[med-svn] [artfastqgenerator] 04/04: More packaging stuff
Andreas Tille
tille at debian.org
Tue Feb 16 13:24:37 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository artfastqgenerator.
commit da04a8ae08a98c07180fc78bc79309c9f77c8483
Author: Andreas Tille <tille at debian.org>
Date: Tue Feb 16 14:21:49 2016 +0100
More packaging stuff
---
debian/artfastqgenerator-doc.install | 1 +
debian/artfastqgenerator-examples.install | 1 +
debian/artfastqgenerator.links | 1 +
debian/control | 40 ++++++++++++++++++++++++++++---
debian/copyright | 24 +++++++++++++++----
debian/doc-base | 18 ++++++++++++++
debian/docs | 1 +
debian/jlibs | 1 +
debian/manifest | 6 +++++
debian/rules | 19 +++++----------
10 files changed, 92 insertions(+), 20 deletions(-)
diff --git a/debian/artfastqgenerator-doc.install b/debian/artfastqgenerator-doc.install
new file mode 100644
index 0000000..1d88d21
--- /dev/null
+++ b/debian/artfastqgenerator-doc.install
@@ -0,0 +1 @@
+doc/* usr/share/doc/artfastqgenerator/html
diff --git a/debian/artfastqgenerator-examples.install b/debian/artfastqgenerator-examples.install
new file mode 100644
index 0000000..062d12e
--- /dev/null
+++ b/debian/artfastqgenerator-examples.install
@@ -0,0 +1 @@
+*.fasta usr/share/doc/artfastqgenerator/examples
diff --git a/debian/artfastqgenerator.links b/debian/artfastqgenerator.links
new file mode 100644
index 0000000..7cb59aa
--- /dev/null
+++ b/debian/artfastqgenerator.links
@@ -0,0 +1 @@
+usr/share/java/artfastqgenerator.jar usr/bin/artfastqgenerator
diff --git a/debian/control b/debian/control
index 024ba81..a5131a8 100644
--- a/debian/control
+++ b/debian/control
@@ -3,15 +3,17 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 9)
+Build-Depends: debhelper (>= 9),
+ javahelper,
+ default-jdk
Standards-Version: 3.9.7
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/artfastqgenerator.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/artfastqgenerator.git
Homepage: https://sourceforge.net/projects/artfastqgen/
Package: artfastqgenerator
-Architecture: any
-Depends: ${shlibs:Depends},
+Architecture: all
+Depends: ${java:Depends},
${misc:Depends}
Description: ouputs artificial FASTQ files derived from a reference genome
ArtificialFastqGenerator takes the reference genome (in FASTA format) as
@@ -23,3 +25,35 @@ Description: ouputs artificial FASTQ files derived from a reference genome
insertions and deletions (indels)). This enables evaluation of a Next
Generation Sequencing (NGS) analysis pipeline which aligns reads to the
reference genome and then calls the variants.
+
+Package: artfastqgenerator-doc
+Architecture: all
+Depends: ${misc:Depends}
+Description: ouputs artificial FASTQ files derived from a reference genome (doc)
+ ArtificialFastqGenerator takes the reference genome (in FASTA format) as
+ input and outputs artificial FASTQ files in the Sanger format. It can
+ accept Phred base quality scores from existing FASTQ files, and use them
+ to simulate sequencing errors. Since the artificial FASTQs are derived
+ from the reference genome, the reference genome provides a gold-standard
+ for calling variants (Single Nucleotide Polymorphisms (SNPs) and
+ insertions and deletions (indels)). This enables evaluation of a Next
+ Generation Sequencing (NGS) analysis pipeline which aligns reads to the
+ reference genome and then calls the variants.
+ .
+ This package contains the Java API documentation for artfastqgenerator.
+
+Package: artfastqgenerator-examples
+Architecture: all
+Depends: ${misc:Depends}
+Description: ouputs artificial FASTQ files derived from a reference genome (examples)
+ ArtificialFastqGenerator takes the reference genome (in FASTA format) as
+ input and outputs artificial FASTQ files in the Sanger format. It can
+ accept Phred base quality scores from existing FASTQ files, and use them
+ to simulate sequencing errors. Since the artificial FASTQs are derived
+ from the reference genome, the reference genome provides a gold-standard
+ for calling variants (Single Nucleotide Polymorphisms (SNPs) and
+ insertions and deletions (indels)). This enables evaluation of a Next
+ Generation Sequencing (NGS) analysis pipeline which aligns reads to the
+ reference genome and then calls the variants.
+ .
+ This package contains example data for artfastqgenerator.
diff --git a/debian/copyright b/debian/copyright
index f545d38..c58a1f8 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,11 +1,27 @@
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: ArtificialFastqGenerator
+Upstream-Contact: Matthew Frampton <Matthew.Frampton at icr.ac.uk>
Source: https://sourceforge.net/projects/artfastqgen/files/
Files: *
-Copyright: © 20xx-20yy <upstream>
-License: <license>
+Copyright: 2010-2012 Matthew Frampton <Matthew.Frampton at icr.ac.uk>
+ Richard Houlston
+License: GPL-3+
Files: debian/*
-Copyright: © 2016 maintainername <maintainer at e.mail>
-License: <license>
+Copyright: 2016 Andreas Tille <tille at debian.org>
+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, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ On Debian systems you find a copy of the GNU General Public License
+ at /usr/share/common-licenses/GPL-3.
diff --git a/debian/doc-base b/debian/doc-base
new file mode 100644
index 0000000..a24d2a3
--- /dev/null
+++ b/debian/doc-base
@@ -0,0 +1,18 @@
+Document: artfastqgenerator
+Title: API documentation for artfastqgenerator
+Author: Matthew Frampton, Richard Houlston
+Abstract: ouputs artificial FASTQ files derived from a reference genome
+ ArtificialFastqGenerator takes the reference genome (in FASTA format) as
+ input and outputs artificial FASTQ files in the Sanger format. It can
+ accept Phred base quality scores from existing FASTQ files, and use them
+ to simulate sequencing errors. Since the artificial FASTQs are derived
+ from the reference genome, the reference genome provides a gold-standard
+ for calling variants (Single Nucleotide Polymorphisms (SNPs) and
+ insertions and deletions (indels)). This enables evaluation of a Next
+ Generation Sequencing (NGS) analysis pipeline which aligns reads to the
+ reference genome and then calls the variants.
+Section: Science/Biology
+
+Format: html
+Index: /usr/share/doc/artfastqgenerator/html/index.html
+Files: /usr/share/doc/artfastqgenerator/html/*
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..71dfd5b
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+README.txt
diff --git a/debian/jlibs b/debian/jlibs
new file mode 100644
index 0000000..77d57a4
--- /dev/null
+++ b/debian/jlibs
@@ -0,0 +1 @@
+artfastqgenerator.jar
diff --git a/debian/manifest b/debian/manifest
new file mode 100644
index 0000000..2a7fbc1
--- /dev/null
+++ b/debian/manifest
@@ -0,0 +1,6 @@
+/usr/share/java/artfastqgenerator.jar:
+ Main-Class: artificialFastqGenerator.Main
+
+
+
+
diff --git a/debian/rules b/debian/rules
index 40d2a0a..e8d48fe 100755
--- a/debian/rules
+++ b/debian/rules
@@ -2,21 +2,14 @@
# 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.
+DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
%:
- dh $@
+ dh $@ --with javahelper
+
+override_dh_auto_build:
+ javac artificialFastqGenerator/*.java && \
+ jar -cmf META-INF/MANIFEST.MF $(DEBPKGNAME).jar artificialFastqGenerator/*.class
get-orig-source:
. debian/get-orig-source
--
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