[med-svn] [SCM] grinder branch, master, updated. 6c40bfc7e3f31f3cca6930f6c2b4c8c27cb98136

Fri Jan 20 01:21:14 UTC 2012

The following commit has been merged in the master branch:
commit 6c40bfc7e3f31f3cca6930f6c2b4c8c27cb98136
Author: Florent Angly <florent.angly at gmail.com>
Date:   Fri Jan 20 11:21:55 2012 +1000

    Created Debian files

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..ba96811
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+grinder (0.4.4-1) UNRELEASED; urgency=low
+
+  * Initial Release. Closes: #654394
+
+ -- Florent Angly <florent.angly at gmail.com>  Fri, 20 Jan 2012 10:24:54 +1000
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..45a4fb7
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+8
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..b67a071
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,37 @@
+Source: grinder
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Florent Angly <florent.angly at gmail.com>
+DM-Upload-Allowed: yes
+Build-Depends: debhelper (>= 8)
+Build-Depends-Indep: libbio-perl-perl,
+ libgetopt-euclid-perl (>= 0.2.8),
+ libmath-random-mt-perl (>= 1.13),
+ perl,
+ help2man
+Standards-Version: 3.9.2
+Homepage: http://sourceforge.net/projects/biogrinder/
+Vcs-Git: git://git.debian.org/debian-med/grinder.git
+Vcs-Browser: http://git.debian.org/?p=debian-med/grinder.git
+
+Package: grinder
+Architecture: all
+Depends: ${misc:Depends}, ${perl:Depends},
+ libbio-perl-perl,
+ libgetopt-euclid-perl (>= 0.2.8),
+ libmath-random-mt-perl (>= 1.13),
+ perl
+Description: Versatile omics shotgun and amplicon sequencing read simulator
+ Grinder is a versatile program to create random shotgun and amplicon sequence
+ libraries based on DNA, RNA or proteic reference sequences provided in a
+ FASTA file.
+ .
+ Grinder can produce genomic, metagenomic, transcriptomic, metatranscriptomic,
+ proteomic, metaproteomic shotgun and amplicon datasets from current
+ sequencing technologies such as Sanger, 454, Illumina. These simulated
+ datasets can be used to test the accuracy of bioinformatic tools under
+ specific hypothesis, e.g. with or without sequencing errors, or with low or
+ high community diversity. Grinder may also be used to help decide between
+ alternative sequencing methods for a sequence-based project, e.g. should the
+ library be paired-end or not, how many reads should be sequenced.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..e62d728
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,21 @@
+Format-Specification: http://anonscm.debian.org/viewvc/dep/web/deps/dep5.mdwn?view=markup&pathrev=135
+Maintainer: Florent Angly <florent.angly at gmail.com>
+Source: http://sourceforge.net/projects/biogrinder/files/
+Name: Grinder
+
+Files: *
+Copyright: Florent Angly <florent.angly at gmail.com>
+License: GPL-3+
+
+Files: debian/*
+Copyright: 2012, Florent Angly <florent.angly at gmail.com>
+License: GPL-3+
+
+License: GPL-3+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; version 3 dated June, 2007, or (at your
+ option) any later version.
+ .
+ On Debian systems, the complete text of version 3 of the GNU General
+ Public License can be found in `/usr/share/common-licenses/GPL-3'.
diff --git a/debian/grinder.docs b/debian/grinder.docs
new file mode 100644
index 0000000..ea4c277
--- /dev/null
+++ b/debian/grinder.docs
@@ -0,0 +1,2 @@
+README.htm
+README
diff --git a/debian/grinder.manpages b/debian/grinder.manpages
new file mode 100644
index 0000000..7eba1b2
--- /dev/null
+++ b/debian/grinder.manpages
@@ -0,0 +1 @@
+debian/man/grinder.1 debian/man/average_genome_size.1 debian/man/change_paired_read_orientation.1
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..23ef15c
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,55 @@
+#!/usr/bin/make -f
+
+PACKAGE = grinder
+AUTHOR  = Florent Angly <florent.angly at gmail.com>
+VERSION = 0.4.2
+SECTION = 1
+MANDIR  = debian/man
+
+NAME1   = $(PACKAGE)
+SCRIPT1 = script/$(NAME1)
+DESC1   = 'Versatile omics shotgun and amplicon sequencing read simulator'
+MAN1    = $(MANDIR)/$(NAME1).$(SECTION)
+
+NAME2   = average_genome_size
+SCRIPT2 = utils/$(NAME2)
+DESC2   = 'Calculate the average genome size in Grinder libraries'
+MAN2    = $(MANDIR)/$(NAME2).$(SECTION)
+
+NAME3   = change_paired_read_orientation
+SCRIPT3 = utils/$(NAME3)
+DESC3   = 'Reverses the orientation of each paired\-end FASTA sequence'
+MAN3    = $(MANDIR)/$(NAME3).$(SECTION)
+
+define MORE
+[author]
+$(AUTHOR)
+[see also]
+.BR grinder (7),
+.BR $(NAME1) ($(SECTION)),
+.BR $(NAME2) ($(SECTION))
+and
+.BR $(NAME3) ($(SECTION)).
+endef
+export MORE
+MOREFILE = $(MANDIR)/more.$(SECTION)
+
+
+%:
+	dh $@
+
+# Because of Grinder's random output, some tests may fail... Skip all tests.
+override_dh_auto_test:
+
+override_dh_auto_build:
+	mkdir -p $(MANDIR)
+	echo "$$MORE" > $(MOREFILE)
+	help2man --no-discard-stderr --name $(DESC1) --section $(SECTION) --version-string $(VERSION) --no-info --include $(MOREFILE) --output $(MAN1) $(SCRIPT1)
+	help2man --no-discard-stderr --name $(DESC2) --section $(SECTION) --version-string $(VERSION) --no-info --include $(MOREFILE) --output $(MAN2) $(SCRIPT2)
+	help2man --no-discard-stderr --name $(DESC3) --section $(SECTION) --version-string $(VERSION) --no-info --include $(MOREFILE) --output $(MAN3) $(SCRIPT3)
+	rm $(MOREFILE)
+	echo $(MAN1) $(MAN2) $(MAN3) > debian/$(PACKAGE).manpages
+	dh_auto_build
+
+override_dh_auto_clean:
+	rm -rf $(MANDIR)
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..14308be
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,2 @@
+version=3
+http://sf.net/biogrinder/Grinder-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$

-- 
Versatile shotgun and amplicon read simulator

