[med-svn] [phast] 02/02: Initial Debian packaging

[Andreas Tille]

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tille pushed a commit to branch master
in repository phast.

commit d57a5470f2a96e6a75100f9e656644cc90b731b3
Author: Andreas Tille <tille at debian.org>
Date:   Thu Apr 21 10:39:59 2016 +0200

    Initial Debian packaging
---
 debian/changelog             |  5 +++++
 debian/compat                |  1 +
 debian/control               | 30 ++++++++++++++++++++++++++++++
 debian/copyright             | 11 +++++++++++
 debian/patches/lapacke.patch | 13 +++++++++++++
 debian/patches/series        |  1 +
 debian/rules                 | 22 ++++++++++++++++++++++
 debian/source/format         |  1 +
 debian/upstream/metadata     | 12 ++++++++++++
 debian/watch                 |  3 +++
 10 files changed, 99 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..2403071
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+phast (1.4-1) UNRELEASED; urgency=medium
+
+  * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org>  Thu, 21 Apr 2016 10:12:37 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..9701ba2
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,30 @@
+Source: phast
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+               liblapacke-dev,
+#               libf2c2-dev
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/phast.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/phast.git
+Homepage: http://compgen.cshl/edu/phast
+
+Package: phast
+Architecture: any
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
+Description: phylogenetic analysis with space/time models
+ PHAST is a software package for comparative and evolutionary genomics.
+ It consists of about half a dozen major programs, plus more than a dozen
+ utilities for manipulating sequence alignments, phylogenetic trees, and
+ genomic annotations. For the most part, PHAST focuses on two kinds of
+ applications: the identification of novel functional elements, including
+ protein-coding exons and evolutionarily conserved sequences; and
+ statistical phylogenetic modeling, including estimation of model
+ parameters, detection of signatures of selection, and reconstruction of
+ ancestral sequences.
+ .
+ PHAST does not support phylogeny reconstruction or sequence alignment,
+ and it is designed for use with DNA sequences only (see Comparison).
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..552ad2a
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,11 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: <pkg>
+Source: <path_to_download>
+
+Files: *
+Copyright: © 20xx-20yy <upstream>
+License: <license>
+
+Files: debian/*
+Copyright: © 2016 maintainername <maintainer at e.mail>
+License: <license>
diff --git a/debian/patches/lapacke.patch b/debian/patches/lapacke.patch
new file mode 100644
index 0000000..cedc904
--- /dev/null
+++ b/debian/patches/lapacke.patch
@@ -0,0 +1,13 @@
+--- a/include/external_libs.h
++++ b/include/external_libs.h
+@@ -39,8 +39,8 @@
+ #else
+ 
+ #ifndef SKIP_LAPACK 
+-#include <f2c.h>  
+-#include <clapack.h> 
++/* #include <f2c.h> */
++#include <lapacke.h> 
+ #define LAPACK_INT integer
+ #define LAPACK_DOUBLE doublereal
+ #endif  /*ifndef SKIP_LAPACK */
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..8a9a701
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+lapacke.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..1d11ebc
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,22 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+# 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 $@
+
+#get-orig-source:
+#	. debian/get-orig-source
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..d8b5812
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+  Author: 
+  Title: 
+  Journal: 
+  Year: 
+  Volume: 
+  Number: 
+  Pages: 
+  DOI: 
+  PMID:
+  URL: 
+  eprint: 
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..10211f3
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+https://github.com/CshlSiepelLab/phast/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)

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