[med-svn] [Git][med-team/hts-nim-tools][master] Partial packaging - still missing deps
Steffen Möller
gitlab at salsa.debian.org
Mon Nov 2 20:36:51 GMT 2020
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 <moeller at debian.org> 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 <moeller at debian.org>
+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 <moeller 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.
=====================================
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
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