[med-svn] r22079 - in trunk/packages/garli/trunk/debian: . bin

[Andreas Tille]

Author: tille
Date: 2016-06-02 20:28:05 +0000 (Thu, 02 Jun 2016)
New Revision: 22079

Added:
   trunk/packages/garli/trunk/debian/bin/
   trunk/packages/garli/trunk/debian/bin/garli
   trunk/packages/garli/trunk/debian/garli-examples.examples
   trunk/packages/garli/trunk/debian/garli.docs
   trunk/packages/garli/trunk/debian/garli.examples
   trunk/packages/garli/trunk/debian/garli.install
Modified:
   trunk/packages/garli/trunk/debian/clean
   trunk/packages/garli/trunk/debian/control
   trunk/packages/garli/trunk/debian/rules
Log:
Some progress in packaging


Added: trunk/packages/garli/trunk/debian/bin/garli
===================================================================
--- trunk/packages/garli/trunk/debian/bin/garli	                        (rev 0)
+++ trunk/packages/garli/trunk/debian/bin/garli	2016-06-02 20:28:05 UTC (rev 22079)
@@ -0,0 +1,15 @@
+#!/bin/sh
+
+if [ ! -e garli.conf ] ; then
+    cp -a /usr/share/doc/garli/examples/basic/garli.conf .
+    cat <<EOT
+You need to create a garli.conf file first.
+There was a basic example copied to your current directory which you
+most probably need to adapt.  For more information please read
+
+    zless /usr/share/doc/garli/QuickStart.txt*
+
+EOT
+    exit 1
+fi
+/usr/lib/garli/bin/Garli $*

Modified: trunk/packages/garli/trunk/debian/clean
===================================================================
--- trunk/packages/garli/trunk/debian/clean	2016-06-02 19:00:08 UTC (rev 22078)
+++ trunk/packages/garli/trunk/debian/clean	2016-06-02 20:28:05 UTC (rev 22079)
@@ -1,2 +1,5 @@
 tests/*.log
 tests/*.tre
+tests/*.check
+tests/out*.phy
+tests/test.out.*.nex

Modified: trunk/packages/garli/trunk/debian/control
===================================================================
--- trunk/packages/garli/trunk/debian/control	2016-06-02 19:00:08 UTC (rev 22078)
+++ trunk/packages/garli/trunk/debian/control	2016-06-02 20:28:05 UTC (rev 22079)
@@ -8,8 +8,8 @@
                libncl-dev (>= 2.1.18+dfsg-2),
                ncl-tools,
                bc
-Standards-Version: 3.9.6
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/garli/trunk/
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/garli/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/garle/trunk/
 Homepage: https://github.com/Ashod/garli
 
@@ -25,3 +25,17 @@
  score. It implements nucleotide, amino acid and codon-based models of
  sequence evolution, and runs on all platforms. The latest version adds
  support for partitioned models and morphology-like datatypes.
+
+Package: garli-examples
+Architecture: all
+Depends: ${misc:Depends}
+Description: phylogenetic analysis of molecular sequence data using maximum-likelihood (examples)
+ GARLI, Genetic Algorithm for Rapid Likelihood Inference is a program for
+ inferring phylogenetic trees. Using an approach similar to a classical
+ genetic algorithm, it rapidly searches the space of evolutionary trees
+ and model parameters to find the solution maximizing the likelihood
+ score. It implements nucleotide, amino acid and codon-based models of
+ sequence evolution, and runs on all platforms. The latest version adds
+ support for partitioned models and morphology-like datatypes.
+ .
+ This package contains example data for garli.

Added: trunk/packages/garli/trunk/debian/garli-examples.examples
===================================================================
--- trunk/packages/garli/trunk/debian/garli-examples.examples	                        (rev 0)
+++ trunk/packages/garli/trunk/debian/garli-examples.examples	2016-06-02 20:28:05 UTC (rev 22079)
@@ -0,0 +1 @@
+example/partition

Added: trunk/packages/garli/trunk/debian/garli.docs
===================================================================
--- trunk/packages/garli/trunk/debian/garli.docs	                        (rev 0)
+++ trunk/packages/garli/trunk/debian/garli.docs	2016-06-02 20:28:05 UTC (rev 22079)
@@ -0,0 +1 @@
+*.txt

Added: trunk/packages/garli/trunk/debian/garli.examples
===================================================================
--- trunk/packages/garli/trunk/debian/garli.examples	                        (rev 0)
+++ trunk/packages/garli/trunk/debian/garli.examples	2016-06-02 20:28:05 UTC (rev 22079)
@@ -0,0 +1 @@
+example/basic

Added: trunk/packages/garli/trunk/debian/garli.install
===================================================================
--- trunk/packages/garli/trunk/debian/garli.install	                        (rev 0)
+++ trunk/packages/garli/trunk/debian/garli.install	2016-06-02 20:28:05 UTC (rev 22079)
@@ -0,0 +1,2 @@
+usr/bin		usr/lib/garli
+debian/bin	usr

Modified: trunk/packages/garli/trunk/debian/rules
===================================================================
--- trunk/packages/garli/trunk/debian/rules	2016-06-02 19:00:08 UTC (rev 22078)
+++ trunk/packages/garli/trunk/debian/rules	2016-06-02 20:28:05 UTC (rev 22079)
@@ -1,22 +1,9 @@
 #!/usr/bin/make -f
 
-# DH_VERBOSE := 1
+DEBPKGNAME     := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
 
-# some helpful variables - uncomment them if needed
-# shamelessly stolen from http://jmtd.net/log/awk/
-#DEBVERS        := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
-#VERSION        := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
-#DEBFLAVOR      := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
-#DEBPKGNAME     := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
-#DEBIAN_BRANCH  := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
-#GIT_TAG        := $(subst ~,_,$(VERSION))
-
-# alternatively to manually set those variables, you can
-#  include /usr/share/dpkg/default.mk
-# and use what is set there.
-
 %:
 	dh $@ --with autoreconf
 
 override_dh_auto_configure:
-	dh_auto_configure -- --with-ncl=/usr
\ No newline at end of file
+	dh_auto_configure -- --with-ncl=/usr