[med-svn] r11112 - in trunk/packages/strap/trunk/debian: . bin2 man

Wed May 30 23:10:34 UTC 2012

Author: christophgil-guest
Date: 2012-05-30 23:10:33 +0000 (Wed, 30 May 2012)
New Revision: 11112

Added:
   trunk/packages/strap/trunk/debian/Sed.sh
   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
   trunk/packages/strap/trunk/debian/man/
   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
   trunk/packages/strap/trunk/debian/man/toXXX.1
   trunk/packages/strap/trunk/debian/strap.install
   trunk/packages/strap/trunk/debian/strap.manpages
Log:


Added: trunk/packages/strap/trunk/debian/Sed.sh
===================================================================

--- trunk/packages/strap/trunk/debian/Sed.sh	                        (rev 0)
+++ trunk/packages/strap/trunk/debian/Sed.sh	2012-05-30 23:10:33 UTC (rev 11112)
@@ -0,0 +1,12 @@
+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 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
+
+cat man/toXXX.1 | sed 's|toXXX|toMultipleFasta|1;s|FORMAT|multiple fasta|1;s|OUTPUT|A single file in multiple fasta format is written.|1' > man/strap_util_toMultipleFasta.1
+
+
+cat man/toXXX.1 | sed 's|toXXX|toFasta|1;s|FORMAT|fasta|1;s|OUTPUT|Fore each amino acid sequence a fasta file is generated.|1' > man/strap_util_toFasta.1
+


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

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 23:10:33 UTC (rev 11112)
@@ -0,0 +1,17 @@
+#! /bin/sh
+
+. /usr/lib/java-wrappers/java-wrappers.sh
+find_java_runtime java6
+
+# Java option max heap size 
+xmx=-Xmx100M
+
+for i in $*; do
+    if [ $i != ${i##-Xmx} ]; then xmx=$i; fi
+    if [ $i != ${i##-cp=} ]; then CP=${i##-cp=}":"$CP; fi
+done
+
+
+$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toClustal $*
+
+ 
\ No newline at end of file


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 23:10:33 UTC (rev 11112)
@@ -0,0 +1,17 @@
+#! /bin/sh
+
+. /usr/lib/java-wrappers/java-wrappers.sh
+find_java_runtime java6
+
+# Java option max heap size 
+xmx=-Xmx100M
+
+for i in $*; do
+    if [ $i != ${i##-Xmx} ]; then xmx=$i; fi
+    if [ $i != ${i##-cp=} ]; then CP=${i##-cp=}":"$CP; fi
+done
+
+
+$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toFasta $*
+
+ 
\ No newline at end of file


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 23:10:33 UTC (rev 11112)
@@ -0,0 +1,17 @@
+#! /bin/sh
+
+. /usr/lib/java-wrappers/java-wrappers.sh
+find_java_runtime java6
+
+# Java option max heap size 
+xmx=-Xmx100M
+
+for i in $*; do
+    if [ $i != ${i##-Xmx} ]; then xmx=$i; fi
+    if [ $i != ${i##-cp=} ]; then CP=${i##-cp=}":"$CP; fi
+done
+
+
+$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toMultipleFasta $*
+
+ 
\ No newline at end of file


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 23:10:33 UTC (rev 11112)
@@ -0,0 +1,17 @@
+#! /bin/sh
+
+. /usr/lib/java-wrappers/java-wrappers.sh
+find_java_runtime java6
+
+# Java option max heap size 
+xmx=-Xmx100M
+
+for i in $*; do
+    if [ $i != ${i##-Xmx} ]; then xmx=$i; fi
+    if [ $i != ${i##-cp=} ]; then CP=${i##-cp=}":"$CP; fi
+done
+
+
+$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -toXXX $*
+
+ 
\ No newline at end of file


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

Added: trunk/packages/strap/trunk/debian/man/strap_util_toClustal.1
===================================================================
--- trunk/packages/strap/trunk/debian/man/strap_util_toClustal.1	                        (rev 0)
+++ trunk/packages/strap/trunk/debian/man/strap_util_toClustal.1	2012-05-30 23:10:33 UTC (rev 11112)
@@ -0,0 +1,52 @@
+.TH strap_util_toClustal 1 "October 2011"
+.SH NAME
+
+
+Strap-utility \- Converts amino acid sequences to clustal format.
+
+.SH Synopsis
+
+.B strap_util_toFasta [\fIprotein_files\fR]
+
+.SH DESCRIPTION
+
+One or several amino acid sequences are loaded from files.
+Several file formats are supported: PDB, Swissprot, Embl, Genbank,
+GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom,
+Pfam, Stockholm and HSSP.
+A single file in clustal format is written.
+
+.SS Home-Page
+
+http://3d-alignment.eu/
+
+http://www.bioinformatics.org/strap/
+
+.SS File Compression
+
+The following file compression methods are supported: .gz, .bz2 and .Z
+
+.SS Parts of proteins
+
+To load only a subset of a proteins, a suffix is appended to the
+protein file name.  Residue subsets are specified by an exclamation
+mark and a subset expression after the protein file. Example:
+"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To
+refer to pdb-residue numbers use the Rasmol/Jmol syntax
+\fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A".
+
+.SH COPYRIGHT
+
+Christoph Gille \(co 1999-2011 
+
+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)

Added: trunk/packages/strap/trunk/debian/man/strap_util_toFasta.1
===================================================================
--- trunk/packages/strap/trunk/debian/man/strap_util_toFasta.1	                        (rev 0)
+++ trunk/packages/strap/trunk/debian/man/strap_util_toFasta.1	2012-05-30 23:10:33 UTC (rev 11112)
@@ -0,0 +1,52 @@
+.TH strap_util_toFasta 1 "October 2011"
+.SH NAME
+
+
+Strap-utility \- Converts amino acid sequences to fasta format.
+
+.SH Synopsis
+
+.B strap_util_toFasta [\fIprotein_files\fR]
+
+.SH DESCRIPTION
+
+One or several amino acid sequences are loaded from files.
+Several file formats are supported: PDB, Swissprot, Embl, Genbank,
+GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom,
+Pfam, Stockholm and HSSP.
+Fore each amino acid sequence a fasta file is generated.
+
+.SS Home-Page
+
+http://3d-alignment.eu/
+
+http://www.bioinformatics.org/strap/
+
+.SS File Compression
+
+The following file compression methods are supported: .gz, .bz2 and .Z
+
+.SS Parts of proteins
+
+To load only a subset of a proteins, a suffix is appended to the
+protein file name.  Residue subsets are specified by an exclamation
+mark and a subset expression after the protein file. Example:
+"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To
+refer to pdb-residue numbers use the Rasmol/Jmol syntax
+\fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A".
+
+.SH COPYRIGHT
+
+Christoph Gille \(co 1999-2011 
+
+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)

Added: trunk/packages/strap/trunk/debian/man/strap_util_toMultipleFasta.1
===================================================================
--- trunk/packages/strap/trunk/debian/man/strap_util_toMultipleFasta.1	                        (rev 0)
+++ trunk/packages/strap/trunk/debian/man/strap_util_toMultipleFasta.1	2012-05-30 23:10:33 UTC (rev 11112)
@@ -0,0 +1,52 @@
+.TH strap_util_toMultipleFasta 1 "October 2011"
+.SH NAME
+
+
+Strap-utility \- Converts amino acid sequences to multiple fasta format.
+
+.SH Synopsis
+
+.B strap_util_toFasta [\fIprotein_files\fR]
+
+.SH DESCRIPTION
+
+One or several amino acid sequences are loaded from files.
+Several file formats are supported: PDB, Swissprot, Embl, Genbank,
+GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom,
+Pfam, Stockholm and HSSP.
+A single file in multiple fasta format is written.
+
+.SS Home-Page
+
+http://3d-alignment.eu/
+
+http://www.bioinformatics.org/strap/
+
+.SS File Compression
+
+The following file compression methods are supported: .gz, .bz2 and .Z
+
+.SS Parts of proteins
+
+To load only a subset of a proteins, a suffix is appended to the
+protein file name.  Residue subsets are specified by an exclamation
+mark and a subset expression after the protein file. Example:
+"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To
+refer to pdb-residue numbers use the Rasmol/Jmol syntax
+\fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A".
+
+.SH COPYRIGHT
+
+Christoph Gille \(co 1999-2011 
+
+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)

Added: trunk/packages/strap/trunk/debian/man/toXXX.1
===================================================================
--- trunk/packages/strap/trunk/debian/man/toXXX.1	                        (rev 0)
+++ trunk/packages/strap/trunk/debian/man/toXXX.1	2012-05-30 23:10:33 UTC (rev 11112)
@@ -0,0 +1,52 @@
+.TH strap_util_toXXX 1 "October 2011"
+.SH NAME
+
+
+Strap-utility \- Converts amino acid sequences to FORMAT format.
+
+.SH Synopsis
+
+.B strap_util_toFasta [\fIprotein_files\fR]
+
+.SH DESCRIPTION
+
+One or several amino acid sequences are loaded from files.
+Several file formats are supported: PDB, Swissprot, Embl, Genbank,
+GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom,
+Pfam, Stockholm and HSSP.
+OUTPUT
+
+.SS Home-Page
+
+http://3d-alignment.eu/
+
+http://www.bioinformatics.org/strap/
+
+.SS File Compression
+
+The following file compression methods are supported: .gz, .bz2 and .Z
+
+.SS Parts of proteins
+
+To load only a subset of a proteins, a suffix is appended to the
+protein file name.  Residue subsets are specified by an exclamation
+mark and a subset expression after the protein file. Example:
+"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To
+refer to pdb-residue numbers use the Rasmol/Jmol syntax
+\fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A".
+
+.SH COPYRIGHT
+
+Christoph Gille \(co 1999-2011 
+
+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)

Added: trunk/packages/strap/trunk/debian/strap.install
===================================================================
--- trunk/packages/strap/trunk/debian/strap.install	                        (rev 0)
+++ trunk/packages/strap/trunk/debian/strap.install	2012-05-30 23:10:33 UTC (rev 11112)
@@ -0,0 +1,4 @@
+debian/bin/strap_util_toFasta      usr/bin
+debian/bin/strap_util_toMultipleFasta      usr/bin
+debian/bin/strap_util_toClustal      usr/bin
+


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

Added: trunk/packages/strap/trunk/debian/strap.manpages
===================================================================
--- trunk/packages/strap/trunk/debian/strap.manpages	                        (rev 0)
+++ trunk/packages/strap/trunk/debian/strap.manpages	2012-05-30 23:10:33 UTC (rev 11112)
@@ -0,0 +1,3 @@
+debian/man/strap_util_toFasta.1
+debian/man/strap_util_toMultipleFasta.1
+debian/man/strap_util_toClustal.1


