[med-svn] r7441 - trunk/packages/circos/trunk/debian
Charles Plessy
plessy at alioth.debian.org
Sat Aug 13 23:30:39 UTC 2011
Author: plessy
Date: 2011-08-13 23:30:39 +0000 (Sat, 13 Aug 2011)
New Revision: 7441
Added:
trunk/packages/circos/trunk/debian/circos.dirs
Removed:
trunk/packages/circos/trunk/debian/circos.1
trunk/packages/circos/trunk/debian/circos.manpages
Modified:
trunk/packages/circos/trunk/debian/rules
Log:
Use original manpage, despite the bad whatis entry.
I like the ASCII art :)
Deleted: trunk/packages/circos/trunk/debian/circos.1
===================================================================
--- trunk/packages/circos/trunk/debian/circos.1 2011-08-13 14:17:13 UTC (rev 7440)
+++ trunk/packages/circos/trunk/debian/circos.1 2011-08-13 23:30:39 UTC (rev 7441)
@@ -1,282 +0,0 @@
-.\" Automatically generated by Pod::Man 2.23 (Pod::Simple 3.14)
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-.\" ========================================================================
-.\"
-.IX Title "CIRCOS 1"
-.TH CIRCOS 1 "2011-07-12" "perl v5.12.4" "User Contributed Perl Documentation"
-.\" For nroff, turn off justification. Always turn off hyphenation; it makes
-.\" way too many mistakes in technical documents.
-.if n .ad l
-.nh
-.SH "NAME"
-circos \- generate publication\-quality, circularly\-composited plots
- of data and annotations layered on chromosome ideograms
-.SH "SYNOPSIS"
-.IX Header "SYNOPSIS"
-.Vb 1
-\& circos \-conf circos.conf [\-silent] [\-debug] [\-help] [\-man]
-.Ve
-.SH "DESCRIPTION"
-.IX Header "DESCRIPTION"
-This is a command line interface to Circos. Most settings are meant to be passed using a configuration file.
-.PP
-All command line options listed below can be defined in the configuration file. Defining them on the command line is useful when using a configuration template for many images.
-.SH QUICK STARTUP
-.IX Header "QUICK STARTUP"
-For a quick start, it is possible to use the given example. To do so, go to /usr/share/circos/example and run "circos -conf circos.conf". An image will be generated.
-.SH "OPTIONS"
-.IX Header "OPTIONS"
-.SS "Configuration"
-.IX Subsection "Configuration"
-.IP "\-configfile \s-1FILE\s0" 4
-.IX Item "-configfile FILE"
-Name of configuration file. This is required.
-.SS "Ideograms"
-.IX Subsection "Ideograms"
-.IP "\-chromosomes \s-1STRING\s0" 4
-.IX Item "-chromosomes STRING"
-.PD 0
-.IP "\-chromosomes_order \s-1STRING\s0" 4
-.IX Item "-chromosomes_order STRING"
-.IP "\-chromosomes_scale \s-1STRING\s0" 4
-.IX Item "-chromosomes_scale STRING"
-.IP "\-chromosomes_radius \s-1STRING\s0" 4
-.IX Item "-chromosomes_radius STRING"
-.PD
-Defines list, order, scale and radius of ideograms.
-.SS "Output Format"
-.IX Subsection "Output Format"
-.IP "\-png" 4
-.IX Item "-png"
-.PD 0
-.IP "\-24bit" 4
-.IX Item "-24bit"
-.IP "\-svg" 4
-.IX Item "-svg"
-.PD
-Toggles output of \s-1PNG\s0 and \s-1SVG\s0 files.
-.Sp
-When using transparency, make sure that \s-1PNG\s0 output is 24\-bit.
-.SS "Output Paths"
-.IX Subsection "Output Paths"
-.IP "\-outputdir \s-1DIR\s0" 4
-.IX Item "-outputdir DIR"
-.PD 0
-.IP "\-outputfile \s-1FILE\s0" 4
-.IX Item "-outputfile FILE"
-.PD
-Change the output directory and filename.
-.SS "Input Format"
-.IX Subsection "Input Format"
-.IP "\-file_delim \s-1DELIMITER\s0" 4
-.IX Item "-file_delim DELIMITER"
-Specify the file delimiter for all input data files. By default this
-is a space. Use a tab if you want to have multi-word records in the
-data files (e.g. multi word labels).
-.SS "Custom Fields"
-.IX Subsection "Custom Fields"
-.IP "\-usertext1 \s-1STRING\s0" 4
-.IX Item "-usertext1 STRING"
-.PD 0
-.IP "\-usertext2 \s-1STRING\s0" 4
-.IX Item "-usertext2 STRING"
-.IP "\-usertext3 \s-1STRING\s0" 4
-.IX Item "-usertext3 STRING"
-.IP "\-usertext4 \s-1STRING\s0" 4
-.IX Item "-usertext4 STRING"
-.PD
-Custom fields that can be used to change any string in the
-configuration file. The fields are referenced in the configuration
-file using \f(CW\*(C`_\|_$CONF{usertext1}_\|_\*(C'\fR, etc. This is useful if you are
-creating multiple versions of an image with different settings.
-.Sp
-For example, in the configuration file you can have
-.Sp
-.Vb 2
-\& <link segdup>
-\& radius = _\|_$CONF{usertext1}_\|_r
-.Ve
-.Sp
-and then call Circos
-.Sp
-.Vb 2
-\& bin/circos ... \-usertext1 0.9
-\& bin/circos ... \-usertext1 0.5
-.Ve
-.SS "Ticks"
-.IX Subsection "Ticks"
-.IP "\-show_ticks, \-noshow_ticks" 4
-.IX Item "-show_ticks, -noshow_ticks"
-.PD 0
-.IP "\-show_tick_labels, \-noshow_tick_labels" 4
-.IX Item "-show_tick_labels, -noshow_tick_labels"
-.PD
-Toggle display of ticks and tick labels.
-.SS "Image Maps"
-.IX Subsection "Image Maps"
-.IP "\-image_map_use" 4
-.IX Item "-image_map_use"
-.PD 0
-.IP "\-image_map_name \s-1MAPNAME\s0" 4
-.IX Item "-image_map_name MAPNAME"
-.IP "\-image_map_file \s-1FILE\s0" 4
-.IX Item "-image_map_file FILE"
-.IP "\-image_map_missing_parameter { exit | removeparam | removeurl }" 4
-.IX Item "-image_map_missing_parameter { exit | removeparam | removeurl }"
-.PD
-Controls image map settings. See
-.Sp
-.Vb 1
-\& http://mkweb.bcgsc.ca/circos/tutorials/lessons/image_maps
-.Ve
-.SS "Debugging"
-.IX Subsection "Debugging"
-.IP "\-silent" 4
-.IX Item "-silent"
-Generate no reporting.
-.IP "\-verbose" 4
-.IX Item "-verbose"
-Generate verbose reporting.
-.IP "\-debug" 4
-.IX Item "-debug"
-Turn on debugging output.
-.SH "AUTHOR"
-.IX Header "AUTHOR"
-Martin Krzywinski <martink at bcgsc.ca> <http://mkweb.bcgsc.ca>
-.SH "RESOURCES"
-.IX Header "RESOURCES"
-<http://mkweb.bcgsc.ca/circos>
-.SH "CITING"
-.IX Header "CITING"
-If you are using Circos in a publication, please cite as
-.PP
-Krzywinski, M., J. Schein, I. Birol, J. Connors, R. Gascoyne,
-D. Horsman, S. Jones, and M. Marra. 2009. Circos: an Information
-Aesthetic for Comparative Genomics. Genome Res 19:1639\-1645.
-.SH "CONTRIBUTORS"
-.IX Header "CONTRIBUTORS"
-Ken Youens-Clark <kyclark at gmail.com>
-.SH "SEE ALSO"
-.IX Header "SEE ALSO"
-Hive plots <http://www.hiveplot.com>
Added: trunk/packages/circos/trunk/debian/circos.dirs
===================================================================
--- trunk/packages/circos/trunk/debian/circos.dirs (rev 0)
+++ trunk/packages/circos/trunk/debian/circos.dirs 2011-08-13 23:30:39 UTC (rev 7441)
@@ -0,0 +1 @@
+usr/share/man/man1
Deleted: trunk/packages/circos/trunk/debian/circos.manpages
===================================================================
--- trunk/packages/circos/trunk/debian/circos.manpages 2011-08-13 14:17:13 UTC (rev 7440)
+++ trunk/packages/circos/trunk/debian/circos.manpages 2011-08-13 23:30:39 UTC (rev 7441)
@@ -1 +0,0 @@
-debian/circos.1
Modified: trunk/packages/circos/trunk/debian/rules
===================================================================
--- trunk/packages/circos/trunk/debian/rules 2011-08-13 14:17:13 UTC (rev 7440)
+++ trunk/packages/circos/trunk/debian/rules 2011-08-13 23:30:39 UTC (rev 7441)
@@ -16,6 +16,9 @@
find debian/circos -type f | xargs sed -i 's/include fonts/include \/usr\/share\/circos\/fonts/g'
find debian/circos -type f | xargs sed -i 's/include tiles/include \/usr\/share\/circos\/tiles/g'
+override_dh_installman:
+ pod2man bin/circos > $(CURDIR)/debian/circos/usr/share/man/man1/circos.1
+
override_dh_builddeb:
dh_builddeb -- -Z xz
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