[med-svn] [euler-sr] 11/12: Re-add debian/ dir
Andreas Tille
tille at debian.org
Tue Dec 5 15:29:46 UTC 2017
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tille pushed a commit to branch master
in repository euler-sr.
commit ad099dce2b504588c83077e553649242ace9a372
Author: Andreas Tille <tille at debian.org>
Date: Tue Dec 5 16:27:47 2017 +0100
Re-add debian/ dir
---
debian/README.Debian | 8 ++++++++
debian/README.source | 5 +++++
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 20 ++++++++++++++++++++
debian/copyright | 42 +++++++++++++++++++++++++++++++++++++++++
debian/docs | 1 +
debian/install | 2 ++
debian/patches/20_gcc_4.3.patch | 22 +++++++++++++++++++++
debian/patches/series | 1 +
debian/rules | 23 ++++++++++++++++++++++
debian/upstream/metadata | 12 ++++++++++++
debian/watch | 5 +++++
13 files changed, 147 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..ec6b980
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,8 @@
+euler-sr for Debian
+-------------------
+
+Downloading the source tarball for Euler-SR needs registration at
+the website. So we provide here at least the packaging stuff to
+simplify building Debian packages.
+
+ -- Andreas Tille <tille at debian.org> Thu, 11 Dec 2008 09:51:31 +0200
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..b3c4dde
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,5 @@
+The tarball was downloaded from
+
+ https://web.archive.org/web/20110522113204/http://euler-assembler.ucsd.edu/euler-sr.1.1.2.tgz
+
+using the wayback machine since the project vanished from the web
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..d87f1b9
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+euler-sr (1.1.2-1) UNRELEASED; urgency=low
+
+ * Initial release
+
+ -- Andreas Tille <tille at debian.org> Tue, 05 Dec 2017 16:24:59 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..f599e28
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..cbba7fc
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,20 @@
+Source: euler-sr
+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 (>= 10)
+Standards-Version: 3.9.8
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/euler-sr/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/euler-sr/trunk/
+Homepage: http://cseweb.ucsd.edu/~ppevzner/software.html#EULER-short
+
+Package: euler-sr
+Architecture: any
+Section: science
+Depends: ${shlibs:Depends},
+ graphviz
+Description: correcting errors in short gene sequence reads and assembling them
+ The EULER-SR assembly package contains a suite of programs for
+ correcting errors in short reads and assembling them. Our assembler may
+ take as input classical Sanger reads, 454 sequences, and Illumina reads.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..68eccec
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,42 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: EULER-SR
+Upstream-Contact: Hong−Wen Deng <hdeng2 at tulane.edu>
+Source: http://euler-assembler.ucsd.edu/
+Comment: Download path failed at 2017-01-04
+
+Files: *
+Copyright: (C) 2001-2004 The Regents of the University of California.
+License: non_profit
+ Permission to use any part of this EULER V2.0 software for
+ educational, research and non-profit purposes, without fee, and
+ without a written agreement is hereby granted, provided that the above
+ copyright notice, this paragraph and the following three paragraphs
+ appear in all copies.
+ .
+ Those desiring to incorporate this EULER V2.0 software into commercial
+ products or use for other purposes not specified above should contact
+ the Technology Transfer & Intellectual Property Services, University
+ of California, San Diego, 9500 Gilman Drive, Mail Code 0910, La Jolla,
+ CA 92093-0910, Ph: (858) 534-5815, FAX: (858) 534-7345,
+ E-MAIL:invent at ucsd.edu.
+ .
+ IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY
+ FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES,
+ INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS EULER V2.0
+ SOFTWARE, EVEN IF THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE
+ POSSIBILITY OF SUCH DAMAGE.
+ .
+ THE EULER V2.0 SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND
+ THE UNIVERSITY OF CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE,
+ SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS. THE UNIVERSITY OF
+ CALIFORNIA MAKES NO REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY
+ KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR
+ PURPOSE, OR THAT THE USE OF THE EULER V2.0 SOFTWARE WILL NOT INFRINGE
+ ANY PATENT, TRADEMARK OR OTHER RIGHTS.
+
+Files: debian/*
+Copyright: 2008 Andreas Tille <tille at debian.org> on
+License: GPL
+X-Comment: On Debian systems, the complete text of the GNU General Public
+ License can be found in `/usr/share/common-licenses/GPL'.
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..7dc2f72
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+README.eulersr
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..0127d25
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,2 @@
+binary/* usr/lib/euler-sr
+assembly_utils/* usr/lib/euler-sr
diff --git a/debian/patches/20_gcc_4.3.patch b/debian/patches/20_gcc_4.3.patch
new file mode 100644
index 0000000..5140526
--- /dev/null
+++ b/debian/patches/20_gcc_4.3.patch
@@ -0,0 +1,22 @@
+--- euler-sr.orig/lib/utils.cpp
++++ euler-sr/lib/utils.cpp
+@@ -15,6 +15,7 @@
+ #include <istream>
+ #include <time.h>
+ #include <assert.h>
++#include <string.h>
+
+ using namespace std;
+
+--- euler-sr.orig/lib/tree/NewettTree.cpp
++++ euler-sr/lib/tree/NewettTree.cpp
+@@ -8,6 +8,9 @@
+ * All Rights Reserved
+ * See file LICENSE for details.
+ ***************************************************************************/
++
++#include <stdlib.h>
++
+ #include "NewettTree.h"
+ char Advance(std::ifstream &in) {
+ char next = in.peek();
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..a33e509
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+20_gcc_4.3.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..2ce25a1
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,23 @@
+#!/usr/bin/make -f
+
+MACHTYPE ?= $(shell dpkg-architecture -qDEB_BUILD_ARCH | sed s/i386/i686/)
+
+%:
+ dh $@
+
+override_dh_clean:
+ dh_clean
+ find . -type f -name "lib*.a" -exec rm -f \{\} \;
+ find . -type f -name ".exists" -exec rm -f \{\} \;
+ rm -f lib/make.[dfo][fie]*
+ rm -rf binary
+
+override_dh_auto_build:
+ mkdir -p binary
+ # copy with exception of *.o and *.a
+ (cd assembly; tar -cf - --exclude *.[ao] --exclude .exists $(MACHTYPE)) | (cd binary; tar xfBp -)
+ mv binary/$(MACHTYPE)/* binary
+ rm -rf binary/$(MACHTYPE)
+
+get-orig-source:
+ echo "You have to gegister to obtain the upstream source"
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..2b8e4ac
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Mark J. Chaisson and Pavel A. Pevzner
+ Title: Short read fragment assembly of bacterial genomes
+ Journal: Genome Research
+ Year: 2008
+ Volume: 18
+ Number: 2
+ Pages: 324-30
+ DOI: 10.1101/gr.7088808
+ PMID: 18083777
+ URL: http://genome.cshlp.org/content/early/2007/12/01/gr.7088808.abstract
+ eprint: http://genome.cshlp.org/content/early/2007/12/01/gr.7088808.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..4bc056e
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,5 @@
+version=4
+
+opts=dversionmangle=s/.*/0.No-Release/ \
+ https://people.debian.org/~eriberto/ FakeWatchNoUpstreamReleaseForThisPackage-(\d\S+)\.gz
+
--
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