft link for man page file

Modified: trunk/packages/strap/trunk/debian/bin/strap_protein_alignment
===================================================================
--- trunk/packages/strap/trunk/debian/bin/strap_protein_alignment	2012-12-18 22:25:36 UTC (rev 12694)
+++ trunk/packages/strap/trunk/debian/bin/strap_protein_alignment	2012-12-18 22:26:35 UTC (rev 12695)
@@ -4,10 +4,7 @@
 echo
 
 
-S3D=
-if [ -f /usr/bin/tm-align ]; then S3D="-s3d=tm_align"; fi
 
+/bin/sh /usr/bin/strap_base -probeWebProxy -stdout   $*
 
-/bin/sh /usr/bin/strap_base $S3D -a3d=mustang -aligner2=kalign -v3d=pymol -probeWebProxy -stdout -askUpload   $*
-
  
\ No newline at end of file

Modified: trunk/packages/strap/trunk/debian/strap_protein_alignment.1
===================================================================
--- trunk/packages/strap/trunk/debian/strap_protein_alignment.1	2012-12-18 22:25:36 UTC (rev 12694)
+++ trunk/packages/strap/trunk/debian/strap_protein_alignment.1	2012-12-18 22:26:35 UTC (rev 12695)
@@ -1,4 +1,4 @@
-.\"" Do not edit this file. It has been generated from templateGui.1 with /usr/bin/gpp 
+.\"" Do not edit this file. It is generated by a script. Contact Christoph Gille for changes.
 .TH Strap 1 "October 2011"
 .SH NAME
 
@@ -132,8 +132,13 @@
 -script="open_3D viewName, *" 
 would display all proteins with 3D-coordinates three-dimensionally
 (See -v3d=).  Scripts consisting of more than one line should be
-stored in a file and the file path or URL should be given.
+stored in a file and the file path or URL should be given. 
 
+If scripts are run on a server which allows many instances simultaneously,
+consider to use a database backend instead of the file based cache for computed results
+(See http://www.bioinformatics.org/strap/cache.html)
+
+
 Example:
 
 -script2="open_3D viewName, *" -script3="3D_select $ALL" -script7="3D_ribbons on" -script8="superimpose *"
@@ -195,16 +200,11 @@
 
 \fB\-noCache\fR
 
- Do not use cached results of previous
+Do not use cached results of previous
 computations. This setting can be changed in the graphical user
 interface with a check-box.
+Also see http://www.bioinformatics.org/strap/cache.html.
 
-This setting influences the result of searches in growing
-databases. For example consider the similarity search method
-Blast. With the cache turned on, Strap would present a previously
-computed Blast result even though new sequences might have been
-published since last run.
-
 \fB\-keepFiles\fR 
 
 Do not delete temp-files after the session. This is only important for
@@ -265,6 +265,23 @@
 is deactivated.
 
 
+.SH Parameters for the Java virtual machine
+
+Even if Strap is started indirectly with a UNIX script file, 
+parameters can still be passed directly to the Java command.
+Those parameters need to be  prefixed with "JVM_".
+This does not (yet) work for MS-Windows.
+
+
+Examples: 
+
+\fB JVM_-Xmx200M\fR
+\fB JVM_-Dapple.laf.useScreenMenuBar=true\fR
+\fB JVM_-DproxyHost=realproxy.charite.de  JVM_-DproxyPort=888 \fR
+\fB JVM_-ea\fR
+
+
+
 .SH ALIGNMENT FILE GENERATION
 
 With the options \fB\-toMultipleFasta\fR or \fB\-toClustal\fR or