[med-svn] [Git][med-team/snippy][master] 7 commits: Add autopkgtest
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Nov 1 17:40:27 GMT 2022
Andreas Tille pushed to branch master at Debian Med / snippy
Commits:
d8ebd582 by Andreas Tille at 2022-11-01T18:17:34+01:00
Add autopkgtest
- - - - -
8147a02e by Andreas Tille at 2022-11-01T18:22:10+01:00
conda id
- - - - -
1bb2f3d3 by Andreas Tille at 2022-11-01T18:28:30+01:00
Provide example mask
- - - - -
5b7efc31 by Andreas Tille at 2022-11-01T18:30:06+01:00
enhance autopkgtest
- - - - -
a60a0a26 by Andreas Tille at 2022-11-01T18:30:22+01:00
any2fasta is in new
- - - - -
b0c2548e by Andreas Tille at 2022-11-01T18:35:47+01:00
find snpeff.config at the right place
- - - - -
713412b2 by Andreas Tille at 2022-11-01T18:40:09+01:00
Upload to new
- - - - -
12 changed files:
- + debian/README.Debian
- debian/changelog
- debian/control
- debian/copyright
- − debian/install
- debian/patches/series
- + debian/patches/snpeff.config.patch
- debian/rules
- + debian/snippy-examples.install
- + debian/snippy.install
- debian/tests/run-unit-test
- debian/upstream/metadata
Changes:
=====================================
debian/README.Debian
=====================================
@@ -0,0 +1,15 @@
+snippy for Debian
+=================
+
+From README.md
+
+* If you want to mask certain regions of the genome, you can provide a BED file
+ with the `--mask` parameter. Any SNPs in those regions will be excluded. This
+ is common for genomes like *M.tuberculosis* where pesky repetitive PE/PPE/PGRS
+ genes cause false positives, or masking phage regions. A `--mask` bed file
+ for *M.tb* is provided with Snippy in the `etc/Mtb_NC_000962.3_mask.bed`
+ folder. It is derived from the XLSX file from https://gph.niid.go.jp/tgs-tb/
+
+This example mask file is provided in /usr/share/doc/snippy/etc.
+
+ -- Andreas Tille <tille at debian.org> Tue, 01 Nov 2022 10:07:59 +0100
=====================================
debian/changelog
=====================================
@@ -1,6 +1,5 @@
-snippy (4.6.0+dfsg-1) UNRELEASED; urgency=medium
+snippy (4.6.0+dfsg-1) unstable; urgency=medium
- * Initial release (Closes: #<bug>)
- TODO: https://github.com/tseemann/any2fasta
+ * Initial release (Closes: #1023283)
- -- Andreas Tille <tille at debian.org> Tue, 01 Nov 2022 10:07:59 +0100
+ -- Andreas Tille <tille at debian.org> Tue, 01 Nov 2022 18:39:47 +0100
=====================================
debian/control
=====================================
@@ -26,8 +26,8 @@ Homepage: https://github.com/tseemann/snippy/
Rules-Requires-Root: no
Package: snippy
-Architecture: any
-Depends: ${shlibs:Depends},
+Architecture: all
+Depends: ${perl:Depends},
${misc:Depends},
any2fasta,
bcftools,
@@ -53,3 +53,19 @@ Description: rapid haploid variant calling and core genome alignment
folder. It can then take a set of Snippy results using the same
reference and generate a core SNP alignment (and ultimately a
phylogenomic tree).
+
+Package: snippy-examples
+Architecture: all
+Depends: ${misc:Depends}
+Recommends: snippy
+Description: rapid haploid variant calling and core genome alignment (examples)
+ Snippy finds SNPs between a haploid reference genome and your NGS
+ sequence reads. It will find both substitutions (snps) and
+ insertions/deletions (indels). It will use as many CPUs as you can give
+ it on a single computer (tested to 64 cores). It is designed with speed
+ in mind, and produces a consistent set of output files in a single
+ folder. It can then take a set of Snippy results using the same
+ reference and generate a core SNP alignment (and ultimately a
+ phylogenomic tree).
+ .
+ This package contains example data to test snippy.
=====================================
debian/copyright
=====================================
@@ -4,7 +4,7 @@ Source: https://github.com/tseemann/snippy
Files-Excluded: binaries
Files: *
-Copyright: 20xx-20yy <upstream>
+Copyright: 2013-2020 Torsten Seemann
License: GPL-2+
Files: debian/*
=====================================
debian/install deleted
=====================================
@@ -1,2 +0,0 @@
-bin usr
-perl5 usr/share
=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
debian_packaged_libs.patch
+snpeff.config.patch
=====================================
debian/patches/snpeff.config.patch
=====================================
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 01 Nov 2022 10:07:59 +0100
+Description: Find snpeff.config at the right place
+
+--- a/bin/snippy
++++ b/bin/snippy
+@@ -293,7 +293,7 @@ elsif ($subsample < 1) {
+ if ($nfeat > 0) {
+ my $cfg_fn = "$refdir/snpeff.config";
+ msg("Creating $cfg_fn");
+- copy("$BINDIR/../etc/snpeff.config", $cfg_fn);
++ copy("/usr/share/snippy/etc/snpeff.config", $cfg_fn);
+ open my $cfg, '>>', $cfg_fn;
+ print $cfg "ref.genome : Snippy Reference\n";
+ my @id = keys %refseq;
=====================================
debian/rules
=====================================
@@ -6,4 +6,10 @@
dh $@
override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
cd test && $(MAKE)
+endif
+
+override_dh_install:
+ dh_install
+ sed -i 's#../bin/snippy#/usr/bin/snippy#' debian/snippy-examples/usr/share/doc/snippy/examples/Makefile
=====================================
debian/snippy-examples.install
=====================================
@@ -0,0 +1,2 @@
+test/example* usr/share/doc/snippy/examples
+test/Makefile usr/share/doc/snippy/examples
=====================================
debian/snippy.install
=====================================
@@ -0,0 +1,4 @@
+bin usr
+perl5 usr/share
+etc/Mtb_NC_000962.3_mask.bed usr/share/doc/snippy/etc
+etc/snpeff.config usr/share/snippy/etc
=====================================
debian/tests/run-unit-test
=====================================
@@ -1,7 +1,7 @@
#!/bin/bash
set -e
-pkg=#PACKAGENAME#
+pkg=snippy
export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
@@ -12,5 +12,11 @@ fi
cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
+gunzip *.gz
-#do_stuff_to_test_package#
+snippy --version
+snippy --check
+snippy-core --version
+snippy-core --check
+
+make
=====================================
debian/upstream/metadata
=====================================
@@ -1,19 +1,3 @@
-Reference:
- - Author:
- Title:
- Journal:
- Year:
- Volume:
- Number:
- Pages:
- DOI:
- PMID:
- URL:
- eprint:
Registry:
- Name: conda:bioconda
- Entry:
- - Name: SciCrunch
- Entry:
- - Name: bio.tools
- Entry:
+ Entry: snippy
View it on GitLab: https://salsa.debian.org/med-team/snippy/-/compare/761ceaa192da31531cae21de61061015c8840487...713412b2604be1ec5da4518ac9991ddf2fe89e02
--
View it on GitLab: https://salsa.debian.org/med-team/snippy/-/compare/761ceaa192da31531cae21de61061015c8840487...713412b2604be1ec5da4518ac9991ddf2fe89e02
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