Andreas Tille pushed to branch master at Debian Med / snippy
Commits: 661dc9bd by Andreas Tille at 2023-12-06T17:25:09+01:00 Add another test - for the moment just for users local machine in examples since its quite some effort for autopkgtest - - - - - f8c06b27 by Andreas Tille at 2023-12-06T17:28:54+01:00 Set upstream metadata fields: Repository. Changes-By: lintian-brush Fixes: lintian: upstream-metadata-missing-repository See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html - - - - - 1a859387 by Andreas Tille at 2023-12-06T17:35:00+01:00 Revert second part of the patch since it leads to a syntax error in snpeff. Obviously only the build command can consume the said options - - - - - 4b91b246 by Andreas Tille at 2023-12-06T17:36:53+01:00 Upload to unstable - - - - - 5 changed files: - debian/changelog - debian/patches/snpeff_v5.1+.patch - debian/snippy-examples.install - + debian/tests/test_for_working_snpeff_v5.1+ - debian/upstream/metadata Changes: ===================================== debian/changelog ===================================== @@ -1,9 +1,12 @@ -snippy (4.6.0+dfsg-4) UNRELEASED; urgency=medium +snippy (4.6.0+dfsg-4) unstable; urgency=medium * Work with snpeff >= 5.1 Closes: #1029202 + * Add another test - for the moment just for users local machine in + examples since its quite some effort for autopkgtest + * Set upstream metadata fields: Repository. - -- Andreas Tille <ti...@debian.org> Wed, 06 Dec 2023 17:07:28 +0100 + -- Andreas Tille <ti...@debian.org> Wed, 06 Dec 2023 17:35:45 +0100 snippy (4.6.0+dfsg-3) unstable; urgency=medium ===================================== debian/patches/snpeff_v5.1+.patch ===================================== @@ -18,12 +18,3 @@ Last-Update: Wed, 06 Dec 2023 17:07:28 +0100 : () ), # make BAM ($bam ? "samtools view -h -O SAM \Q$bam\E" : "bwa mem $bwaopt -t $cpus $refdir/ref.fa @reads") -@@ -393,7 +393,7 @@ my @cmd = ( - " | bcftools annotate --remove '$KEEP_VCF_TAGS' > $prefix.filt.vcf", - # " > $prefix.filt.vcf", - # call consequences -- ( $nfeat > 0 ? "snpEff ann -noLog -noStats -no-downstream -no-upstream -no-utr" -+ ( $nfeat > 0 ? "snpEff ann -noCheckCds -noCheckProtein -noLog -noStats -no-downstream -no-upstream -no-utr" - ." -c $refdir/snpeff.config -dataDir . ref $prefix.filt.vcf > $prefix.vcf" - : "cp $prefix.filt.vcf $prefix.vcf" ), - # prepare output files ===================================== debian/snippy-examples.install ===================================== @@ -1,2 +1,3 @@ test/example* usr/share/doc/snippy/examples test/Makefile usr/share/doc/snippy/examples +debian/tests/test_for_working_snpeff_v5.1+ usr/share/doc/snippy/examples ===================================== debian/tests/test_for_working_snpeff_v5.1+ ===================================== @@ -0,0 +1,19 @@ +#!/bin/sh + +# This script can be used to test snippy more extensively against +# the problem reported at +# https://github.com/pcingola/SnpEff/issues/455 + +# create tmp dir +TMPDIR=$(mktemp -d /tmp/snippyXXXXX) +cd $TMPDIR +# download public read data +wget -q -N ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR201/004/SRR2014554/SRR2014554_1.fastq.gz +wget -q -N ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR201/004/SRR2014554/SRR2014554_2.fastq.gz +# download reference data +wget -q -N https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.gbff.gz +gunzip GCF_000005845.2_ASM584v2_genomic.gbff.gz +mkdir tmp + +set -x +snippy --cpus 4 --ram 20 --tmpdir ./tmp --reference GCF_000005845.2_ASM584v2_genomic.gbff --R1 SRR2014554_1.fastq.gz --R2 SRR2014554_2.fastq.gz --outdir results --report --mincov 20 ===================================== debian/upstream/metadata ===================================== @@ -3,4 +3,5 @@ Bug-Submit: https://github.com/tseemann/snippy/issues/new Registry: - Name: conda:bioconda Entry: snippy +Repository: https://github.com/tseemann/snippy.git Repository-Browse: https://github.com/tseemann/snippy View it on GitLab: https://salsa.debian.org/med-team/snippy/-/compare/dff0fc3fbbdc9cbe23b2506122b1620949f9f1a3...4b91b246465a7eb224bd55ffb54aef923c19af7e -- View it on GitLab: https://salsa.debian.org/med-team/snippy/-/compare/dff0fc3fbbdc9cbe23b2506122b1620949f9f1a3...4b91b246465a7eb224bd55ffb54aef923c19af7e You're receiving this email because of your account on salsa.debian.org.
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