Steffen Möller pushed to branch master at Debian Med / hts-nim-tools
Commits: b1deb8e9 by Steffen Möller at 2020-11-02T21:36:31+01:00 Partial packaging - still missing deps - - - - - 7 changed files: - + debian/changelog - + debian/control - + debian/copyright - + debian/rules - + debian/salsa-ci.yml - + debian/source/format - + debian/watch Changes: ===================================== debian/changelog ===================================== @@ -0,0 +1,7 @@ +hts-nim-tools (0.2.0-1) UNRELEASED; urgency=medium + + * Initial release (Closes: #973650) + + Misses brentp's nim modules lapper and kexec + + -- Steffen Moeller <[email protected]> Mon, 02 Nov 2020 20:26:54 +0100 ===================================== debian/control ===================================== @@ -0,0 +1,32 @@ +Source: hts-nim-tools +Section: science +Priority: optional +Maintainer: Steffen Moeller <[email protected]> +Build-Depends: debhelper-compat (= 13), + nim, + nim-hts-dev, + nim-docopt-dev, + nim-unicodedb-dev, + nim-unicodeplus-dev, + nim-regex-dev +Standards-Version: 4.5.0 +Homepage: https://github.com/brentp/hts-nim-tools +Vcs-Browser: https://salsa.debian.org/med-team/hts-nim-tools +Vcs-Git: https://salsa.debian.org/med-team/hts-nim-tools.git +Rules-Requires-Root: no + +Package: hts-nim-tools +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: tools biological sequences: bam-filter, count-reads, vcf-check + This package provides several tools that (at least at the time of their creation) + provide functionalities beyond the routine provided by samtools and other reverse + dependencies of the htslib. + . + These new tools are + • bam-filter : filter BAM/CRAM/SAM files with a simple expression language + • count-reads : count BAM/CRAM reads in regions given in a BED file + • vcf-check : check regions of a VCF against a background for missing chunks + . + and yes, as the name suggests, these tools are all implemented in nim, using the + nim-hts (upstream: hts-nim) wrapper for the htslib. ===================================== debian/copyright ===================================== @@ -0,0 +1,30 @@ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: hts-nim-tools +Source: https://github.com/brentp/hts-nim-tools + +Files: * +Copyright: 2018 Brent Pedersen <@brentp> +License: MIT + +Files: debian/* +Copyright: 2020 Steffen Moeller <[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. ===================================== debian/rules ===================================== @@ -0,0 +1,19 @@ +#!/usr/bin/make -f +export DH_VERBOSE = 1 + +%: + dh $@ + +override_dh_auto_build: + # needs kexpr + #nim c -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/hts src/bam_filter.nim + # nim c -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/hts src/hts_nim_tools.nim + # needs lapper + # nim c -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/hts src/count_reads.nim + # nim c -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/hts src/copy_number_sampler.nim + # works! + nim c -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/hts src/vcf_check.nim + +override_dh_auto_clean: + rm -f src/version src/vcf_check src/bam_filter src/hts_nim_tools src/count_reads + ===================================== debian/salsa-ci.yml ===================================== @@ -0,0 +1,11 @@ +# For more information on what jobs are run see: +# https://salsa.debian.org/salsa-ci-team/pipeline +# +# To enable the jobs, go to your repository (at salsa.debian.org) +# and click over Settings > CI/CD > Expand (in General pipelines). +# In "Custom CI config path" write debian/salsa-ci.yml and click +# in "Save Changes". The CI tests will run after the next commit. +--- +include: + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml ===================================== debian/source/format ===================================== @@ -0,0 +1 @@ +3.0 (quilt) ===================================== debian/watch ===================================== @@ -0,0 +1,3 @@ +version=4 +opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%hts-nim-tools-$1.tar.gz%" \ + https://github.com/brentp/hts-nim-tools/tags (?:.*?/)?v?(\d[\d.]*)\.tar\.gz View it on GitLab: https://salsa.debian.org/med-team/hts-nim-tools/-/commit/b1deb8e91ec0e64e5f611bfbc35085691aab81c8 -- View it on GitLab: https://salsa.debian.org/med-team/hts-nim-tools/-/commit/b1deb8e91ec0e64e5f611bfbc35085691aab81c8 You're receiving this email because of your account on salsa.debian.org.
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