[Blends-commit] [Git][blends-team/med][master] 4 commits: Rename guppy to bio-guppy to not mess up with existing Debian package guppy
Andreas Tille
gitlab at salsa.debian.org
Tue May 12 08:25:06 BST 2020
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
6f63bf36 by Andreas Tille at 2020-05-12T08:25:04+02:00
Rename guppy to bio-guppy to not mess up with existing Debian package guppy
- - - - -
6610381f by Andreas Tille at 2020-05-12T08:37:25+02:00
Use temporary table to allow more flexibility
- - - - -
81223c9f by Andreas Tille at 2020-05-12T09:02:25+02:00
Use Debian binary package names
- - - - -
2e727e5a by Andreas Tille at 2020-05-12T09:24:44+02:00
Mark packages in non-free
- - - - -
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
=====================================
@@ -58,115 +58,122 @@ done
output="bio_covid-19_dependencies_result"
-if which psql-public-udd >/dev/null ; then
- RUNPSQL=psql-public-udd
-else
- RUNPSQL="psql $SERVICE"
-fi
-
echo "Last-Update: `date -R`" > "$output"
echo >> "$output"
-$RUNPSQL >>"$output" <<EOT
-SELECT package, string_agg(architecture, ',') as architectures FROM (
- SELECT DISTINCT package, architecture FROM packages WHERE
- architecture in ('all', 'amd64', 'arm64', 'ppc64el' ) and
- package in (
-'nextflow',
-'snakemake',
-'nf-core',
-'abacas',
-'allelecount',
-'ascat',
-'bcftools',
-'bedtools',
-'biopython',
-'ncbi-blast+',
-'bowtie2',
-'busco',
-'bustools',
-'bwa',
-'cat',
-'centrifuge',
-'changeo',
-'cutadapt',
-'diamond',
-'deeptools',
-'drop-seq-tools',
-'fastp',
-'fastqc',
-'filtlong',
-'freebayes',
-'gatk',
-'graphmap2',
-'guppy',
-'htslib',
-'htseq',
-'ivar',
-'java',
-'kallisto',
-'kraken2',
-'krona',
-'lumpy',
-'manta',
-'megahit',
-'metabat',
-'minia',
-'minimap2',
-'multiqc',
-'muscle',
-'nanolyse',
-'nanoplot',
-'numpy',
-'pandas',
-'parallel-fastq-dump',
-'picard',
-'porechop',
-'presto',
-'prodigal',
-'pycoqc',
-'qcat',
-'qualimap',
-'quast',
-'r-cran-alakazam',
-'r-cran-ggplot2',
-'r-cran-rmarkdown',
-'r-cran-shazam',
-'r-cran-tigger',
-'r-cran-locfit',
-'r-bioc-deseq2',
-'r-bioc-tximport',
-'r-cran-data.table',
-'r-cran-rlang',
-'r-cran-ggrepel',
-'r-cran-dt',
-'r-cran-pheatmap',
-'r-cran-corrplot',
-'r-cran-reshape2',
-'r-cran-plotly',
-'r-cran-scales',
-'r-cran-crosstalk',
-'r-cran-gprofiler',
-'r-bioc-summarizedexperiment',
-'r-bioc-rtracklayer',
-'r-cran-rjson',
-'salmon',
-'samtools',
-'snpeff',
-'snpsift',
-'spades',
-'sra-toolkit',
-'rna-star',
-'strelka',
-'tiddit',
-'trim-galore',
-'unicycler',
-'varscan2',
-'vcftools',
-'vep',
-'vg'
-)
- ORDER BY package, architecture
-) tmp GROUP by package ORDER BY package
+psql --quiet $SERVICE >>"$output" <<EOT
+BEGIN;
+
+CREATE TEMPORARY TABLE covid19_packages ( package text ) ;
+INSERT INTO covid19_packages VALUES
+('nextflow'),
+('snakemake'),
+('nf-core'),
+('abacas'),
+('allelecount'),
+('ascat'),
+('bcftools'),
+('bedtools'),
+('python3-biopython'),
+('ncbi-blast+'), -- == blast
+('bowtie2'),
+('busco'),
+('bustools'),
+('bwa'),
+('cat'),
+('centrifuge'),
+('changeo'),
+('cutadapt'),
+('diamond'),
+('python3-deeptools'),
+('drop-seq-tools'),
+('fastp'),
+('fastqc'),
+('filtlong'),
+('freebayes'),
+('gatk'),
+('graphmap2'),
+('bio-guppy'),
+('libhts-dev'),
+('python3-htseq'),
+('ivar'),
+('kallisto'),
+('kraken2'),
+('radiant'), -- == krona - Debian had to change the name
+('lumpy'),
+('manta'),
+('megahit'),
+('metabat'),
+('minia'),
+('minimap2'),
+('multiqc'),
+('muscle'),
+('nanolyse'),
+('nanoplot'),
+('python3-numpy'),
+('python3-pandas'),
+('parallel-fastq-dump'),
+('picard-tools'),
+('porechop'),
+('presto'),
+('prodigal'),
+('pycoqc'),
+('qcat'),
+('qualimap'),
+('quast'),
+('r-cran-alakazam'),
+('r-cran-ggplot2'),
+('r-cran-rmarkdown'),
+('r-cran-shazam'),
+('r-cran-tigger'),
+('r-cran-locfit'),
+('r-bioc-deseq2'),
+('r-bioc-tximport'),
+('r-cran-data.table'),
+('r-cran-rlang'),
+('r-cran-ggrepel'),
+('r-cran-dt'),
+('r-cran-pheatmap'),
+('r-cran-corrplot'),
+('r-cran-reshape2'),
+('r-cran-plotly'),
+('r-cran-scales'),
+('r-cran-crosstalk'),
+('r-cran-gprofiler'),
+('r-bioc-summarizedexperiment'),
+('r-bioc-rtracklayer'),
+('r-cran-rjson'),
+('salmon'),
+('samtools'),
+('snpeff'),
+('snpsift'),
+('spades'),
+('sra-toolkit'),
+('rna-star'),
+('strelka'),
+('tiddit'),
+('trim-galore'),
+('unicycler'),
+('varscan'),
+('vcftools'),
+('vep'),
+('vg')
+;
+
+SELECT co.package, architectures, s.section FROM covid19_packages co
+ LEFT JOIN (
+ SELECT package, string_agg(architecture, ',') AS architectures FROM (
+ SELECT DISTINCT package, architecture FROM packages WHERE
+ architecture IN ('all', 'amd64', 'arm64', 'ppc64el' ) AND
+ package IN (SELECT * FROM covid19_packages)
+ ORDER BY package, architecture
+ ) tmp GROUP BY package
+ ) p ON p.package = co.package
+ LEFT JOIN (
+ 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
+ ORDER BY package
;
+END;
EOT
=====================================
covid-19_doc/bio_covid-19_dependencies_result
=====================================
@@ -1,63 +1,98 @@
-Last-Update: Mon, 11 May 2020 21:59:45 +0200
+Last-Update: Tue, 12 May 2020 09:23:52 +0200
- package | architectures
------------------------------+-------------------------
- abacas | all
- bcftools | amd64,arm64,ppc64el
- bedtools | amd64,arm64,ppc64el
- bowtie2 | amd64,arm64,ppc64el
- bustools | amd64
- bwa | amd64,arm64,ppc64el
- centrifuge | amd64
- changeo | all
- cutadapt | all
- diamond | all
- fastp | amd64,arm64,ppc64el
- fastqc | all
- freebayes | amd64,arm64,ppc64el
- kallisto | amd64,arm64,ppc64el
- kraken2 | amd64,arm64,ppc64el
- minia | amd64,arm64,ppc64el
- minimap2 | amd64,arm64,ppc64el
- multiqc | all
- muscle | amd64,arm64,ppc64el
- ncbi-blast+ | amd64,arm64,ppc64el
- picard | amd64,arm64,ppc64el
- porechop | amd64,arm64,ppc64el
- prodigal | amd64,arm64,ppc64el
- pycoqc | all
- qcat | all
- r-bioc-deseq2 | amd64,arm64,ppc64el
- r-bioc-rtracklayer | amd64,arm64,ppc64el
- r-bioc-summarizedexperiment | all
- r-bioc-tximport | all
- r-cran-alakazam | amd64,arm64,ppc64el
- r-cran-corrplot | all
- r-cran-crosstalk | all
- r-cran-data.table | amd64,arm64,ppc64el
- r-cran-dt | all
- r-cran-ggplot2 | all
- r-cran-ggrepel | amd64,arm64,ppc64el
- r-cran-gprofiler | all
- r-cran-locfit | amd64,arm64,ppc64el
- r-cran-pheatmap | all
- r-cran-plotly | all
- r-cran-reshape2 | all,amd64,arm64,ppc64el
- r-cran-rjson | amd64,arm64,ppc64el
- r-cran-rlang | amd64,arm64,ppc64el
- r-cran-rmarkdown | all
- r-cran-scales | all,amd64,arm64,ppc64el
- r-cran-shazam | all
- r-cran-tigger | all
- rna-star | amd64,arm64,ppc64el
- salmon | amd64
- samtools | amd64,arm64,ppc64el
- snakemake | all
- spades | amd64
- sra-toolkit | amd64
- trim-galore | all
- unicycler | amd64
- vcftools | amd64,arm64,ppc64el
- vg | amd64
-(57 Zeilen)
+ 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
+(92 Zeilen)
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/5c05edc9953f2dfb1ff543e8833ddf76516320b1...2e727e5a9c1fbce435e4db6bdbf3a21746d69e53
--
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/5c05edc9953f2dfb1ff543e8833ddf76516320b1...2e727e5a9c1fbce435e4db6bdbf3a21746d69e53
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