[med-svn] r22079 - in trunk/packages/garli/trunk/debian: . bin
Andreas Tille
tille at moszumanska.debian.org
Thu Jun 2 20:28:06 UTC 2016
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
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