[med-svn] r12832 - in trunk/packages/strap-base/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Thu Jan 24 08:36:29 UTC 2013
Author: tille
Date: 2013-01-24 08:36:29 +0000 (Thu, 24 Jan 2013)
New Revision: 12832
Added:
trunk/packages/strap-base/trunk/debian/patches/
trunk/packages/strap-base/trunk/debian/patches/manpages.patch
trunk/packages/strap-base/trunk/debian/patches/series
Log:
Fix lintian issues in upstream manpages
Added: trunk/packages/strap-base/trunk/debian/patches/manpages.patch
===================================================================
--- trunk/packages/strap-base/trunk/debian/patches/manpages.patch (rev 0)
+++ trunk/packages/strap-base/trunk/debian/patches/manpages.patch 2013-01-24 08:36:29 UTC (rev 12832)
@@ -0,0 +1,251 @@
+Author: Andreas Tille <tille at debian.org>
+Description: Fix lintian issues in upstream manpages
+
+--- a/man/strap_base.1
++++ b/man/strap_base.1
+@@ -86,13 +86,13 @@ refer to pdb-residue numbers use the Ras
+
+ Program options start with a dash. The values \fBtrue\fR and
+ \fBfalse\fR can be abbreviated by \fBt\fR and \fBf\fR. The "=true" or
+-"=t" can be ommitted. For example \fB-noSeqres=true\fR can be written
++"=t" can be omitted. For example \fB-noSeqres=true\fR can be written
+ as \fB-noSeqres=t\fR or \fB-noSeqres\fR. For most settings there is an
+ equivalent check-box or choice menu in the graphical user interface.
+
+ If the Web-start script http://www.bioinformatics.org/strap/strap.php
+ is started, the options are given as web-variable without the leading
+-dash. For example for -noSeqres include \fBnoSeqres=t\fR into the
++dash. For example for \fB-noSeqres\fR include \fBnoSeqres=t\fR into the
+ URL.
+
+ \fB-help\fR
+@@ -116,7 +116,7 @@ Do not load a sequence identical to an a
+ Opens a certain dialog at start.
+ The Java class name of a dialog is shown in the tool tip of the help button when the shift key is pressed.
+
+-Examples: -dialog=DialogAlign or -dialog=DialogBlast or or -dialog=DialogDotPlot
++Examples: \-dialog=DialogAlign or \-dialog=DialogBlast or or \-dialog=DialogDotPlot
+
+ \fB\-script\fR=\fIURL_or_FilePath_or_ScriptText\fR
+
+@@ -128,16 +128,16 @@ presence of a slash and the absence of w
+ Named pipes are accepted. See Interprocess communication for details.
+
+ Two or more script files are possible:
+--script5=\fIhttp://...../file\fR -script7=\fIhttp://...../file\fR.
++\-script5=\fIhttp://...../file\fR \-script7=\fIhttp://...../file\fR.
+ The optional number suffix defines the order of consecutively executed scripts.
+
+
+-A list of all script commands is printed with the program parameter -help=script.
++A list of all script commands is printed with the program parameter \-help=script.
+ Script commands can be given directly. Consider a few protein files
+ in PDB format loaded by Strap. The option
+--script="open_3D viewName, *"
+-would display all proteins with 3D-coordinates three-dimensionally
+-(See -v3d=). Scripts consisting of more than one line should be
++\-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.
+
+ If scripts are run on a server which allows many instances simultaneously,
+@@ -147,7 +147,7 @@ consider to use a database backend inste
+
+ Example:
+
+--script2="open_3D viewName, *" -script3="3D_select $ALL" -script7="3D_ribbons on" -script8="superimpose *"
++\-script2="open_3D viewName, *" \-script3="3D_select $ALL" \-script7="3D_ribbons on" \-script8="superimpose *"
+
+ \fB\-scriptOutput\fR=\fIoutput file name\fR
+
+@@ -165,26 +165,26 @@ Sets the Java class for superimposing pr
+
+ The short name or the full Java class name can be used such as "tm_align" for "Superimpose_TM_align".
+
+-Example: -s3d=tm_align or -s3d=ce or -s3d=gangstaplus
++Example: \-s3d=tm_align or \-s3d=ce or \-s3d=gangstaplus
+
+ \fB\-a3d\fR=\fIJavaClass\fR
+
+ Sets the Java class to compute structure based sequence alignments.
+
+-Examples: -a3d=tm_align or -a3d=mapsci or -a3d=matt or -a3d=mustang
++Examples: \-a3d=tm_align or \-a3d=mapsci or \-a3d=matt or \-a3d=mustang
+
+ \fB\-v3d\fR=\fIJavaClass\fR
+
+ Sets the Java class to display 3D-structures.
+
+-Example: -v3d=jmol or -v3d=pymol or -v3d=astex
++Example: \-v3d=jmol or \-v3d=pymol or \-v3d=astex
+
+ \fB\-aligner2\fR=\fIJavaClass\fR
+
+ Sets the Java class for aligning two amino acid sequences. Preferably an implementation in Java because native executables take longer to start.
+ Default value is PairAlignerNeoBioPROXY.
+
+-Example: -aligner2=MultipleAlignerClustalW
++Example: \-aligner2=MultipleAlignerClustalW
+
+
+ \fB\-alignerP\fR=\fIJavaClass\fR
+@@ -192,7 +192,7 @@ Example: -aligner2=MultipleAlignerClusta
+ Sets the Java class for aligning sequences and structures.
+ The default is clustalW.
+
+-Example: -alignerP=t_coffee
++Example: \-alignerP=t_coffee
+
+
+ \fB\-log3d\fR
+@@ -232,20 +232,20 @@ height 333, horizontal screen position 1
+
+ Examples:
+
+--laf=com.sun.java.swing.plaf.motif.MotifLookAndFeel ( or short -laf=m)
++\-laf=com.sun.java.swing.plaf.motif.MotifLookAndFeel ( or short \-laf=m)
+
+--laf=com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel ( or short -laf=N)
++\-laf=com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel ( or short \-laf=N)
+
+--laf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel ( or short -laf=G)
++\-laf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel ( or short \-laf=G)
+
+--laf=javax.swing.plaf.metal.MetalLookAndFeel ( or short -laf=M)
++\-laf=javax.swing.plaf.metal.MetalLookAndFeel ( or short \-laf=M)
+
+ Also non-standard Look-and-Feels can be used. Consider tinylaf which
+ can be installed as a Debian package. The following two options would
+ apply tinylaf:
+
+ \fB-cp=\fR/usr/share/java/tinylaf.jar
+--laf=de.muntjak.tinylookandfeel.TinyLookAndFeel
++\-laf=de.muntjak.tinylookandfeel.TinyLookAndFeel
+
+ See also http://en.wikipedia.org/wiki/Look_and_feel.
+
+@@ -256,7 +256,7 @@ Generates a sequence file in Fasta forma
+ .SS Interprocess communication
+
+ Strap can be controled from another application using named pipes.
+-The -script option does not only take files and URLS but also named
++The \-script option does not only take files and URLS but also named
+ pipes. Other applications can write script commands to the pipe which
+ are then executed by Strap.
+
+--- a/man/strap_to_clustal.1
++++ b/man/strap_to_clustal.1
+@@ -7,9 +7,9 @@ strap_to_clustal \- Reads amino acid seq
+
+ strap_to_clustal [\fIprotein or alignment files\fR]
+
+-strap_to_clustal [\fIprotein or alignment files\fR] -o=\fIoutput-file\fR
++strap_to_clustal [\fIprotein or alignment files\fR] \-o=\fIoutput-file\fR
+
+-strap_to_clustal [\fIprotein or alignment files\fR] -script="align *"
++strap_to_clustal [\fIprotein or alignment files\fR] \-script="align *"
+
+
+
+@@ -66,7 +66,7 @@ Instead of computing the alignment, the
+ In this case no sequence files need to be given and the align command is not required.
+ 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.
+-A list of all script commands is printed with the program parameter -help=script.
++A list of all script commands is printed with the program parameter \-help=script.
+ See http://www.bioinformatics.org/strap/alignment-to-html.html for details.
+
+ If computations are performed within the script and if more than one Strap instances are running at the same time,
+--- a/man/strap_to_html.1
++++ b/man/strap_to_html.1
+@@ -7,9 +7,9 @@ strap_to_html \- Reads amino acid sequen
+
+ strap_to_html [\fIprotein or alignment files\fR]
+
+-strap_to_html [\fIprotein or alignment files\fR] -o=\fIoutput-file\fR
++strap_to_html [\fIprotein or alignment files\fR] \-o=\fIoutput-file\fR
+
+-strap_to_html [\fIprotein or alignment files\fR] -script="align *"
++strap_to_html [\fIprotein or alignment files\fR] \-script="align *"
+
+
+
+@@ -66,7 +66,7 @@ Instead of computing the alignment, the
+ In this case no sequence files need to be given and the align command is not required.
+ 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.
+-A list of all script commands is printed with the program parameter -help=script.
++A list of all script commands is printed with the program parameter \-help=script.
+ See http://www.bioinformatics.org/strap/alignment-to-html.html for details.
+
+ If computations are performed within the script and if more than one Strap instances are running at the same time,
+--- a/man/strap_to_msf.1
++++ b/man/strap_to_msf.1
+@@ -7,9 +7,9 @@ strap_to_msf \- Reads amino acid sequenc
+
+ strap_to_msf [\fIprotein or alignment files\fR]
+
+-strap_to_msf [\fIprotein or alignment files\fR] -o=\fIoutput-file\fR
++strap_to_msf [\fIprotein or alignment files\fR] \-o=\fIoutput-file\fR
+
+-strap_to_msf [\fIprotein or alignment files\fR] -script="align *"
++strap_to_msf [\fIprotein or alignment files\fR] \-script="align *"
+
+
+
+@@ -66,7 +66,7 @@ Instead of computing the alignment, the
+ In this case no sequence files need to be given and the align command is not required.
+ 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.
+-A list of all script commands is printed with the program parameter -help=script.
++A list of all script commands is printed with the program parameter \-help=script.
+ See http://www.bioinformatics.org/strap/alignment-to-html.html for details.
+
+ If computations are performed within the script and if more than one Strap instances are running at the same time,
+--- a/man/strap_to_multiple_fasta.1
++++ b/man/strap_to_multiple_fasta.1
+@@ -7,9 +7,9 @@ strap_to_multiple_fasta \- Reads amino a
+
+ strap_to_multiple_fasta [\fIprotein or alignment files\fR]
+
+-strap_to_multiple_fasta [\fIprotein or alignment files\fR] -o=\fIoutput-file\fR
++strap_to_multiple_fasta [\fIprotein or alignment files\fR] \-o=\fIoutput-file\fR
+
+-strap_to_multiple_fasta [\fIprotein or alignment files\fR] -script="align *"
++strap_to_multiple_fasta [\fIprotein or alignment files\fR] \-script="align *"
+
+
+
+@@ -66,7 +66,7 @@ Instead of computing the alignment, the
+ In this case no sequence files need to be given and the align command is not required.
+ 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.
+-A list of all script commands is printed with the program parameter -help=script.
++A list of all script commands is printed with the program parameter \-help=script.
+ See http://www.bioinformatics.org/strap/alignment-to-html.html for details.
+
+ If computations are performed within the script and if more than one Strap instances are running at the same time,
+--- a/man/strap_to_word.1
++++ b/man/strap_to_word.1
+@@ -7,9 +7,9 @@ strap_to_word \- Reads amino acid sequen
+
+ strap_to_word [\fIprotein or alignment files\fR]
+
+-strap_to_word [\fIprotein or alignment files\fR] -o=\fIoutput-file\fR
++strap_to_word [\fIprotein or alignment files\fR] \-o=\fIoutput-file\fR
+
+-strap_to_word [\fIprotein or alignment files\fR] -script="align *"
++strap_to_word [\fIprotein or alignment files\fR] \-script="align *"
+
+
+
+@@ -66,7 +66,7 @@ Instead of computing the alignment, the
+ In this case no sequence files need to be given and the align command is not required.
+ 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.
+-A list of all script commands is printed with the program parameter -help=script.
++A list of all script commands is printed with the program parameter \-help=script.
+ See http://www.bioinformatics.org/strap/alignment-to-html.html for details.
+
+ If computations are performed within the script and if more than one Strap instances are running at the same time,
Added: trunk/packages/strap-base/trunk/debian/patches/series
===================================================================
--- trunk/packages/strap-base/trunk/debian/patches/series (rev 0)
+++ trunk/packages/strap-base/trunk/debian/patches/series 2013-01-24 08:36:29 UTC (rev 12832)
@@ -0,0 +1 @@
+manpages.patch
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