[Blends-commit] [Git][blends-team/med][master] 2 commits: Base architectures on sid only to avoid noise
Andreas Tille
gitlab at salsa.debian.org
Tue May 12 08:52:57 BST 2020
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
8707b023 by Andreas Tille at 2020-05-12T09:27:55+02:00
Base architectures on sid only to avoid noise
- - - - -
6f3899b8 by Andreas Tille at 2020-05-12T09:52:43+02:00
Add release
- - - - -
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
=====================================
@@ -84,7 +84,7 @@ INSERT INTO covid19_packages VALUES
('centrifuge'),
('changeo'),
('cutadapt'),
-('diamond'),
+('diamond-aligner'),
('python3-deeptools'),
('drop-seq-tools'),
('fastp'),
@@ -160,10 +160,10 @@ INSERT INTO covid19_packages VALUES
('vg')
;
-SELECT co.package, architectures, s.section FROM covid19_packages co
+SELECT co.package, architectures, s.section, r.releases FROM covid19_packages co
LEFT JOIN (
SELECT package, string_agg(architecture, ',') AS architectures FROM (
- SELECT DISTINCT package, architecture FROM packages WHERE
+ SELECT DISTINCT package, architecture FROM packages WHERE release in ('sid') AND
architecture IN ('all', 'amd64', 'arm64', 'ppc64el' ) AND
package IN (SELECT * FROM covid19_packages)
ORDER BY package, architecture
@@ -173,6 +173,15 @@ SELECT co.package, architectures, s.section FROM covid19_packages co
SELECT DISTINCT package, CASE WHEN substring(section from 0 for 10) = 'non-free/' THEN 'non-free' ELSE 'main' END AS section FROM packages WHERE release in ('sid') AND
package IN (SELECT * FROM covid19_packages)
) s ON s.package = co.package
+ LEFT JOIN (
+ SELECT package, string_agg(release, ',') AS releases FROM (
+ SELECT DISTINCT p.package, p.release, s.sort FROM packages p
+ JOIN releases s ON p.release = s.release
+ WHERE p.release in ('sid', 'bullseye', 'buster') AND
+ package IN (SELECT * FROM covid19_packages)
+ ORDER BY p.package, s.sort, p.release
+ ) tmp GROUP BY package
+ ) r ON r.package = co.package
ORDER BY package
;
END;
=====================================
covid-19_doc/bio_covid-19_dependencies_result
=====================================
@@ -1,98 +1,98 @@
-Last-Update: Tue, 12 May 2020 09:23:52 +0200
+Last-Update: Tue, 12 May 2020 09:52:09 +0200
- package | architectures | section
------------------------------+-------------------------+----------
- abacas | all | main
- allelecount | |
- ascat | |
- bcftools | amd64,arm64,ppc64el | main
- bedtools | amd64,arm64,ppc64el | main
- bio-guppy | |
- bowtie2 | amd64,arm64,ppc64el | main
- busco | |
- bustools | amd64 | main
- bwa | amd64,arm64,ppc64el | main
- cat | |
- centrifuge | amd64 | main
- changeo | all | main
- cutadapt | all | main
- diamond | all |
- drop-seq-tools | |
- fastp | amd64,arm64,ppc64el | main
- fastqc | all | main
- filtlong | |
- freebayes | amd64,arm64,ppc64el | main
- gatk | |
- graphmap2 | |
- ivar | |
- kallisto | amd64,arm64,ppc64el | main
- kraken2 | amd64,arm64,ppc64el | main
- libhts-dev | amd64,arm64,ppc64el | main
- lumpy | |
- manta | |
- megahit | |
- metabat | |
- minia | amd64,arm64,ppc64el | main
- minimap2 | amd64,arm64,ppc64el | main
- multiqc | all | main
- muscle | amd64,arm64,ppc64el | main
- nanolyse | |
- nanoplot | |
- ncbi-blast+ | amd64,arm64,ppc64el | main
- nextflow | |
- nf-core | |
- parallel-fastq-dump | |
- picard-tools | all,amd64 | main
- porechop | amd64,arm64,ppc64el | main
- presto | |
- prodigal | amd64,arm64,ppc64el | main
- pycoqc | all | main
- python3-biopython | amd64,arm64,ppc64el | main
- python3-deeptools | all | main
- python3-htseq | amd64,arm64,ppc64el | main
- python3-numpy | amd64,arm64,ppc64el | main
- python3-pandas | all | main
- qcat | all | main
- qualimap | |
- quast | |
- radiant | all | main
- r-bioc-deseq2 | amd64,arm64,ppc64el | main
- r-bioc-rtracklayer | amd64,arm64,ppc64el | main
- r-bioc-summarizedexperiment | all | main
- r-bioc-tximport | all | main
- r-cran-alakazam | amd64,arm64,ppc64el | main
- r-cran-corrplot | all | main
- r-cran-crosstalk | all | main
- r-cran-data.table | amd64,arm64,ppc64el | main
- r-cran-dt | all | main
- r-cran-ggplot2 | all | main
- r-cran-ggrepel | amd64,arm64,ppc64el | main
- r-cran-gprofiler | all | main
- r-cran-locfit | amd64,arm64,ppc64el | main
- r-cran-pheatmap | all | main
- r-cran-plotly | all | main
- r-cran-reshape2 | all,amd64,arm64,ppc64el | main
- r-cran-rjson | amd64,arm64,ppc64el | main
- r-cran-rlang | amd64,arm64,ppc64el | main
- r-cran-rmarkdown | all | main
- r-cran-scales | all,amd64,arm64,ppc64el | main
- r-cran-shazam | all | main
- r-cran-tigger | all | main
- rna-star | amd64,arm64,ppc64el | main
- salmon | amd64 | main
- samtools | amd64,arm64,ppc64el | main
- snakemake | all | main
- snpeff | |
- snpsift | |
- spades | amd64 | main
- sra-toolkit | amd64 | main
- strelka | |
- tiddit | |
- trim-galore | all | main
- unicycler | amd64 | main
- varscan | amd64 | non-free
- vcftools | amd64,arm64,ppc64el | main
- vep | |
- vg | amd64 | main
+ package | architectures | section | releases
+-----------------------------+---------------------+----------+---------------------
+ abacas | all | main | buster,bullseye,sid
+ allelecount | | |
+ ascat | | |
+ bcftools | amd64,arm64,ppc64el | main | buster,bullseye,sid
+ bedtools | amd64,arm64,ppc64el | main | buster,bullseye,sid
+ bio-guppy | | |
+ bowtie2 | amd64,arm64,ppc64el | main | buster,bullseye,sid
+ busco | | |
+ bustools | amd64 | main | bullseye,sid
+ bwa | amd64,arm64,ppc64el | main | buster,bullseye,sid
+ cat | | |
+ centrifuge | amd64 | main | buster,bullseye,sid
+ changeo | all | main | buster,bullseye,sid
+ cutadapt | all | main | buster,bullseye,sid
+ diamond-aligner | amd64,arm64,ppc64el | main | buster,bullseye,sid
+ drop-seq-tools | | |
+ fastp | amd64,arm64,ppc64el | main | buster,bullseye,sid
+ fastqc | all | main | buster,bullseye,sid
+ filtlong | | |
+ freebayes | amd64,arm64,ppc64el | main | buster,bullseye,sid
+ gatk | | |
+ 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 | | |
+ 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 | | |
+ ncbi-blast+ | amd64,arm64,ppc64el | main | buster,bullseye,sid
+ nextflow | | |
+ nf-core | | |
+ parallel-fastq-dump | | |
+ picard-tools | amd64 | main | buster,bullseye,sid
+ porechop | amd64,arm64,ppc64el | main | buster,bullseye,sid
+ presto | | |
+ prodigal | amd64,arm64,ppc64el | main | buster,bullseye,sid
+ pycoqc | all | main | sid
+ python3-biopython | amd64,arm64,ppc64el | main | buster,bullseye,sid
+ python3-deeptools | all | main | bullseye,sid
+ 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
+ qcat | all | main | bullseye,sid
+ qualimap | | |
+ 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
+ r-bioc-summarizedexperiment | all | main | buster,bullseye,sid
+ r-bioc-tximport | all | main | bullseye,sid
+ r-cran-alakazam | amd64,arm64,ppc64el | main | buster,bullseye,sid
+ r-cran-corrplot | all | main | bullseye,sid
+ r-cran-crosstalk | all | main | buster,bullseye,sid
+ r-cran-data.table | amd64,arm64,ppc64el | main | buster,bullseye,sid
+ r-cran-dt | all | main | buster,bullseye,sid
+ r-cran-ggplot2 | all | main | buster,bullseye,sid
+ r-cran-ggrepel | amd64,arm64,ppc64el | main | bullseye,sid
+ r-cran-gprofiler | all | main | bullseye,sid
+ r-cran-locfit | amd64,arm64,ppc64el | main | bullseye,sid
+ r-cran-pheatmap | all | main | buster,bullseye,sid
+ r-cran-plotly | all | main | buster,bullseye,sid
+ r-cran-reshape2 | amd64,arm64,ppc64el | main | buster,bullseye,sid
+ r-cran-rjson | amd64,arm64,ppc64el | main | buster,bullseye,sid
+ r-cran-rlang | amd64,arm64,ppc64el | main | buster,bullseye,sid
+ r-cran-rmarkdown | all | main | buster,bullseye,sid
+ r-cran-scales | all | main | buster,bullseye,sid
+ r-cran-shazam | all | main | buster,bullseye,sid
+ r-cran-tigger | all | main | buster,bullseye,sid
+ rna-star | amd64,arm64,ppc64el | main | buster,bullseye,sid
+ salmon | amd64 | main | buster,bullseye,sid
+ samtools | amd64,arm64,ppc64el | main | buster,bullseye,sid
+ snakemake | all | main | buster,bullseye,sid
+ snpeff | | |
+ snpsift | | |
+ spades | amd64 | main | buster,bullseye,sid
+ sra-toolkit | amd64 | main | buster,bullseye,sid
+ strelka | | |
+ tiddit | | |
+ trim-galore | all | main | bullseye,sid
+ unicycler | amd64 | main | buster,bullseye,sid
+ varscan | amd64 | non-free | buster,bullseye,sid
+ vcftools | amd64,arm64,ppc64el | main | buster,bullseye,sid
+ vep | | |
+ vg | amd64 | main | bullseye,sid
(92 Zeilen)
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/2e727e5a9c1fbce435e4db6bdbf3a21746d69e53...6f3899b8aaae9be5011455efad1367ec30b72557
--
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/2e727e5a9c1fbce435e4db6bdbf3a21746d69e53...6f3899b8aaae9be5011455efad1367ec30b72557
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