[med-svn] [sniffles] 02/02: releasing package sniffles version 0.0.1+ds-1
Afif Elghraoui
afif at moszumanska.debian.org
Sat Jun 18 23:28:36 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository sniffles.
commit ef83e42a736452239f94db80366f66ffb54267ed
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Sat Jun 18 16:23:08 2016 -0700
releasing package sniffles version 0.0.1+ds-1
---
debian/changelog | 5 +++
debian/compat | 1 +
debian/control | 29 ++++++++++++++
debian/copyright | 32 +++++++++++++++
debian/install | 1 +
debian/manpages | 1 +
debian/patches/external-libs.patch | 37 +++++++++++++++++
debian/patches/no-extra-binary.patch | 39 ++++++++++++++++++
debian/patches/series | 2 +
debian/rules | 26 ++++++++++++
debian/sniffles.1.md | 77 ++++++++++++++++++++++++++++++++++++
debian/source/format | 1 +
debian/watch | 5 +++
13 files changed, 256 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..eac6439
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+sniffles (0.0.1+ds-1) unstable; urgency=medium
+
+ * Initial release (Closes: #827638)
+
+ -- Afif Elghraoui <afif at debian.org> Sat, 18 Jun 2016 13:38:07 -0700
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..0081ed2
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,29 @@
+Source: sniffles
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Afif Elghraoui <afif at debian.org>
+Build-Depends:
+ debhelper (>=9),
+ cmake (>=2.8),
+ libbamtools-dev,
+ libtclap-dev,
+ zlib1g-dev,
+ pandoc,
+Standards-Version: 3.9.8
+Homepage: http://fritzsedlazeck.github.io/Sniffles
+Vcs-Git: https://anonscm.debian.org/git/debian-med/sniffles.git
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/sniffles.git
+
+Package: sniffles
+Architecture: any
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+Suggests:
+ bwa,
+Description: structural variation caller using third-generation sequencing
+ Sniffles is a structural variation caller using third-generation sequencing
+ data such as those from Pacific Biosciences or Oxford Nanopore platforms.
+ It detects all types of SVs using evidence from split-read alignments,
+ high-mismatch regions, and coverage analysis.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..7a5e367
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,32 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: sniffles
+Upstream-Contact: Fritz Sedlazeck <fritz.sedlazeck at gmail.com>
+Source: https://github.com/fritzsedlazeck/Sniffles
+Files-Excluded: lib
+
+Files: *
+Copyright: 2015-2016 Fritz Sedlazeck <fritz.sedlazeck at gmail.com>
+License: MIT
+
+Files: debian/*
+Copyright: 2016 Afif Elghraoui <afif at debian.org>
+License: MIT
+
+License: MIT
+ 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.
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..da6f74c
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+bin/sniffles-*/* /usr/bin/
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..51cf52c
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/sniffles.1
diff --git a/debian/patches/external-libs.patch b/debian/patches/external-libs.patch
new file mode 100644
index 0000000..53ad912
--- /dev/null
+++ b/debian/patches/external-libs.patch
@@ -0,0 +1,37 @@
+Description: Use system libraries
+Author: Afif Elghraoui <afif at debian.org>
+Forwarded: not-needed
+Last-Update: 2016-06-18
+
+--- sniffles.orig/CMakeLists.txt
++++ sniffles/CMakeLists.txt
+@@ -30,7 +30,5 @@
+ endif()
+
+
+-add_subdirectory(lib/zlib-1.2.7)
+-add_subdirectory(lib/bamtools-2.3.0)
+
+ add_subdirectory(src)
+--- sniffles.orig/src/CMakeLists.txt
++++ sniffles/src/CMakeLists.txt
+@@ -1,6 +1,8 @@
+ cmake_minimum_required(VERSION 2.8)
+ project(Sniffles)
+
++include_directories(${CMAKE_INCLUDE_PATH})
++
+ include_directories (../lib/bamtools-2.3.0/src)
+ include_directories(../lib/tclap-1.2.1/include)
+
+@@ -28,8 +30,8 @@
+ )
+
+ #target_link_libraries(ngm-core pthread)
+-TARGET_LINK_LIBRARIES(sniffles BamTools-static)
+-TARGET_LINK_LIBRARIES(sniffles zlibstatic)
++TARGET_LINK_LIBRARIES(sniffles bamtools)
++TARGET_LINK_LIBRARIES(sniffles z)
+
+ add_executable(sniffles-debug
+ Alignment.cpp
diff --git a/debian/patches/no-extra-binary.patch b/debian/patches/no-extra-binary.patch
new file mode 100644
index 0000000..abadd97
--- /dev/null
+++ b/debian/patches/no-extra-binary.patch
@@ -0,0 +1,39 @@
+Description: Do not build <target>-debug programs
+ The default build creates two versions of the program:
+ sniffles and sniffles-debug. We don't need the latter.
+Author: Afif Elghraoui <afif at debian.org>
+Forwarded: not-needed
+Last-Update: 2016-06-18
+--- sniffles.orig/src/CMakeLists.txt
++++ sniffles/src/CMakeLists.txt
+@@ -33,30 +33,3 @@
+ TARGET_LINK_LIBRARIES(sniffles bamtools)
+ TARGET_LINK_LIBRARIES(sniffles z)
+
+-add_executable(sniffles-debug
+- Alignment.cpp
+- BamParser.cpp
+- Parser.cpp
+- Sniffles.cpp
+- Ignore_Regions.cpp
+- tree/Intervall_bed.cpp
+- sub/Detect_Breakpoints.cpp
+- sub/Breakpoint.cpp
+- tree/IntervallTree.cpp
+- realign/SWCPU.cpp
+- realign/Realign.cpp
+- print/VCFPrinter.cpp
+- print/BedePrinter.cpp
+- print/MariaPrinter.cpp
+- print/IPrinter.cpp
+- phasing/PhaserSV.cpp
+- tree/BinTree.cpp
+- print/NGMPrinter.cpp
+- )
+-
+-SET_TARGET_PROPERTIES(sniffles-debug PROPERTIES COMPILE_FLAGS "-g3 -O0")
+-
+-#target_link_libraries(sniffles-debug pthread)
+-TARGET_LINK_LIBRARIES(sniffles-debug BamTools-static)
+-TARGET_LINK_LIBRARIES(sniffles-debug zlibstatic)
+-
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..5026758
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+external-libs.patch
+no-extra-binary.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..955a2da
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,26 @@
+#!/usr/bin/make -f
+
+#export DH_VERBOSE = 1
+
+INCLUDE_PATHS = /usr/include/bamtools
+
+space=
+space+=
+
+%:
+ dh $@ --parallel
+
+
+override_dh_auto_build: debian/sniffles.1
+ dh_auto_build
+
+override_dh_auto_configure:
+ dh_auto_configure -- \
+ -DCMAKE_INCLUDE_PATH="$(subst $(space),:,$(strip $(INCLUDE_PATHS)))"
+
+override_dh_auto_clean:
+ dh_auto_clean
+ $(RM) debian/sniffles.1
+
+%.1: %.1.md
+ pandoc --from markdown --to man -s $< -o $@
diff --git a/debian/sniffles.1.md b/debian/sniffles.1.md
new file mode 100644
index 0000000..484a77c
--- /dev/null
+++ b/debian/sniffles.1.md
@@ -0,0 +1,77 @@
+% SNIFFLES(1) 0.0.1
+% Fritz Sedlazeck <fritz.sedlazech at gmail.com>
+%
+
+# NAME
+
+sniffles - structural variation caller for third-generation sequencing data
+
+# SYNOPSIS
+
+**sniffles** -m *string* [-s *int*] [--max_num_splits *int*] [-q *int*]
+ [-l *int*] [-v *string*] [--bede *string*] [-c *int*] [-t
+ *int*] [-d *int*] [-n *int*] [--use_MD_Cigar] [--]
+ [--version] [-h]
+
+**sniffles** **-m** *reads.bam* **-v** *calls.vcf*
+
+# DESCRIPTION
+Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Please note the current version of Sniffles requires output from BWA-MEM with the optional SAM attributes enabled!
+
+# OPTIONS
+
+ -m *string*, --mapped_reads *string*
+: (required) Bam File
+
+ -s *int*, --min_support *int*
+: Minimum number of reads that support a SV. Default: 10
+
+ --max_num_splits *int*
+: Maximum number of splits per read to be still taken into account.
+ Default: 4
+
+ -q *int*, --minmapping_qual *int*
+: Minimum Mapping Quality. Default: 20
+
+ -l *int*, --min_length *int*
+: Minimum length of SV to be reported. Default:0
+
+ -v *string*, --vcf *string*
+: VCF output file name
+
+ --bede *string*
+: Simplified format of bede Format.
+
+ -c *int*, --min_cigar_event *int*
+: Minimum Cigar Event (e.g. Insertion, deletion) to take into account.
+ Default:50
+
+ -t *int*, --threads *int*
+: Number of threads to use. Default: 3
+
+ -d *int*, --max_distance *int*
+: Maximum distance to group SV together. Default: 1kb
+
+ -n *int*, --num_reads_report *int*
+: Report up to N reads that support the SV. Default: 0
+
+ --use_MD_Cigar
+: Enables Sniffles to use the alignment information to screen for
+ suspicious regions.
+
+ --, --ignore_rest
+: Ignores the rest of the labeled arguments following this flag.
+
+ --version
+: Displays version information and exits.
+
+ -h, --help
+: Displays usage information and exits.
+
+# BUGS
+
+If you experience problems or have suggestions please contact: fritz.sedlazeck at gmail.com
+
+# SEE ALSO
+
+**bwa**(1)
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..ba3ecbb
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,5 @@
+version=4
+
+opts="repack,repacksuffix=+ds,dversionmangle=s/\+ds\d*$//,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%sniffles-$1.tar.gz%" \
+ https://github.com/fritzsedlazeck/sniffles/tags \
+ (?:.*?/)?v?(\d[\d.]*)\.tar\.gz debian uupdate
--
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