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commit ef83e42a736452239f94db80366f66ffb54267ed Author: Afif Elghraoui <[email protected]> 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 <[email protected]> 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 <[email protected]> +Uploaders: Afif Elghraoui <[email protected]> +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 <[email protected]> +Source: https://github.com/fritzsedlazeck/Sniffles +Files-Excluded: lib + +Files: * +Copyright: 2015-2016 Fritz Sedlazeck <[email protected]> +License: MIT + +Files: debian/* +Copyright: 2016 Afif Elghraoui <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 <[email protected]> +% + +# 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: [email protected] + +# 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sniffles.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
