[med-svn] [mothur-lookup-files] 02/02: Initial packaging. These are the missing .pat files that used to be in the main Mothur source. See get-orig-source.

[Timothy Booth]

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tbooth-guest pushed a commit to branch master
in repository mothur-lookup-files.

commit 0c4a1480572261167cd36d7238cf0e5d0e7f8ef1
Author: Tim Booth <tbooth at ceh.ac.uk>
Date:   Mon Sep 14 11:54:55 2015 +0100

    Initial packaging.  These are the missing .pat files that used to be in
    the main Mothur source.  See get-orig-source.
---
 debian/changelog       | 12 ++++++++++++
 debian/compat          |  1 +
 debian/control         | 18 ++++++++++++++++++
 debian/copyright       | 10 ++++++++++
 debian/get-orig-source | 30 ++++++++++++++++++++++++++++++
 debian/install         |  1 +
 debian/rules           | 17 +++++++++++++++++
 debian/source/format   |  1 +
 8 files changed, 90 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..a46ac45
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,12 @@
+mothur-lookup-files (1-0biolinux2) trusty; urgency=medium
+
+  * Add conflict with old mothur, following guidance in policy
+    section 7.6.1
+
+ -- Tim Booth <tbooth at ceh.ac.uk>  Thu, 10 Sep 2015 16:18:02 +0100
+
+mothur-lookup-files (1-0biolinux1) trusty; urgency=medium
+
+  * Package to hold the lookup files required by Mothur.
+
+ -- Tim Booth <tbooth at ceh.ac.uk>  Thu, 10 Sep 2015 12:26:59 +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..a7711cb
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,18 @@
+Source: mothur-lookup-files
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Tim Booth <tbooth at ceh.ac.uk>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9), unzip
+Standards-Version: 3.9.5
+Homepage: http://www.mothur.org
+
+Package: mothur-lookup-files
+Architecture: all
+Depends: ${misc:Depends}
+Suggests: mothur
+Replaces: mothur (<< 1.36.0)
+Breaks: mothur (<< 1.36.0)
+Description: .pat lookup files for Mothur
+ If you are using Mothur on 454 data and running shhhercommand or
+ sffmultiplecommand then you will want these files.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..2981bf3
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,10 @@
+These are the lookup files that are needed to run shhh.flows.
+They were taken from Chris Quince's old site:
+http://userweb.eng.gla.ac.uk/christopher.quince/Software/PyroNoise.html
+
+The file formats are slightly different, but contain the same data.
+
+As these files are not creative works they are not subject to copyright.
+
+The files in debian/ were written by Tim Booth <tbooth at ceh.ac.uk> and may
+be re-used for any purpose with or without attribution.
diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100755
index 0000000..03e3c0c
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,30 @@
+#!/bin/sh
+# script to download the pattern files wanted by mothus as
+# a single .orig.tar.xz file.
+# The files should not change.  Bump the version if you add more.
+
+set -e
+
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=1
+
+if [ -z "$PKG" ] ; then
+    echo "Failed to parse debian/changelog"
+    exit 1
+fi
+
+mkdir -p ../tarballs
+cd ../tarballs
+#If we're running this I assume we want to re-download.
+rm -rf "$PKG"-"$VERSION"
+mkdir "$PKG"-"$VERSION"
+cd "$PKG"-"$VERSION"
+
+wget http://www.mothur.org/w/images/9/96/LookUp_Titanium.zip
+wget http://www.mothur.org/w/images/8/84/LookUp_GSFLX.zip
+wget http://www.mothur.org/w/images/7/7b/LookUp_GS20.zip
+
+cd ..
+tar -cvaf ../"$PKG"_"$VERSION".orig.tar.xz "$PKG"-"$VERSION"
+
+echo DONE
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..fcef1f1
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+lookupFiles/* /usr/share/mothur
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..77dc5e7
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,17 @@
+#!/usr/bin/make -f
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+	dh $@
+
+override_dh_auto_clean:
+	rm -rf lookupFiles
+
+override_dh_auto_build:
+	mkdir -p lookupFiles
+	cd lookupFiles && for f in ../*.zip ; do unzip "$$f" ; done
+
+get-orig-source:
+	./debian/get_original_source.sh
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)

-- 
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