[Blends-commit] [Git][blends-team/med][master] 2 commits: Add conda name
Andreas Tille
gitlab at salsa.debian.org
Tue May 12 09:56:10 BST 2020
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
3cc416a9 by Andreas Tille at 2020-05-12T10:48:45+02:00
Add conda name
- - - - -
dd6b6285 by Andreas Tille at 2020-05-12T10:51:12+02:00
Add bio.tools entry
- - - - -
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
=====================================
@@ -166,7 +166,9 @@ SELECT co.package, architectures, s.section,
CASE WHEN vcs.vcs_browser IS NULL THEN '' ELSE vcs.vcs_browser END
ELSE 'new' END
ELSE r.releases
- END AS releases
+ END AS releases,
+ conda.conda,
+ bt.biotools AS "bio.tools"
FROM covid19_packages co
LEFT JOIN (
SELECT package, string_agg(architecture, ',') AS architectures FROM (
@@ -191,6 +193,14 @@ SELECT co.package, architectures, s.section,
) 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
+ LEFT JOIN (SELECT DISTINCT package, entry AS conda FROM (
+ 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 = 'conda:bioconda') tmp) conda ON conda.package = co.package
+ LEFT JOIN (SELECT DISTINCT package, entry AS biotools FROM (
+ 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
ORDER BY package
;
END;
=====================================
covid-19_doc/bio_covid-19_dependencies_result
=====================================
@@ -1,99 +1,98 @@
-Last-Update: Tue, 12 May 2020 10:13:05 +0200
+Last-Update: Tue, 12 May 2020 10:50:33 +0200
- 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 | | | https://salsa.debian.org/med-team/filtlong
- freebayes | amd64,arm64,ppc64el | main | buster,bullseye,sid
- 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 | | | 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 | | | https://salsa.debian.org/med-team/nanoplot
- ncbi-blast+ | amd64,arm64,ppc64el | main | buster,bullseye,sid
- nextflow | | | https://salsa.debian.org/med-team/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
- python3-pauvre | | | new
- qcat | all | main | bullseye,sid
- 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
- 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 | | | https://salsa.debian.org/med-team/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
-(93 Zeilen)
+ package | architectures | section | releases | conda | bio.tools
+-----------------------------+---------------------+----------+---------------------------------------------+--------------------------+--------------
+ abacas | all | main | buster,bullseye,sid | |
+ allelecount | | | | |
+ ascat | | | | |
+ 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 | | | | |
+ bustools | amd64 | main | bullseye,sid | bustools | BUStools
+ bwa | amd64,arm64,ppc64el | main | buster,bullseye,sid | bwa | BWA
+ 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 | | | | |
+ fastp | amd64,arm64,ppc64el | main | buster,bullseye,sid | fastp |
+ fastqc | all | main | buster,bullseye,sid | fastqc | FastQC
+ filtlong | | | https://salsa.debian.org/med-team/filtlong | |
+ freebayes | amd64,arm64,ppc64el | main | buster,bullseye,sid | freebayes | freebayes
+ gatk | | | https://salsa.debian.org/med-team/gatk | |
+ graphmap2 | | | https://salsa.debian.org/med-team/graphmap2 | |
+ ivar | | | | |
+ kallisto | amd64,arm64,ppc64el | main | bullseye,sid | kallisto | kallisto
+ kraken2 | amd64,arm64,ppc64el | main | bullseye,sid | kraken2 | kraken
+ libhts-dev | amd64,arm64,ppc64el | main | buster,bullseye,sid | htslib |
+ lumpy | | | | |
+ 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 | | 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 | | | | |
+ nanoplot | | | https://salsa.debian.org/med-team/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 | | | | |
+ picard-tools | amd64 | main | buster,bullseye,sid | picard | Picard_tools
+ 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 | | Biopython
+ python3-deeptools | all | main | bullseye,sid | deeptools | deeptools
+ python3-htseq | amd64,arm64,ppc64el | main | buster,bullseye,sid | | htseq
+ python3-numpy | amd64,arm64,ppc64el | main | buster,bullseye,sid | |
+ python3-pandas | all | main | buster,bullseye,sid | |
+ qcat | all | main | bullseye,sid | |
+ qualimap | | | https://salsa.debian.org/med-team/qualimap | |
+ quast | | | https://salsa.debian.org/med-team/quast | |
+ radiant | all | main | buster,bullseye,sid | | krona
+ r-bioc-deseq2 | amd64,arm64,ppc64el | main | buster,bullseye,sid | bioconductor-deseq2 | deseq2
+ r-bioc-rtracklayer | amd64,arm64,ppc64el | main | buster,bullseye,sid | bioconductor-rtracklayer | rtracklayer
+ r-bioc-summarizedexperiment | all | main | buster,bullseye,sid | |
+ r-bioc-tximport | all | main | bullseye,sid | bioconductor-tximport | tximport
+ 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-dt |
+ 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-shazam |
+ r-cran-tigger | all | main | buster,bullseye,sid | r-tigger |
+ rna-star | amd64,arm64,ppc64el | main | buster,bullseye,sid | star | star
+ salmon | amd64 | main | buster,bullseye,sid | salmon | salmon
+ samtools | amd64,arm64,ppc64el | main | buster,bullseye,sid | samtools | samtools
+ snakemake | all | main | buster,bullseye,sid | snakemake | snakemake
+ snpeff | | | https://salsa.debian.org/med-team/snpeff | |
+ snpsift | | | | |
+ spades | amd64 | main | buster,bullseye,sid | spades | Spades
+ sra-toolkit | amd64 | main | buster,bullseye,sid | sra-tools | sra-tools
+ strelka | | | | |
+ tiddit | | | | |
+ trim-galore | all | main | bullseye,sid | trim-galore |
+ 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
+ vep | | | | |
+ vg | amd64 | main | bullseye,sid | |
+(92 Zeilen)
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/cf47dafbca50463e7436f934c5f03e4fde6d3081...dd6b6285a4d648b26774268147052a2926d09b14
--
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/cf47dafbca50463e7436f934c5f03e4fde6d3081...dd6b6285a4d648b26774268147052a2926d09b14
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