[Blends-commit] [Git][blends-team/med][master] Add column test suite
Andreas Tille
gitlab at salsa.debian.org
Thu May 28 08:06:44 BST 2020
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
61c72573 by Andreas Tille at 2020-05-28T09:06:23+02:00
Add column test suite
- - - - -
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
=====================================
@@ -193,7 +193,8 @@ SELECT co.package, architectures, s.section,
ELSE r.releases
END AS releases,
conda.conda,
- bt.biotools AS "bio.tools"
+ bt.biotools AS "bio.tools",
+ t.testsuite
FROM covid19_packages co
LEFT JOIN (
SELECT package, string_agg(architecture, ',') AS architectures FROM (
@@ -233,6 +234,8 @@ SELECT co.package, architectures, s.section,
SELECT p.source, p.package, entry FROM registry r
JOIN (SELECT DISTINCT source, package FROM packages WHERE release in ('sid')) p ON r.source = p.source
WHERE name = 'bio.tools') tmp) bt ON bt.package = co.package
+ LEFT OUTER JOIN (SELECT DISTINCT p.package, p.source, s.testsuite FROM packages p
+ LEFT JOIN (SELECT source, testsuite FROM sources WHERE release = 'sid') s ON p.source = s.source ) t ON co.package = t.package
ORDER BY package
;
END;
=====================================
covid-19_doc/bio_covid-19_dependencies_result
=====================================
@@ -1,102 +1,104 @@
-Last-Update: Wed, 27 May 2020 23:05:59 +0200
+Last-Update: Thu, 28 May 2020 08:48:01 +0200
- package | architectures | section | releases | conda | bio.tools
----------------------+---------------------+----------+----------------------------------------------+----------------------+--------------
- abacas | all | main | buster,bullseye,sid | |
- allelecount | amd64,arm64,ppc64el | main | bullseye,sid | cancerit-allelecount |
- augustus | amd64,arm64,ppc64el | main | buster,bullseye,sid | augustus | AUGUSTUS
- bandage | amd64,arm64,ppc64el | main | buster,bullseye,sid | bandage | bandage
- bcftools | amd64,arm64,ppc64el | main | buster,bullseye,sid | bcftools | bcftools
- bedtools | amd64,arm64,ppc64el | main | buster,bullseye,sid | biotools | bedtools
- bio-guppy | | | | |
- bowtie2 | amd64,arm64,ppc64el | main | buster,bullseye,sid | bowtie2 | bowtie2
- busco | all | main | bullseye,sid | busco |
- bustools | amd64,arm64,ppc64el | main | bullseye,sid | bustools | BUStools
- bwa | amd64,arm64,ppc64el | main | buster,bullseye,sid | bwa | BWA
- cat-bat | amd64,arm64,ppc64el | main | sid | cat |
- centrifuge | amd64 | main | buster,bullseye,sid | centrifuge | Centrifuge
- changeo | all | main | buster,bullseye,sid | changeo |
- cutadapt | all | main | buster,bullseye,sid | cutadapt | cutadapt
- diamond-aligner | amd64,arm64,ppc64el | main | buster,bullseye,sid | diamond | Diamond
- drop-seq-tools | all | main | sid | dropseq_tools |
- fastp | amd64,arm64,ppc64el | main | buster,bullseye,sid | fastp |
- fastqc | all | main | buster,bullseye,sid | fastqc | FastQC
- filtlong | amd64,arm64,ppc64el | main | bullseye,sid | filtlong |
- flash | amd64,arm64,ppc64el | main | sid | flash |
- freebayes | amd64,arm64,ppc64el | main | buster,bullseye,sid | freebayes | freebayes
- gatk | | | https://salsa.debian.org/med-team/gatk | gatk4 |
- graphmap2 | | | https://salsa.debian.org/med-team/graphmap2 | graphmap |
- ivar | amd64,arm64 | main | sid | ivar |
- kallisto | amd64,arm64,ppc64el | main | bullseye,sid | kallisto | kallisto
- kmc | amd64,arm64,ppc64el | main | buster,bullseye,sid | kmc | KMC
- kraken2 | amd64,arm64,ppc64el | main | bullseye,sid | kraken2 | kraken
- libhts-dev | amd64,arm64,ppc64el | main | buster,bullseye,sid | htslib |
- lighter | | | | |
- lumpy-sv | | | https://salsa.debian.org/med-team/lumpy-sv | lumpy-sv |
- magicblast | | | | |
- manta | | | https://salsa.debian.org/med-team/manta | manta |
- mash | amd64,arm64,ppc64el | main | buster,bullseye,sid | mash |
- megahit | | | new | megahit |
- metabat | | | | |
- metaspades | | | | |
- minia | amd64,arm64,ppc64el | main | buster,bullseye,sid | minia | minia
- minimap2 | amd64,arm64,ppc64el | main | buster,bullseye,sid | minimap2 |
- multiqc | all | main | bullseye,sid | multiqc | multiqc
- muscle | amd64,arm64,ppc64el | main | buster,bullseye,sid | muscle | MUSCLE
- nanolyse | | | https://salsa.debian.org/med-team/nanolyse | nanolyse |
- nanoplot | | | https://salsa.debian.org/med-team/nanoplot | nanoplot |
- ncbi-blast+ | amd64,arm64,ppc64el | main | buster,bullseye,sid | blast | blast
- nextflow | | | https://salsa.debian.org/med-team/nextflow | |
- nf-core | | | | |
- parallel-fastq-dump | all | main | sid | parallel-fastq-dump |
- picard-tools | amd64 | main | buster,bullseye,sid | picard | Picard_tools
- pilon | all | main | buster,bullseye,sid | pilon | pilon
- porechop | amd64,arm64,ppc64el | main | buster,bullseye,sid | porechop |
- pplacer | | | https://salsa.debian.org/med-team/pplacer | pplacer |
- presto | | | | |
- prinseq-lite | all | main | bullseye,sid | |
- prodigal | amd64,arm64,ppc64el | main | buster,bullseye,sid | prodigal |
- pycoqc | all | main | bullseye,sid | pycoqc |
- python3-anndata | | | new | anndata |
- python3-biopython | amd64,arm64,ppc64el | main | buster,bullseye,sid | | Biopython
- python3-deeptools | all | main | bullseye,sid | deeptools | deeptools
- python3-h5py | all | main | buster,bullseye,sid | |
- python3-htseq | amd64,arm64,ppc64el | main | buster,bullseye,sid | htseq | htseq
- python3-numpy | amd64,arm64,ppc64el | main | buster,bullseye,sid | |
- python3-pandas | all | main | buster,bullseye,sid | |
- qcat | all | main | bullseye,sid | qcat |
- qualimap | | | https://salsa.debian.org/med-team/qualimap | qualimap |
- quast | | | https://salsa.debian.org/med-team/quast | quast |
- radiant | all | main | buster,bullseye,sid | | krona
- r-cran-alakazam | amd64,arm64,ppc64el | main | buster,bullseye,sid | |
- r-cran-shazam | all | main | buster,bullseye,sid | r-shazam |
- r-cran-tigger | all | main | buster,bullseye,sid | r-tigger |
- rna-star | amd64,arm64,ppc64el | main | buster,bullseye,sid | star | star
- r-other-ascat | all | main | sid | ascat |
- salmon | amd64 | main | buster,bullseye,sid | salmon | salmon
- samclip | | | https://salsa.debian.org/med-team/samclip | samclip |
- samtools | amd64,arm64,ppc64el | main | buster,bullseye,sid | samtools | samtools
- sepp | | | https://salsa.debian.org/med-team/sepp | sepp |
- seqtk | amd64,arm64,ppc64el | main | buster,bullseye,sid | seqtk | seqtk
- seqwish | | | https://salsa.debian.org/med-team/seqwish | seqwish |
- skesa | amd64 | main | bullseye,sid | skesa |
- snakemake | all | main | buster,bullseye,sid | snakemake | snakemake
- snpeff | | | https://salsa.debian.org/med-team/snpeff | snpeff |
- snpsift | | | https://salsa.debian.org/med-team/snpeff | snpeff |
- spades | amd64 | main | buster,bullseye,sid | spades | Spades
- sra-toolkit | amd64 | main | buster,bullseye,sid | sra-tools | sra-tools
- strelka | | | https://salsa.debian.org/med-team/strelka | strelka |
- tiddit | | | https://salsa.debian.org/med-team/tiddit | tiddit |
- tigr-glimmer | amd64,arm64,ppc64el | main | buster,bullseye,sid | glimmer | glimmer
- trim-galore | all | main | bullseye,sid | trim-galore |
- trimmomatic | all | main | buster,bullseye,sid | trimmomatic | Trimmomatic
- umap-learn | | | https://salsa.debian.org/med-team/umap-learn | |
- unicycler | amd64 | main | buster,bullseye,sid | unicycler | unicycler
- varscan | amd64 | non-free | buster,bullseye,sid | varscan | varscan
- vcftools | amd64,arm64,ppc64el | main | buster,bullseye,sid | vcftools | vcftools
- velvet | amd64,arm64,ppc64el | main | buster,bullseye,sid | velvet | velvet
- vep | | | | |
- vg | amd64 | main | bullseye,sid | vg |
- vsearch | amd64,ppc64el | main | buster,bullseye,sid | vsearch | vsearch
-(96 Zeilen)
+ package | architectures | section | releases | conda | bio.tools | testsuite
+---------------------+---------------------+----------+----------------------------------------------+----------------------+--------------+-------------------------------------
+ abacas | all | main | buster,bullseye,sid | | |
+ allelecount | amd64,arm64,ppc64el | main | bullseye,sid | cancerit-allelecount | | autopkgtest-pkg-perl
+ augustus | amd64,arm64,ppc64el | main | buster,bullseye,sid | augustus | AUGUSTUS | autopkgtest
+ bandage | amd64,arm64,ppc64el | main | buster,bullseye,sid | bandage | bandage |
+ bcftools | amd64,arm64,ppc64el | main | buster,bullseye,sid | bcftools | bcftools | autopkgtest
+ bedtools | amd64,arm64,ppc64el | main | buster,bullseye,sid | biotools | bedtools | autopkgtest
+ bio-guppy | | | | | |
+ bowtie2 | amd64,arm64,ppc64el | main | buster,bullseye,sid | bowtie2 | bowtie2 | autopkgtest
+ busco | all | main | bullseye,sid | busco | |
+ bustools | amd64,arm64,ppc64el | main | bullseye,sid | bustools | BUStools |
+ bwa | amd64,arm64,ppc64el | main | buster,bullseye,sid | bwa | BWA | autopkgtest
+ cat-bat | amd64,arm64,ppc64el | main | sid | cat | |
+ centrifuge | amd64 | main | buster,bullseye,sid | centrifuge | Centrifuge |
+ changeo | all | main | buster,bullseye,sid | changeo | | autopkgtest-pkg-python
+ cutadapt | all | main | buster,bullseye,sid | cutadapt | cutadapt | autopkgtest-pkg-python
+ diamond-aligner | amd64,arm64,ppc64el | main | buster,bullseye,sid | diamond | Diamond | autopkgtest
+ diamond-aligner | amd64,arm64,ppc64el | main | buster,bullseye,sid | diamond | Diamond |
+ drop-seq-tools | all | main | sid | dropseq_tools | |
+ fastp | amd64,arm64,ppc64el | main | buster,bullseye,sid | fastp | | autopkgtest
+ fastqc | all | main | buster,bullseye,sid | fastqc | FastQC | autopkgtest
+ filtlong | amd64,arm64,ppc64el | main | bullseye,sid | filtlong | | autopkgtest
+ flash | amd64,arm64,ppc64el | main | sid | flash | |
+ freebayes | amd64,arm64,ppc64el | main | buster,bullseye,sid | freebayes | freebayes |
+ gatk | | | https://salsa.debian.org/med-team/gatk | gatk4 | |
+ graphmap2 | | | https://salsa.debian.org/med-team/graphmap2 | graphmap | |
+ ivar | amd64,arm64 | main | sid | ivar | |
+ kallisto | amd64,arm64,ppc64el | main | bullseye,sid | kallisto | kallisto | autopkgtest
+ kmc | amd64,arm64,ppc64el | main | buster,bullseye,sid | kmc | KMC | autopkgtest
+ kraken2 | amd64,arm64,ppc64el | main | bullseye,sid | kraken2 | kraken | autopkgtest
+ libhts-dev | amd64,arm64,ppc64el | main | buster,bullseye,sid | htslib | | autopkgtest
+ lighter | | | | | |
+ lumpy-sv | | | https://salsa.debian.org/med-team/lumpy-sv | lumpy-sv | |
+ magicblast | | | | | |
+ manta | | | https://salsa.debian.org/med-team/manta | manta | |
+ mash | amd64,arm64,ppc64el | main | buster,bullseye,sid | mash | | autopkgtest
+ megahit | | | new | megahit | |
+ metabat | | | | | |
+ metaspades | | | | | |
+ minia | amd64,arm64,ppc64el | main | buster,bullseye,sid | minia | minia | autopkgtest
+ minimap2 | amd64,arm64,ppc64el | main | buster,bullseye,sid | minimap2 | | autopkgtest
+ multiqc | all | main | bullseye,sid | multiqc | multiqc |
+ muscle | amd64,arm64,ppc64el | main | buster,bullseye,sid | muscle | MUSCLE | autopkgtest
+ nanolyse | | | https://salsa.debian.org/med-team/nanolyse | nanolyse | |
+ nanoplot | | | https://salsa.debian.org/med-team/nanoplot | nanoplot | |
+ ncbi-blast+ | amd64,arm64,ppc64el | main | buster,bullseye,sid | blast | blast | autopkgtest
+ nextflow | | | https://salsa.debian.org/med-team/nextflow | | |
+ nf-core | | | | | |
+ parallel-fastq-dump | all | main | sid | parallel-fastq-dump | |
+ picard-tools | amd64 | main | buster,bullseye,sid | picard | Picard_tools | autopkgtest
+ pilon | all | main | buster,bullseye,sid | pilon | pilon |
+ porechop | amd64,arm64,ppc64el | main | buster,bullseye,sid | porechop | | autopkgtest
+ pplacer | | | https://salsa.debian.org/med-team/pplacer | pplacer | |
+ presto | | | | | |
+ prinseq-lite | all | main | bullseye,sid | | | autopkgtest
+ prodigal | amd64,arm64,ppc64el | main | buster,bullseye,sid | prodigal | | autopkgtest
+ pycoqc | all | main | bullseye,sid | pycoqc | |
+ python3-anndata | | | new | anndata | |
+ python3-biopython | amd64,arm64,ppc64el | main | buster,bullseye,sid | | Biopython | autopkgtest
+ python3-deeptools | all | main | bullseye,sid | deeptools | deeptools | autopkgtest, autopkgtest-pkg-python
+ python3-h5py | all | main | buster,bullseye,sid | | | autopkgtest
+ python3-htseq | amd64,arm64,ppc64el | main | buster,bullseye,sid | htseq | htseq | autopkgtest
+ python3-numpy | amd64,arm64,ppc64el | main | buster,bullseye,sid | | | autopkgtest
+ python3-numpy | amd64,arm64,ppc64el | main | buster,bullseye,sid | | | autopkgtest
+ python3-pandas | all | main | buster,bullseye,sid | | | autopkgtest
+ qcat | all | main | bullseye,sid | qcat | | autopkgtest
+ qualimap | | | https://salsa.debian.org/med-team/qualimap | qualimap | |
+ quast | | | https://salsa.debian.org/med-team/quast | quast | |
+ radiant | all | main | buster,bullseye,sid | | krona |
+ r-cran-alakazam | amd64,arm64,ppc64el | main | buster,bullseye,sid | | | autopkgtest-pkg-r
+ r-cran-shazam | all | main | buster,bullseye,sid | r-shazam | | autopkgtest-pkg-r
+ r-cran-tigger | all | main | buster,bullseye,sid | r-tigger | | autopkgtest-pkg-r
+ rna-star | amd64,arm64,ppc64el | main | buster,bullseye,sid | star | star | autopkgtest
+ r-other-ascat | all | main | sid | ascat | | autopkgtest-pkg-r
+ salmon | amd64 | main | buster,bullseye,sid | salmon | salmon |
+ samclip | | | https://salsa.debian.org/med-team/samclip | samclip | |
+ samtools | amd64,arm64,ppc64el | main | buster,bullseye,sid | samtools | samtools | autopkgtest
+ sepp | | | https://salsa.debian.org/med-team/sepp | sepp | |
+ seqtk | amd64,arm64,ppc64el | main | buster,bullseye,sid | seqtk | seqtk | autopkgtest
+ seqwish | | | https://salsa.debian.org/med-team/seqwish | seqwish | |
+ skesa | amd64 | main | bullseye,sid | skesa | |
+ snakemake | all | main | buster,bullseye,sid | snakemake | snakemake | autopkgtest
+ snpeff | | | https://salsa.debian.org/med-team/snpeff | snpeff | |
+ snpsift | | | https://salsa.debian.org/med-team/snpeff | snpeff | |
+ spades | amd64 | main | buster,bullseye,sid | spades | Spades | autopkgtest
+ sra-toolkit | amd64 | main | buster,bullseye,sid | sra-tools | sra-tools | autopkgtest
+ strelka | | | https://salsa.debian.org/med-team/strelka | strelka | |
+ tiddit | | | https://salsa.debian.org/med-team/tiddit | tiddit | |
+ tigr-glimmer | amd64,arm64,ppc64el | main | buster,bullseye,sid | glimmer | glimmer | autopkgtest
+ trim-galore | all | main | bullseye,sid | trim-galore | | autopkgtest
+ trimmomatic | all | main | buster,bullseye,sid | trimmomatic | Trimmomatic | autopkgtest
+ umap-learn | | | https://salsa.debian.org/med-team/umap-learn | | |
+ unicycler | amd64 | main | buster,bullseye,sid | unicycler | unicycler | autopkgtest
+ varscan | amd64 | non-free | buster,bullseye,sid | varscan | varscan |
+ vcftools | amd64,arm64,ppc64el | main | buster,bullseye,sid | vcftools | vcftools | autopkgtest
+ velvet | amd64,arm64,ppc64el | main | buster,bullseye,sid | velvet | velvet | autopkgtest
+ vep | | | | | |
+ vg | amd64 | main | bullseye,sid | vg | | autopkgtest
+ vsearch | amd64,ppc64el | main | buster,bullseye,sid | vsearch | vsearch |
+(98 Zeilen)
View it on GitLab: https://salsa.debian.org/blends-team/med/-/commit/61c7257337b27b3e41bfb1f86a61a2722c80e57a
--
View it on GitLab: https://salsa.debian.org/blends-team/med/-/commit/61c7257337b27b3e41bfb1f86a61a2722c80e57a
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