[Blends-commit] [Git][blends-team/med][master] Add new packages and packages in Salsa
Andreas Tille
gitlab at salsa.debian.org
Tue May 12 09:14:31 BST 2020
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
cf47dafb by Andreas Tille at 2020-05-12T10:14:07+02:00
Add new packages and packages in Salsa
- - - - -
2 changed files:
- covid-19_doc/bio_covid-19_dependencies_query
- covid-19_doc/bio_covid-19_dependencies_result
Changes:
=====================================
covid-19_doc/bio_covid-19_dependencies_query
=====================================
@@ -160,7 +160,14 @@ INSERT INTO covid19_packages VALUES
('vg')
;
-SELECT co.package, architectures, s.section, r.releases FROM covid19_packages co
+SELECT co.package, architectures, s.section,
+ CASE WHEN r.releases IS NULL THEN
+ CASE WHEN n.component IS NULL THEN
+ CASE WHEN vcs.vcs_browser IS NULL THEN '' ELSE vcs.vcs_browser END
+ ELSE 'new' END
+ ELSE r.releases
+ END AS releases
+ FROM covid19_packages co
LEFT JOIN (
SELECT package, string_agg(architecture, ',') AS architectures FROM (
SELECT DISTINCT package, architecture FROM packages WHERE release in ('sid') AND
@@ -182,6 +189,8 @@ SELECT co.package, architectures, s.section, r.releases FROM covid19_packages co
ORDER BY p.package, s.sort, p.release
) tmp GROUP BY package
) r ON r.package = co.package
+ LEFT JOIN (SELECT package, component FROM new_packages) n ON n.package = co.package
+ LEFT JOIN (SELECT package, vcs_browser FROM blends_prospectivepackages) vcs ON vcs.package = co.package
ORDER BY package
;
END;
=====================================
covid-19_doc/bio_covid-19_dependencies_result
=====================================
@@ -1,7 +1,7 @@
-Last-Update: Tue, 12 May 2020 09:52:09 +0200
+Last-Update: Tue, 12 May 2020 10:13:05 +0200
- package | architectures | section | releases
------------------------------+---------------------+----------+---------------------
+ package | architectures | section | releases
+-----------------------------+---------------------+----------+---------------------------------------------
abacas | all | main | buster,bullseye,sid
allelecount | | |
ascat | | |
@@ -20,26 +20,26 @@ Last-Update: Tue, 12 May 2020 09:52:09 +0200
drop-seq-tools | | |
fastp | amd64,arm64,ppc64el | main | buster,bullseye,sid
fastqc | all | main | buster,bullseye,sid
- filtlong | | |
+ filtlong | | | https://salsa.debian.org/med-team/filtlong
freebayes | amd64,arm64,ppc64el | main | buster,bullseye,sid
- gatk | | |
- graphmap2 | | |
+ gatk | | | https://salsa.debian.org/med-team/gatk
+ graphmap2 | | | https://salsa.debian.org/med-team/graphmap2
ivar | | |
kallisto | amd64,arm64,ppc64el | main | bullseye,sid
kraken2 | amd64,arm64,ppc64el | main | bullseye,sid
libhts-dev | amd64,arm64,ppc64el | main | buster,bullseye,sid
lumpy | | |
- manta | | |
- megahit | | |
+ manta | | | https://salsa.debian.org/med-team/manta
+ megahit | | | https://salsa.debian.org/med-team/megahit
metabat | | |
minia | amd64,arm64,ppc64el | main | buster,bullseye,sid
minimap2 | amd64,arm64,ppc64el | main | buster,bullseye,sid
multiqc | all | main | bullseye,sid
muscle | amd64,arm64,ppc64el | main | buster,bullseye,sid
nanolyse | | |
- nanoplot | | |
+ nanoplot | | | https://salsa.debian.org/med-team/nanoplot
ncbi-blast+ | amd64,arm64,ppc64el | main | buster,bullseye,sid
- nextflow | | |
+ nextflow | | | https://salsa.debian.org/med-team/nextflow
nf-core | | |
parallel-fastq-dump | | |
picard-tools | amd64 | main | buster,bullseye,sid
@@ -52,9 +52,10 @@ Last-Update: Tue, 12 May 2020 09:52:09 +0200
python3-htseq | amd64,arm64,ppc64el | main | buster,bullseye,sid
python3-numpy | amd64,arm64,ppc64el | main | buster,bullseye,sid
python3-pandas | all | main | buster,bullseye,sid
+ python3-pauvre | | | new
qcat | all | main | bullseye,sid
- qualimap | | |
- quast | | |
+ qualimap | | | https://salsa.debian.org/med-team/qualimap
+ quast | | | https://salsa.debian.org/med-team/quast
radiant | all | main | buster,bullseye,sid
r-bioc-deseq2 | amd64,arm64,ppc64el | main | buster,bullseye,sid
r-bioc-rtracklayer | amd64,arm64,ppc64el | main | buster,bullseye,sid
@@ -82,7 +83,7 @@ Last-Update: Tue, 12 May 2020 09:52:09 +0200
salmon | amd64 | main | buster,bullseye,sid
samtools | amd64,arm64,ppc64el | main | buster,bullseye,sid
snakemake | all | main | buster,bullseye,sid
- snpeff | | |
+ snpeff | | | https://salsa.debian.org/med-team/snpeff
snpsift | | |
spades | amd64 | main | buster,bullseye,sid
sra-toolkit | amd64 | main | buster,bullseye,sid
@@ -94,5 +95,5 @@ Last-Update: Tue, 12 May 2020 09:52:09 +0200
vcftools | amd64,arm64,ppc64el | main | buster,bullseye,sid
vep | | |
vg | amd64 | main | bullseye,sid
-(92 Zeilen)
+(93 Zeilen)
View it on GitLab: https://salsa.debian.org/blends-team/med/-/commit/cf47dafbca50463e7436f934c5f03e4fde6d3081
--
View it on GitLab: https://salsa.debian.org/blends-team/med/-/commit/cf47dafbca50463e7436f934c5f03e4fde6d3081
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