[med-svn] [baitfisher] 02/03: Import Debian patch 1.0+dfsg-1
Olivier Sallou
osallou at debian.org
Sat Jan 14 07:48:49 UTC 2017
This is an automated email from the git hooks/post-receive script.
osallou pushed a commit to branch master
in repository baitfisher.
commit 74f0c40bb34142acca9e86c465bd6d928f817d62
Author: Olivier Sallou <osallou at debian.org>
Date: Fri Jan 13 10:27:13 2017 +0000
Import Debian patch 1.0+dfsg-1
---
debian/README.source | 2 ++
debian/baitfisher.docs | 0
debian/baitfisher.manpages | 1 +
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 37 +++++++++++++++++++++++++++++++++++++
debian/copyright | 41 +++++++++++++++++++++++++++++++++++++++++
debian/dirs | 2 ++
debian/patches/fix_gcc6.patch | 17 +++++++++++++++++
debian/patches/series | 1 +
debian/rules | 26 ++++++++++++++++++++++++++
debian/source/format | 1 +
debian/watch | 4 ++++
13 files changed, 138 insertions(+)
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..8b71a49
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,2 @@
+Remove Documentation from source package because there is no source file for the moment.
+A bug has been created to ask for source document: https://github.com/cmayer/BaitFisher-package/issues/6
diff --git a/debian/baitfisher.docs b/debian/baitfisher.docs
new file mode 100644
index 0000000..e69de29
diff --git a/debian/baitfisher.manpages b/debian/baitfisher.manpages
new file mode 100644
index 0000000..f7e585b
--- /dev/null
+++ b/debian/baitfisher.manpages
@@ -0,0 +1 @@
+*.1
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..f6e644b
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+baitfisher (1.0+dfsg-1) unstable; urgency=medium
+
+ * Initial release (Closes: #NNNN)
+
+ -- Olivier Sallou <osallou at debian.org> Fri, 13 Jan 2017 10:27:13 +0000
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/control b/debian/control
new file mode 100644
index 0000000..62fd941
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,37 @@
+Source: baitfisher
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>
+Build-Depends: debhelper (>= 9),
+ help2man
+Standards-Version: 3.9.8
+Homepage: https://github.com/cmayers/BaitFisher-package
+Vcs-Git: https://anonscm.debian.org/debian-med/baitfisher.git
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/baitfisher.git
+
+Package: baitfisher
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: software package for designing hybrid enrichment probes
+ The BaitFisher package consists of two programs: BaitFisher and BaitFilter.
+ .
+ BaitFisher was been designed to construct hybrid enrichment baits from
+ multiple sequence alignments (MSAs) or annotated features in MSAs. The main
+ goal of BaitFisher is to avoid redundancy in the construction of baits by
+ designing fewer baits in conserved regions of the MSAs and designing more baits
+ in variable regions. This makes use of the fact that hybrid enrichment baits
+ can differ to some extends from the target region, which they should capture
+ in the enrichment procedure.
+ By specifying the allowed distance between baits and the sequences in the MSAs
+ the user can control the allowed bait-to-target distance and the degree of
+ reduction in the number of baits that are designed.
+ See the BaitFisher paper for details.
+ .
+ BaitFilter was designed (i) to determine whether baits bind unspecifically to
+ a reference genome, (ii) to filter baits that only have partial length matches
+ to a reference genome, (iii) to determine the optimal bait region in a MSA and
+ to convert baits to a format that can be uploaded at a bait constructing
+ company. The optimal bait region can be the most conserved region in the MSA
+ or the region with the highest number of sequences without gaps or ambiguous
+ nucleotides.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..74dedd7
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,41 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: BaitFisher
+Source: https://github.com/cmayer/BaitFisher-package
+Files-Excluded: Documentation
+
+Files: *
+Copyright: 2011-2016
+License: GPL-2
+ This package 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 2 of the License.
+ .
+ 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 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+Files: debian/*
+Copyright: 2017 Olivier Sallou <osallou at debian.org>
+License: GPL-2+
+ This package 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 2 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 2 can be found in "/usr/share/common-licenses/GPL-2".
diff --git a/debian/dirs b/debian/dirs
new file mode 100644
index 0000000..5942cb9
--- /dev/null
+++ b/debian/dirs
@@ -0,0 +1,2 @@
+usr/share/doc/bedops
+usr/bin
diff --git a/debian/patches/fix_gcc6.patch b/debian/patches/fix_gcc6.patch
new file mode 100644
index 0000000..992965a
--- /dev/null
+++ b/debian/patches/fix_gcc6.patch
@@ -0,0 +1,17 @@
+Subject: fix gcc6 compilation
+Description: fails to build with gcc 6
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2017-01-13
+Forwarded: yes
+Bug: https://github.com/cmayer/BaitFisher-package/issues/5
+--- a/CBlastParser.h
++++ b/CBlastParser.h
+@@ -539,7 +539,7 @@
+ void add(CBlastHit* p)
+ {
+ lbh.push_back(p);
+- bh_map.insert(bh_map.end(), std::make_pair<faststring, CBlastHit*>(p->get_query_seq_name(), p));
++ bh_map.insert(bh_map.end(), std::make_pair(p->get_query_seq_name(), p));
+ }
+
+ public:
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..ac462d5
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+fix_gcc6.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..0394e83
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,26 @@
+#!/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
+
+include /usr/share/dpkg/pkg-info.mk
+
+%:
+ dh $@
+
+override_dh_install:
+ cp BaitFilter-v* debian/baitfisher/usr/bin/BaitFiler
+ cp BaitFisher-v* debian/baitfisher/usr/bin/BaitFisher
+ dh_install
+
+override_dh_installman:
+ help2man --no-discard-stderr -o BaitFilter.1 BaitFilter-v*
+ help2man --no-discard-stderr -o BaitFisher.1 BaitFisher-v*
+ dh_installman
+
+
+
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/watch b/debian/watch
new file mode 100644
index 0000000..80afa57
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=4
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz,filenamemangle=s/.+\/v?(\d\S+)\.tar\.gz/baitfisher-$1\.tar\.gz/" \
+ https://github.com/cmayer/BaitFisher-package/tags .*/v?(\d\S+)\.tar\.gz
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