[med-svn] [condetri] 01/01: Seems like I previously for got add something.
Steffen Möller
moeller at moszumanska.debian.org
Sun Mar 6 20:22:06 UTC 2016
This is an automated email from the git hooks/post-receive script.
moeller pushed a commit to branch master
in repository condetri.
commit 7bab4764200e02d70c2ee0b4bcc5776f54236d56
Author: Steffen Moeller <moeller at debian.org>
Date: Sun Mar 6 21:21:34 2016 +0100
Seems like I previously for got add something.
---
debian/README.Debian | 12 ++++++++++++
debian/changelog | 7 +++++++
debian/compat | 1 +
debian/condetri-doc.docs | 2 ++
debian/condetri.docs | 2 ++
debian/condetri.install | 2 ++
debian/control | 23 +++++++++++++++++++++++
debian/copyright | 11 +++++++++++
debian/rules | 22 ++++++++++++++++++++++
debian/source/format | 1 +
debian/upstream/edam | 14 ++++++++++++++
debian/upstream/metadata | 12 ++++++++++++
debian/watch | 12 ++++++++++++
13 files changed, 121 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..98f9b22
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,12 @@
+ConDeTri
+========
+
+Steffen is in contact with half the upstream authors to get the source
+tree in share for its redistribution with a Linux distribution. So far
+missing are:
+ * license information
+ * sources for the PDF
+which was communicated back after a look at version 2.3.
+
+ --
+ Steffen Moeller <moeller at debian.org> Sun, 06 Mar 2016 17:40:38 +0100
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..bf3b583
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,7 @@
+condetri (2.3-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #816925)
+ * The package is not yet ready for upload.
+ * Missing man pages.
+
+ -- Steffen Moeller <moeller at debian.org> Sun, 06 Mar 2016 16:58:42 +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/condetri-doc.docs b/debian/condetri-doc.docs
new file mode 100644
index 0000000..884f927
--- /dev/null
+++ b/debian/condetri-doc.docs
@@ -0,0 +1,2 @@
+MANUAL_ConDeTri.pdf
+wiki
diff --git a/debian/condetri.docs b/debian/condetri.docs
new file mode 100644
index 0000000..8840bf2
--- /dev/null
+++ b/debian/condetri.docs
@@ -0,0 +1,2 @@
+README.md
+wiki
diff --git a/debian/condetri.install b/debian/condetri.install
new file mode 100644
index 0000000..4281463
--- /dev/null
+++ b/debian/condetri.install
@@ -0,0 +1,2 @@
+condetri.pl usr/bin
+filterPCRdupl.pl usr/bin
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..bcd3caf
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,23 @@
+Source: condetri
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.7
+Vcs-Browser: git://anonscm.debian.org/cgit/debian-med/packages/condetri
+Vcs-Git: git://anonscm.debian.org/debian-med/packages/condetri
+Homepage: https://github.com/linneas/condetri/
+
+Package: condetri
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}, perl
+Description: straight-forward trimming of FASTQ sequences
+ This package is a simplistic contribution to the wealth of tools for
+ trimming of sequences of current Next-Generation-Sequencing data. It
+ was developed in the context of de novo whole-genome assembly.
+ .
+ The tool reads from the 3'-end and extract reads (or read pairs) of good
+ quality. If the reads are paired, the filtering is done pairwise, and
+ if one read in a pair has low quality, the remaining read is saved as
+ single end.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..e628cc7
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,11 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: condetri
+Source: https://github.com/linneas/condetri
+
+Files: *
+Copyright: © 2011-2015 Linnéa Smeds, Axel Künstner
+License: <license>
+
+Files: debian/*
+Copyright: © 2016 Steffen Moeller <moeller at debian.org>
+License: <license>
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/edam b/debian/upstream/edam
new file mode 100644
index 0000000..e1781b9
--- /dev/null
+++ b/debian/upstream/edam
@@ -0,0 +1,14 @@
+ontology: EDAM (1.12)
+topic:
+ - Sequencing
+scopes:
+ - name: summary
+ function:
+ - Sequence trimmimg
+ - Sequencing quality control
+ inputs:
+ - data: Sequence
+ formats: [FASTQ]
+ outputs:
+ - data: Sequence
+ formats: [FASTQ]
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..4b2a3b6
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Linnéa Smeds, Axel Künstner
+ Title: ConDeTri - A Concent Dependent Read Trimmer for Illumina Data
+ Journal: PLoS ONE
+ Year: 2011
+ Volume: 6
+ Number: 10
+ Pages: e26314
+ DOI: 10.1371/journal.pone.0026314
+ PMID: 22039460
+ URL: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0026314
+ eprint: http://journals.plos.org/plosone/article/asset?id=10.1371%2Fjournal.pone.0026314.PDF
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..1c45dfd
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,12 @@
+version=3
+
+# Uncomment to find new files on Github
+# - when using releases:
+https://github.com/linneas/condetri/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+
+# if tweaking of source is needed
+# \
+# debian debian/get-orig-source
+
+# if you need to repack and choose +dfsg prefix
+# opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,compress=xz" \
--
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