[med-svn] [gwamar] 02/02: Add initial Debian packaging
Andreas Tille
tille at debian.org
Sat Nov 21 16:22:30 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository gwamar.
commit cbd77079f786fd35eb66c448578c400fcc74d547
Author: Andreas Tille <tille at debian.org>
Date: Sat Nov 21 13:02:24 2015 +0100
Add initial Debian packaging
---
debian/bin/gwamar | 2 ++
debian/changelog | 5 ++++
debian/compat | 1 +
debian/control | 29 ++++++++++++++++++++++
debian/copyright | 14 +++++++++++
debian/install | 5 ++++
.../adapt_debian_locations_of_binaries.patch | 23 +++++++++++++++++
debian/patches/series | 1 +
debian/rules | 7 ++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 +++++++++
debian/watch | 6 +++++
12 files changed, 106 insertions(+)
diff --git a/debian/bin/gwamar b/debian/bin/gwamar
new file mode 100644
index 0000000..6a6d522
--- /dev/null
+++ b/debian/bin/gwamar
@@ -0,0 +1,2 @@
+#!/bin/sh
+python /usr/share/gwamar/gwamar.py $@
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..dec47cb
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+gwamar (1.14+dfsg-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Sat, 21 Nov 2015 12:31:04 +0100
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..182c9b3
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,29 @@
+Source: gwamar
+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),
+ dh-python,
+ python-all-dev
+Standards-Version: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/gwamar.git
+Vcs-Git: git://anonscm.debian.org/debian-med/gwamar.git
+Homepage: http://bioputer.mimuw.edu.pl/gwamar/
+
+Package: gwamar
+Architecture: any
+Depends: ${misc:Depends},
+ ${python:Depends},
+ phylip,
+ raxml,
+ phyml
+Description: genome-wide assessment of mutations associated with drug resistance in bacteria
+ GWAMAR is a tool for detecting of drug resistance-associated mutations
+ in bacteria through comparative analysis of whole-genome sequences. The
+ pipeline of GWAMAR comprises several steps. First, for a set of closely
+ related bacterial genomes, it employs eCAMBer to identify homologous
+ gene families. Second, based on multiple alignments of the gene
+ families, it identifies mutations among the strains of interest. Third,
+ it calculates several statistics to identify which mutations are the
+ most associated with drug resistance.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..f37d95a
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,14 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: <pkg>
+Upstream-Contact: m.wozniak at mimuw.edu.pl
+Source: https://bitbucket.org/mimowo/gwamar
+Files-Excluded: */*/__pycache__
+ *.pyc
+
+Files: *
+Copyright: 20xx-20yy <upstream>
+License: <license>
+
+Files: debian/*
+Copyright: 2015 Andreas Tille <tille at debian.org>
+License: <license>
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..fdad0da
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,5 @@
+*.py usr/share/gwamar
+src usr/share/gwamar
+config usr/share/gwamar
+datasets usr/share/gwamar
+debian/bin usr
diff --git a/debian/patches/adapt_debian_locations_of_binaries.patch b/debian/patches/adapt_debian_locations_of_binaries.patch
new file mode 100644
index 0000000..bb3c34b
--- /dev/null
+++ b/debian/patches/adapt_debian_locations_of_binaries.patch
@@ -0,0 +1,23 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 21 Nov 2015 12:31:04 +0100
+Description: Adapt local PATHes of authors to Debian locations
+
+--- a/config/config_params.txt
++++ b/config/config_params.txt
+@@ -32,12 +32,12 @@ A_OUTPUT_TYPE:txt
+
+ TREE_ID:
+ CMP_PROFILES:Fluoroquinolones,Streptomycin,Isoniazid,Ethambutol,Rifampicin,Pyrazinamide # drug resistance profiles used for comparison
+-PHYLIP_PATH:/home/misias/phylip/exe/
++PHYLIP_PATH:/usr/lib/phylip/bin/
+ PHYLIP_EXE:PHYLIP_PATH:/dnamlk
+-PHYML_PATH:/home/misias/phyml/
++PHYML_PATH:/usr/bin
+ PHYML_EXE:PHYML_PATH:/phyml
+-RAXML_PATH:/home/misias/raxml/
+-RAXML_EXE:RAXML_PATH:/raxml
++RAXML_PATH:/usr/bin
++RAXML_EXE:RAXML_PATH:/raxmlHPC
+ RAXML_REP:11
+ RAXML_TYPE:MR
+ TREE_SOFT:phyml
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..fc58033
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+adapt_debian_locations_of_binaries.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..4eb5571
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,7 @@
+#!/usr/bin/make -f
+
+%:
+ dh $@ --with python2
+
+get-orig-source:
+ uscan --verbose --force-download --repack --compress xz
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..814681b
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,6 @@
+version=3
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g" \
+ http://bioputer.mimuw.edu.pl/gwamar/software.html software/gwamar_v([\d.]+)/gwamar\.zip
+
+# https://bitbucket.org/mimowo/gwamar/downloads .*/(\d\S*)\.tar\.gz
--
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