debian/changelog

-gmap (2018-07-04-1) UNRELEASED; urgency=medium
+gmap (2018-07-04-1) unstable; urgency=medium
 
+  [ Steffen Möller ]
+  * Updated bio.tools RRID in d/u/metadata
+  * Update metadata
+
+  [ Andreas Tille ]
   * Cleanup d/rules
   * New upstream version
   * debhelper 11
   * Point Vcs fields to salsa.debian.org
   * Standards-Version: 4.1.5
-  * libgmap1-dev Depends: gmap, libgmap1 (instead of alternative)
-    Closes: #903793
 
- -- Andreas Tille <tille@debian.org>  Tue, 17 Jul 2018 07:24:19 +0200
+  [ Alexandre Mestiashvili ]
+  * Refresh patches
+  * d/control:
+    - update Uploader's email
+    - drop libgmap1{,-dev} as there is no use cases so far
+      Closes: #903793
+  * Update d/rules:
+    - remove --enable-shared as we dropped libgmap1
+    - add stanza to install tests files to examples
+  * Remove install files for libgmap1*
+  * Update d/copyright, remove section for src/saca-k*, update email
+  * Update lintian-overrides, remove *.nosimd binaries
+  * Update d/filter.pl to fix gmap man page
+  * Add autopkgtest
+
+ -- Alexandre Mestiashvili <mestia@debian.org>  Tue, 17 Jul 2018 17:07:39 +0200
 
 gmap (2017-11-15-1) unstable; urgency=medium
 

debian/control

@@ -2,7 +2,7 @@ Source: gmap
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Shaun Jackman <sjackman@debian.org>,
            Andreas Tille <tille@debian.org>,
-           Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
+           Alexandre Mestiashvili <mestia@debian.org>
 Section: non-free/science
 XS-Autobuild: no
 Priority: optional
@@ -32,36 +32,3 @@ Description: spliced and SNP-tolerant alignment for mRNA and short reads
   * known splice sites and identify novel splice sites.
   * known single-nucleotide polymorphisms (SNPs).
  GSNAP can align bisulfite-treated DNA.
-
-Package: libgmap1
-Architecture: any
-Section: non-free/libs
-Depends: ${misc:Depends},
-         ${shlibs:Depends}
-Description: library for gmap tool
- This package contains library for gmap tool.
- GMAP (Genomic Mapping and Alignment Program) is a tool for aligning
- EST, mRNA and cDNA sequences.
- GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for
- aligning single-end and paired-end transcriptome reads.
- Both tools can use a database of
-  * known splice sites and identify novel splice sites.
-  * known single-nucleotide polymorphisms (SNPs).
- GSNAP can align bisulfite-treated DNA.
-
-Package: libgmap1-dev
-Architecture: any
-Section: non-free/libdevel
-Depends: gmap (= ${binary:Version}),
-         libgmap1 (= ${binary:Version}),
-         ${misc:Depends}
-Description: development files for gmap
- This package contains header files for gmap.
- GMAP (Genomic Mapping and Alignment Program) is a tool for aligning
- EST, mRNA and cDNA sequences.
- GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for
- aligning single-end and paired-end transcriptome reads.
- Both tools can use a database of
-  * known splice sites and identify novel splice sites.
-  * known single-nucleotide polymorphisms (SNPs).
- GSNAP can align bisulfite-treated DNA.

debian/copyright

@@ -2,6 +2,8 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: GMAP
 Upstream-Contact: Thomas Wu <twu@gene.com>, Colin K. Watanabe <ckw@gene.com>
 Source: http://research-pub.gene.com/gmap/
+Comment: gmap is in contirb/non-free due to the license,
+ see also https://lists.debian.org/debian-med/2017/09/msg00013.html
 
 Files: *
 Copyright: 2011-2014 Genentech, Inc.
@@ -105,27 +107,6 @@ License: X11
  dealings in this Software without prior written authorization from the X
  Consortium.
 
-Files: src/saca-k*
-Copyright: 2012 Ge Nong <issng@mail.sysu.edu.cn>
-License: Expat
- Permission is hereby granted, free of charge, to any person obtaining a copy
- of this software and associated documentation files (the "Software"), to deal
- in the Software without restriction, including without limitation the rights
- to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- copies of the Software, and to permit persons to whom the Software is
- furnished to do so, subject to the following conditions:
- .
- The above copyright notice and this permission notice shall be included in
- all copies or substantial portions of the Software.
- .
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- THE SOFTWARE.
-
 Files: src/fastlog.h
 Copyright: 2012 Paul Mineiro <paul@mineiro.com>
 License: BSD-3-clause
@@ -165,7 +146,7 @@ License: BSD-3-clause
 Files: debian/*
 Copyright: 2011 Shaun Jackman <sjackman@debian.org>
            2012-2014 Andreas Tille <tille@debian.org>
-           2016 Alex Mestiashvili <alex@biotec.tu-dresden.de>
+           2016 Alex Mestiashvili <mestia@debian.org>
 License: ISC
  Permission to use, copy, modify, and/or distribute this software for any
  purpose with or without fee is hereby granted, provided that the above

debian/filter.pl

@@ -30,7 +30,15 @@ while ( <STDIN> ) {
     s/(^5\s{6}see\snote\s.*)/           $1/gmxs;
     s/(^Examples:\n\.TP)/\.TP\n$1/gmsx;
     s/(.*be\schanged)\n\.TP\n(by\sproviding.*)/$1 $2/gmsx;
+    #gmap aligning
     #fix gmap_build header
+    #s/(^Batch\smode\s\(default\s=\s2\)\n)(Mode.*)/$1\n         $2/gmxs;
+    s/(^\.TP\n)(0)(\n)(mmap\s.*)/           $2      $4/gmxs;
+    s/(^\.TP\n)(1)(\n)(mmap\s.*)/           $2      $4/gmxs;
+    s/(^\.TP\n)(\(default\))(\n)(2\s{6}mmap.*)/ $2 $4/gmxs;
+    s/(^3\s{6}allocate.*)/           $1/gmxs;
+    s/(^4\s{6}allocate.*)/           $1/gmxs;
+    s/(^5\s{6}allocate.*)/           $1/gmxs;
     s/(^\.SH\sDESCRIPTION\n)Unknown.*\.PP/$1/gmsx;
     print;
 }

debian/gmap.install

-usr/lib/gmap/* usr/lib/gmap

debian/gmap.lintian-overrides

 gmap: binary-without-manpage usr/bin/gmap.sse41
-gmap: binary-without-manpage usr/bin/gmap.nosimd
 gmap: binary-without-manpage usr/bin/gsnap.sse41
-gmap: binary-without-manpage usr/bin/gsnap.nosimd
 gmap: binary-without-manpage usr/bin/gmapl
 gmap: binary-without-manpage usr/bin/gmapl.sse41
-gmap: binary-without-manpage usr/bin/gmapl.nosimd
 gmap: binary-without-manpage usr/bin/gsnapl
 gmap: binary-without-manpage usr/bin/gsnapl.sse41
-gmap: binary-without-manpage usr/bin/gsnapl.nosimd

debian/libgmap1-dev.install

-#! /usr/bin/dh-exec
-usr/include/* usr/include/gmap
-src/.libs/libgmap.a usr/lib/${DEB_HOST_MULTIARCH}
-src/.libs/libgmap.so usr/lib/${DEB_HOST_MULTIARCH}
-

debian/libgmap1.install

-#! /usr/bin/dh-exec
-src/.libs/libgmap.so.1 usr/lib/${DEB_HOST_MULTIARCH}
-src/.libs/libgmap.so.1.0.0 usr/lib/${DEB_HOST_MULTIARCH}

debian/patches/install-data-local

@@ -2,7 +2,7 @@ Description: Install data local
 
 --- gmap.orig/Makefile.in
 +++ gmap/Makefile.in
-@@ -846,7 +846,7 @@
+@@ -847,7 +847,7 @@
  
  
  install-data-local:

debian/rules

@@ -18,7 +18,7 @@ HELP2MAN = /usr/bin/help2man --no-info --version-string=${DEB_VERSION}
 	dh  $@
 
 override_dh_auto_configure:
-	dh_auto_configure -- --enable-shared --with-gmapdb=/var/cache/gmap \
+	dh_auto_configure -- --with-gmapdb=/var/cache/gmap \
 	--bindir=/usr/lib/gmap $(EXTRA_CONFIGURE_ARGS)
 
 override_dh_auto_install:
@@ -32,13 +32,22 @@ override_dh_auto_install:
 	dh_auto_install
 
 override_dh_install:
-	dh_install
 	mkdir -p debian/$(DEB_SOURCE)/usr/bin
+	dh_install
 	for bin in `echo gmap gsnap gmap_build gmapl gsnapl; \
-		cd $(CURDIR)/debian/tmp/usr/lib/$(DEB_SOURCE)/; \
+		cd $(CURDIR)/debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/; \
 		ls -1 gmap*.* gsnap*.* `; do \
 		ln -s /usr/lib/gmap/$$bin debian/$(DEB_SOURCE)/usr/bin/$$bin; \
 	done
 
 override_dh_auto_test:
 	dh_auto_test --no-parallel
+
+override_dh_installexamples:
+	mkdir $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples
+	tar --sort=name \
+		--mtime="@${SOURCE_DATE_EPOCH}" \
+		--owner=root --group=root --numeric-owner \
+		--mode=go=rX,u+rw,a-s \
+		-cJf $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples/tests.tar.xz  tests
+	find . -print

debian/tests/control

+Tests: gmap-tests
+Restrictions: allow-stderr

debian/tests/gmap-tests

+#! /bin/bash
+set -e
+
+readonly tmpdir=$(mktemp -d)
+tar -xf /usr/share/doc/gmap/examples/tests.tar.xz -C $tmpdir
+readonly srcdir=${tmpdir}/tests
+
+echo "align.test"
+gmap -A -g ${srcdir}/ss.chr17test ${srcdir}/ss.her2 > align.test.out
+diff align.test.out ${srcdir}/align.test.ok
+rm -f align.test.out
+
+
+echo "coords1.test"
+/usr/lib/gmap/fa_coords -o coords.chr17test ${srcdir}/ss.chr17test
+diff coords.chr17test ${srcdir}/coords1.test.ok
+rm -f coords.chr17test
+
+echo "iit.test"
+/usr/lib/gmap/iit_store -o iittest ${srcdir}/fa.iittest
+diff iittest.iit ${srcdir}/iittest.iit.ok
+
+/usr/lib/gmap/iit_get iittest.iit 20000 > iit_get.out
+diff iit_get.out ${srcdir}/iit_get.out.ok
+
+/usr/lib/gmap/iit_dump iittest.iit > iit_dump.out
+diff iit_dump.out ${srcdir}/fa.iittest
+rm -f iit_get.out
+rm -f iittest.iit
+rm -f iit_dump.out
+
+echo "setup1.test"
+gmap_build -k 15 -B /usr/lib/gmap -D . -d chr17test ${srcdir}/ss.chr17test
+rm -rf chr17test/
+
+rm -rf $tmpdir