Packaging vidjil algo automation

Added automation scripts for building the vidjil algorithm debian
package

packaging/build-algo.sh

+#!/bin/bash
+
+. ./build-generic.sh
+
+MY_PWD="$PWD"
+
+source_files="../algo ../browser ../data ../doc ../germline ../Makefile ../tools"
+dest_files="vidjil"
+exec_dir="$dest_files"
+
+copy_files -s="$source_files" -d="$dest_files"
+
+cd "$MY_PWD/$dest_files/germline"
+make
+cd "$MY_PWD/$dest_files/data"
+
+cd "$MY_PWD/$exec_dir"
+bash "$MY_PWD/mkdeb"
+
+remove_files -s="$source_files" -d="$dest_files"
+exit 0

packaging/vidjil/debian/changelog

+vidjil (2016.08) stable; urgency=medium
+
+  * Resolved error in package
+
+ -- Vidjil Team <team@vidjil.org>  Thu, 11 Aug 2016 14:23:03 +0200

packaging/vidjil/debian/compat

+9

packaging/vidjil/debian/control

+Source: vidjil
+Section: misc
+Priority: optional
+Maintainer: Vidjil Team <team@vidjil.org>
+Build-Depends: debhelper (>=9)
+Standards-Version: 3.9.7
+Homepage: http://www.vidjil.org
+#Vcs-Git: git://anonscm.debian.org/collab-maint/vidjil.git
+#Vcs-Browser: https://anonscm.debian.org/cgit/collab-maint/vidjil.git
+
+Package: vidjil
+Architecture: all
+Depends: vidjil-germline (>=2016.08), zlib1g-dev, libstdc++6, ${misc:Depends}
+Description: Identify majority lymphocyte clones from fasta
+ Vidjil parses a fasta or fastq file in order to identify
+ the major lymphocyte clones in an effort to aid in diagnosis
+ and follow-up of leukaemia patients

packaging/vidjil/debian/copyright

+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: vidjil
+Source: <ur://www.vidjil.org/releases/vidjil-latest.tgz>
+
+Files: *
+Copyright: 2016 Vidjil Team <team@vidjil.org>
+License: GPL-3.0+
+
+Files: debian/*
+Copyright: 2016 Vidjil Team <team@vidjil.org>
+License: GPL-3.0+
+
+License: GPL-3.0+
+ 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 package 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.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <https://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
+
+# Please also look if there are files or directories which have a
+# different copyright/license attached and list them here.
+# Please avoid picking licenses with terms that are more restrictive than the
+# packaged work, as it may make Debian's contributions unacceptable upstream.

packaging/vidjil/debian/install

+vidjil usr/bin/

packaging/vidjil/debian/rules

+#!/usr/bin/make -f
+# See debhelper(7) (uncomment to enable)
+# output every command that modifies files on the build system.
+#export DH_VERBOSE = 1
+
+
+# see FEATURE AREAS in dpkg-buildflags(1)
+#export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+# see ENVIRONMENT in dpkg-buildflags(1)
+# package maintainers to append CFLAGS
+#export DEB_CFLAGS_MAINT_APPEND  = -Wall -pedantic
+# package maintainers to append LDFLAGS
+#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
+
+
+%:
+	dh $@ 
+
+
+# dh_make generated override targets
+# This is example for Cmake (See https://bugs.debian.org/641051 )
+#override_dh_auto_configure:
+#	dh_auto_configure -- #	-DCMAKE_LIBRARY_PATH=$(DEB_HOST_MULTIARCH)
+

packaging/vidjil/debian/source/format

+3.0 (native)

packaging/vidjil/debian/vidjil-docs.docs

+README.source
+README.Debian
+README