Author: tille Date: 2012-01-28 08:12:41 +0000 (Sat, 28 Jan 2012) New Revision: 9470
Added: trunk/packages/phy-spread/trunk/debian/manpages trunk/packages/phy-spread/trunk/debian/patches/encoding.patch trunk/packages/phy-spread/trunk/debian/phy-spread.1 Modified: trunk/packages/phy-spread/trunk/debian/changelog trunk/packages/phy-spread/trunk/debian/control trunk/packages/phy-spread/trunk/debian/patches/series Log: Added manpage Modified: trunk/packages/phy-spread/trunk/debian/changelog =================================================================== --- trunk/packages/phy-spread/trunk/debian/changelog 2012-01-28 07:19:45 UTC (rev 9469) +++ trunk/packages/phy-spread/trunk/debian/changelog 2012-01-28 08:12:41 UTC (rev 9470) @@ -2,4 +2,4 @@ * Initial release. (Closes: #657585) - -- Andreas Tille <[email protected]> Thu, 26 Jan 2012 18:51:29 +0100 + -- Andreas Tille <[email protected]> Sat, 28 Jan 2012 08:59:13 +0100 Modified: trunk/packages/phy-spread/trunk/debian/control =================================================================== --- trunk/packages/phy-spread/trunk/debian/control 2012-01-28 07:19:45 UTC (rev 9469) +++ trunk/packages/phy-spread/trunk/debian/control 2012-01-28 08:12:41 UTC (rev 9470) @@ -7,7 +7,7 @@ Build-Depends: debhelper (>= 8), javahelper (>=0.25), ant, ant-optional, openjdk-6-jdk | default-jdk, libcolorpicker-java, libjebl2-java, libcolt-java, - libprocessing-core-java + libprocessing-core-java, libkmlframework-java Standards-Version: 3.9.2 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/phy-spread/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/phy-spread/trunk/ Added: trunk/packages/phy-spread/trunk/debian/manpages =================================================================== --- trunk/packages/phy-spread/trunk/debian/manpages (rev 0) +++ trunk/packages/phy-spread/trunk/debian/manpages 2012-01-28 08:12:41 UTC (rev 9470) @@ -0,0 +1 @@ +debian/*.1 Added: trunk/packages/phy-spread/trunk/debian/patches/encoding.patch =================================================================== --- trunk/packages/phy-spread/trunk/debian/patches/encoding.patch (rev 0) +++ trunk/packages/phy-spread/trunk/debian/patches/encoding.patch 2012-01-28 08:12:41 UTC (rev 9470) @@ -0,0 +1,16 @@ +Author: Andreas Tille <[email protected]> +Date: Sat, 28 Jan 2012 08:59:13 +0100 +Description: Java called in a pbuilder environment just fails if + finding the '°' character in the comment - so it was replaced + +--- spread-1.0.2.orig/src/utils/Utils.java ++++ spread-1.0.2/src/utils/Utils.java +@@ -414,7 +414,7 @@ + // line + // gives + // dPhi=0 +- // if dLon over 180° take shorter rhumb across 180° meridian: ++ // if dLon over 180 degree take shorter rhumb across 180 degree meridian: + if (dLon > Math.PI) + dLon = 2 * Math.PI - dLon; + double distance = Math.sqrt(dLat * dLat + q * q * dLon * dLon) Modified: trunk/packages/phy-spread/trunk/debian/patches/series =================================================================== --- trunk/packages/phy-spread/trunk/debian/patches/series 2012-01-28 07:19:45 UTC (rev 9469) +++ trunk/packages/phy-spread/trunk/debian/patches/series 2012-01-28 08:12:41 UTC (rev 9470) @@ -1,2 +1,3 @@ follow_hint_from_README.patch build_xml.patch +encoding.patch Added: trunk/packages/phy-spread/trunk/debian/phy-spread.1 =================================================================== --- trunk/packages/phy-spread/trunk/debian/phy-spread.1 (rev 0) +++ trunk/packages/phy-spread/trunk/debian/phy-spread.1 2012-01-28 08:12:41 UTC (rev 9470) @@ -0,0 +1,28 @@ +.TH "SPREAD" "1" "01/28/2012" "SPREAD 1.0.2" "SPREAD Manual" +.SH "NAME" +spread \- analyze and visualize phylogeographic reconstructions +.SH "SYNOPSIS" +\fBphy-spread\fR +.SH "DESCRIPTION" +.PP +SPREAD is a user-friendly application to analyze and visualize +phylogeographic reconstructions resulting from Bayesian inference of +spatio-temporal diffusion. +.PP +There is a tutorial for SPREAD online at +http://www.kuleuven.be/aidslab/phylogeography/tutorial/spread_tutorial.html +.PP +Originally this program is named \fBspread\fR. However, there is just such a +package inside Debian and thus a '\fBphy-\fR' for phylogeny was prepended. +.SH "SEE ALSO" +.PP +\fBbeast-mcmc\fR(1)\&. +.SH "REFERENCES" +.PP +Bielejec F., Rambaut A., Suchard M.A & Lemey P. SPREAD: Spatial Phylogenetic Reconstruction of Evolutionary Dynamics. Bioinformatics, 2011. doi:10.1093 +.SH "AUTHORS" +.PP +The authors of the software \fBSPREAD\fR are Filip Bielejec, Andrew Rambaut, Marc A. Suchard, Philippe Lemey. +.PP +This manual page was written for the Debian distribution by +Andreas Tille <[email protected]>. It can be used freely by others. _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
