[med-svn] [Git][med-team/snippy][master] 4 commits: Add another test - for the moment just for users local machine in examples...

[Andreas Tille (@tille)]

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 <tille at debian.org>  Wed, 06 Dec 2023 17:07:28 +0100
+ -- Andreas Tille <tille at 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
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