[med-svn] r12694 - trunk/packages/strap-base/trunk/debian
Christoph Gille
christophgil-guest at alioth.debian.org
Tue Dec 18 22:25:36 UTC 2012
Author: christophgil-guest
Date: 2012-12-18 22:25:36 +0000 (Tue, 18 Dec 2012)
New Revision: 12694
Removed:
trunk/packages/strap-base/trunk/debian/templates/
Modified:
trunk/packages/strap-base/trunk/debian/copyright
trunk/packages/strap-base/trunk/debian/strap_base.1
trunk/packages/strap-base/trunk/debian/strap_to_clustal.1
trunk/packages/strap-base/trunk/debian/strap_to_fasta.1
trunk/packages/strap-base/trunk/debian/strap_to_html.1
trunk/packages/strap-base/trunk/debian/strap_to_msf.1
trunk/packages/strap-base/trunk/debian/strap_to_multiple_fasta.1
trunk/packages/strap-base/trunk/debian/strap_to_word.1
Log:
Simplified copyright. Updated man pages
Modified: trunk/packages/strap-base/trunk/debian/copyright
===================================================================
--- trunk/packages/strap-base/trunk/debian/copyright 2012-12-18 22:18:34 UTC (rev 12693)
+++ trunk/packages/strap-base/trunk/debian/copyright 2012-12-18 22:25:36 UTC (rev 12694)
@@ -21,21 +21,12 @@
********************************************************************************
Files: debian/* Copyright: © 2012 Christoph Gille License: GPL-3 #
********************************************************************************
-Files: 3d.png browser16.png ledgreen16.png
+Files: 3d.gif browser16.gif ledgreen16.gif
Source: http://www.phoca.cz/demo/gallery-categories/category/22-nuvola-icons
License: LGPL-2.1 Comment: On Debian systems, the complete text of the
Apache license can be found in '/usr/share/common-licenses/LGPL-2.1' #
********************************************************************************
-
-File: visible.png 1.png border_color.png compact_camera.png edit.png
- home.png scales.png stack_of_photos.png zip.png console.png end.png
- import.png mac_os.png scissors.png bug.png search.png umbrella.png
- apply16.png clipboard.png cursor_hand.png folder.png keyboard.png
- pdf.png services.png wifi.png close.png delete.png
- ruler.png settings2.png dna_helix.png globe.png
- lifebuoy.png sandglass.png settings2_26.png windows.png attach.png
- download.png line_chart.png save_as.png skip_to_start.png word.png
- add.png
+Files: *.png
Source: http://icons8.com/ http://www.visualpharm.com/
Citation from Web-site: Use Policy You can use it for your websites
and applications for free. Just link to either You can’t modify the
@@ -44,15 +35,15 @@
# ********************************************************************************
-File: astex.png
+File: astex.gif
Source: http://openastexviewer.net/
License: LPGL
# ********************************************************************************
-File: jmol.jpg
+File: jmol.gif
Source: http://sourceforge.net/projects/jmol/
License: LGPLv2
# ********************************************************************************
-File: pfam.png
+File: pfam.gif
Source: pfam.sanger.ac.uk/
License: Creative Commons Zero ("CC0") licence.
# ********************************************************************************
Modified: trunk/packages/strap-base/trunk/debian/strap_base.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_base.1 2012-12-18 22:18:34 UTC (rev 12693)
+++ trunk/packages/strap-base/trunk/debian/strap_base.1 2012-12-18 22:25:36 UTC (rev 12694)
@@ -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
@@ -135,8 +135,13 @@
-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 *"
@@ -198,16 +203,11 @@
\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
@@ -268,6 +268,23 @@
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
Modified: trunk/packages/strap-base/trunk/debian/strap_to_clustal.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_clustal.1 2012-12-18 22:18:34 UTC (rev 12693)
+++ trunk/packages/strap-base/trunk/debian/strap_to_clustal.1 2012-12-18 22:25:36 UTC (rev 12694)
@@ -1,4 +1,4 @@
-.\"" Do not edit this file. It has been generated from template.1 with /usr/bin/gpp
+.\"" Do not edit this file. It is generated by a script. Contact Christoph Gille for changes.
.TH strap_to_clustal 1 "Mai 2012"
.SH NAME
strap_to_clustal \- Reads amino acid sequences and creates a multiple sequence alignment file in clustal format.
@@ -66,14 +66,34 @@
the secondary structure to be displayed. This information is provided with script commands.
See http://www.bioinformatics.org/strap/strap4services.html for details.
-.SH LIMITATIONS
+If computations are performed within the script like alignment computations, then consider to use an SQL database for the cache rather than the default
+file based cache. This is described in http://www.bioinformatics.org/strap/cache.html.
-Currently, the cache for alignment results should be accessed only by one instance at a time.
-If several instances of Strap are run at the same time (e.g. from web server) the cache may become corrupted.
-Workaround: Deactivate the cache with the option -noCache.
-If you do need a cache in a web server environment, please send a request for feature to the author.
+
+
+
+.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 HOME-PAGE
http://3d-alignment.eu/
Modified: trunk/packages/strap-base/trunk/debian/strap_to_fasta.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_fasta.1 2012-12-18 22:18:34 UTC (rev 12693)
+++ trunk/packages/strap-base/trunk/debian/strap_to_fasta.1 2012-12-18 22:25:36 UTC (rev 12694)
@@ -1,4 +1,4 @@
-.\"" Do not edit this file. It has been generated from template.1 with /usr/bin/gpp
+.\"" Do not edit this file. It is generated by a script. Contact Christoph Gille for changes.
.TH strap_to_fasta 1 "Mai 2012"
.SH NAME
strap_to_fasta \- Reads amino acid sequences and creates a fasta formated sequence file for each sequence.
Modified: trunk/packages/strap-base/trunk/debian/strap_to_html.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_html.1 2012-12-18 22:18:34 UTC (rev 12693)
+++ trunk/packages/strap-base/trunk/debian/strap_to_html.1 2012-12-18 22:25:36 UTC (rev 12694)
@@ -1,4 +1,4 @@
-.\"" Do not edit this file. It has been generated from template.1 with /usr/bin/gpp
+.\"" Do not edit this file. It is generated by a script. Contact Christoph Gille for changes.
.TH strap_to_html 1 "Mai 2012"
.SH NAME
strap_to_html \- Reads amino acid sequences and creates an alignment view for web browsers.
@@ -74,6 +74,12 @@
In HTML output various information can be specified: Important positions can be highlighted, an icon for each protein and
the secondary structure to be displayed. This information is provided with script commands.
See http://www.bioinformatics.org/strap/strap4services.html for details.
+
+If computations are performed within the script like alignment computations, then consider to use an SQL database for the cache rather than the default
+file based cache. This is described in http://www.bioinformatics.org/strap/cache.html.
+
+
+
.SS Residue annotations in HTML alignment output.
Residue positions to be highlighted in the html output need to
@@ -83,14 +89,28 @@
used to attach information. The script may also be used to
define the [gapped] amino acid sequences.
-.SH LIMITATIONS
-Currently, the cache for alignment results should be accessed only by one instance at a time.
-If several instances of Strap are run at the same time (e.g. from web server) the cache may become corrupted.
-Workaround: Deactivate the cache with the option -noCache.
-If you do need a cache in a web server environment, please send a request for feature to the author.
+.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 HOME-PAGE
http://3d-alignment.eu/
Modified: trunk/packages/strap-base/trunk/debian/strap_to_msf.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_msf.1 2012-12-18 22:18:34 UTC (rev 12693)
+++ trunk/packages/strap-base/trunk/debian/strap_to_msf.1 2012-12-18 22:25:36 UTC (rev 12694)
@@ -1,4 +1,4 @@
-.\"" Do not edit this file. It has been generated from template.1 with /usr/bin/gpp
+.\"" Do not edit this file. It is generated by a script. Contact Christoph Gille for changes.
.TH strap_to_msf 1 "Mai 2012"
.SH NAME
strap_to_msf \- Reads amino acid sequences and creates a multiple sequence alignment file in msf format.
@@ -66,14 +66,34 @@
the secondary structure to be displayed. This information is provided with script commands.
See http://www.bioinformatics.org/strap/strap4services.html for details.
-.SH LIMITATIONS
+If computations are performed within the script like alignment computations, then consider to use an SQL database for the cache rather than the default
+file based cache. This is described in http://www.bioinformatics.org/strap/cache.html.
-Currently, the cache for alignment results should be accessed only by one instance at a time.
-If several instances of Strap are run at the same time (e.g. from web server) the cache may become corrupted.
-Workaround: Deactivate the cache with the option -noCache.
-If you do need a cache in a web server environment, please send a request for feature to the author.
+
+
+
+.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 HOME-PAGE
http://3d-alignment.eu/
Modified: trunk/packages/strap-base/trunk/debian/strap_to_multiple_fasta.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_multiple_fasta.1 2012-12-18 22:18:34 UTC (rev 12693)
+++ trunk/packages/strap-base/trunk/debian/strap_to_multiple_fasta.1 2012-12-18 22:25:36 UTC (rev 12694)
@@ -1,4 +1,4 @@
-.\"" Do not edit this file. It has been generated from template.1 with /usr/bin/gpp
+.\"" Do not edit this file. It is generated by a script. Contact Christoph Gille for changes.
.TH strap_to_multiple_fasta 1 "Mai 2012"
.SH NAME
strap_to_multiple_fasta \- Reads amino acid sequences and creates a multiple fast file.
@@ -66,14 +66,34 @@
the secondary structure to be displayed. This information is provided with script commands.
See http://www.bioinformatics.org/strap/strap4services.html for details.
-.SH LIMITATIONS
+If computations are performed within the script like alignment computations, then consider to use an SQL database for the cache rather than the default
+file based cache. This is described in http://www.bioinformatics.org/strap/cache.html.
-Currently, the cache for alignment results should be accessed only by one instance at a time.
-If several instances of Strap are run at the same time (e.g. from web server) the cache may become corrupted.
-Workaround: Deactivate the cache with the option -noCache.
-If you do need a cache in a web server environment, please send a request for feature to the author.
+
+
+
+.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 HOME-PAGE
http://3d-alignment.eu/
Modified: trunk/packages/strap-base/trunk/debian/strap_to_word.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_word.1 2012-12-18 22:18:34 UTC (rev 12693)
+++ trunk/packages/strap-base/trunk/debian/strap_to_word.1 2012-12-18 22:25:36 UTC (rev 12694)
@@ -1,4 +1,4 @@
-.\"" Do not edit this file. It has been generated from template.1 with /usr/bin/gpp
+.\"" Do not edit this file. It is generated by a script. Contact Christoph Gille for changes.
.TH strap_to_word 1 "Mai 2012"
.SH NAME
strap_to_word \- Reads amino acid sequences and creates an alignment view which can be edited in a word processor.
@@ -65,6 +65,12 @@
In HTML output various information can be specified: Important positions can be highlighted, an icon for each protein and
the secondary structure to be displayed. This information is provided with script commands.
See http://www.bioinformatics.org/strap/strap4services.html for details.
+
+If computations are performed within the script like alignment computations, then consider to use an SQL database for the cache rather than the default
+file based cache. This is described in http://www.bioinformatics.org/strap/cache.html.
+
+
+
.SS Residue annotations in HTML alignment output.
Residue positions to be highlighted in the html output need to
@@ -74,14 +80,28 @@
used to attach information. The script may also be used to
define the [gapped] amino acid sequences.
-.SH LIMITATIONS
-Currently, the cache for alignment results should be accessed only by one instance at a time.
-If several instances of Strap are run at the same time (e.g. from web server) the cache may become corrupted.
-Workaround: Deactivate the cache with the option -noCache.
-If you do need a cache in a web server environment, please send a request for feature to the author.
+.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 HOME-PAGE
http://3d-alignment.eu/
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