[Blends-commit] [Git][blends-team/med][master] 2 commits: Inject more packages mentioned in Jun's document
Andreas Tille
gitlab at salsa.debian.org
Sun Jun 7 19:32:20 BST 2020
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
40b6c7e0 by Andreas Tille at 2020-06-07T20:32:10+02:00
Inject more packages mentioned in Jun's document
- - - - -
c71441af by Andreas Tille at 2020-06-07T20:32:10+02:00
Update UDD
- - - - -
3 changed files:
- covid-19_doc/bio_covid-19_dependencies_query
- covid-19_doc/bio_covid-19_dependencies_result
- tasks/covid-19
Changes:
=====================================
covid-19_doc/bio_covid-19_dependencies_query
=====================================
@@ -144,50 +144,58 @@ INSERT INTO covid19_packages VALUES
(DEFAULT,'mosdepth'),
(DEFAULT,'multiqc'),
(DEFAULT,'muscle'),
+(DEFAULT,'nanofilt'),
(DEFAULT,'nanolyse'),
+(DEFAULT,'python3-nanomath'),
+(DEFAULT,'nanopolish'),
+(DEFAULT,'nanook'),
+(DEFAULT,'nanoraw'),
+(DEFAULT,'nanosv'),
+(DEFAULT,'ngmlr'),
+(DEFAULT,'oncofuse'),
+(DEFAULT,'optitype'),
(DEFAULT,'nanoplot'),
-(DEFAULT,'python3-numpy'),
-(DEFAULT,'python3-pandas'),
(DEFAULT,'parallel-fastq-dump'),
+(DEFAULT,'python3-pauvre'),
+(DEFAULT,'picopore'),
+(DEFAULT,'pinfish'),
+(DEFAULT,'plasmidid'),
(DEFAULT,'picard-tools'),
(DEFAULT,'pilon'),
+(DEFAULT,'pomoxis'),
+(DEFAULT,'pore'),
+(DEFAULT,'pore-c'),
(DEFAULT,'porechop'),
+(DEFAULT,'porejuicer'),
+(DEFAULT,'poretools'),
(DEFAULT,'pplacer'),
(DEFAULT,'presto'),
(DEFAULT,'prinseq-lite'),
(DEFAULT,'prodigal'),
+(DEFAULT,'pybedtools-bin'),
+(DEFAULT,'pychopper'),
(DEFAULT,'pycoqc'),
+(DEFAULT,'pyomo'),
+(DEFAULT,'python3-pysam'),
+(DEFAULT,'python3-vcf'),
(DEFAULT,'qcat'),
+(DEFAULT,'qsignature'),
(DEFAULT,'qualimap'),
(DEFAULT,'quast'),
(DEFAULT,'r-cran-alakazam'),
(DEFAULT,'r-cran-shazam'),
(DEFAULT,'r-cran-tigger'),
-/*
-(DEFAULT,'r-cran-ggplot2'),
-(DEFAULT,'r-cran-rmarkdown'),
-(DEFAULT,'r-cran-locfit'),
-(DEFAULT,'r-bioc-deseq2'),
-(DEFAULT,'r-bioc-tximport'),
-(DEFAULT,'r-cran-data.table'),
-(DEFAULT,'r-cran-rlang'),
-(DEFAULT,'r-cran-ggrepel'),
-(DEFAULT,'r-cran-dt'),
-(DEFAULT,'r-cran-pheatmap'),
-(DEFAULT,'r-cran-corrplot'),
-(DEFAULT,'r-cran-reshape2'),
-(DEFAULT,'r-cran-plotly'),
-(DEFAULT,'r-cran-scales'),
-(DEFAULT,'r-cran-crosstalk'),
-(DEFAULT,'r-cran-gprofiler'),
-(DEFAULT,'r-bioc-summarizedexperiment'),
-(DEFAULT,'r-bioc-rtracklayer'),
-(DEFAULT,'r-cran-rjson'),
-*/
+(DEFAULT,'r-bioc-rsamtools'),
+(DEFAULT,'sailfish'),
(DEFAULT,'salmon'),
+(DEFAULT,'samblaster'),
(DEFAULT,'samclip'),
(DEFAULT,'samtools'),
+(DEFAULT,'scrappie'),
(DEFAULT,'sepp'),
+(DEFAULT,'python3-seqcluster'),
+(DEFAULT,'seqlib'),
+(DEFAULT,'seqkit'),
(DEFAULT,'seqtk'),
(DEFAULT,'seqwish'),
(DEFAULT,'skesa'),
@@ -196,10 +204,15 @@ INSERT INTO covid19_packages VALUES
(DEFAULT,'spades'),
(DEFAULT,'sra-toolkit'),
(DEFAULT,'rna-star'),
+(DEFAULT,'streamformatics'),
(DEFAULT,'strelka'),
(DEFAULT,'tiddit'),
+(DEFAULT,'tombo'),
+(DEFAULT,'tophat-recondition'),
+(DEFAULT,'tornado'),
(DEFAULT,'trim-galore'),
(DEFAULT,'trimmomatic'),
+(DEFAULT,'tulip'),
(DEFAULT,'umap-learn'),
(DEFAULT,'unicycler'),
(DEFAULT,'varscan'),
@@ -207,9 +220,16 @@ INSERT INTO covid19_packages VALUES
(DEFAULT,'velvet'),
(DEFAULT,'ensembl-vep'),
(DEFAULT,'vg'),
+(DEFAULT,'viennarna'),
(DEFAULT,'vsearch'),
(DEFAULT,'vt'),
-(DEFAULT,'wham-align')
+(DEFAULT,'wham-align'),
+(DEFAULT,'yanagiba'),
+(DEFAULT,'yanosim'),
+(DEFAULT,'python3-numpy'),
+(DEFAULT,'python3-pandas'),
+(DEFAULT,'python3-toolz'),
+(DEFAULT,'python3-tornado')
;
SELECT co.package, architectures, s.section,
=====================================
covid-19_doc/bio_covid-19_dependencies_result
=====================================
@@ -1,131 +1,172 @@
-Last-Update: Sat, 06 Jun 2020 07:14:46 +0200
+Last-Update: Sun, 07 Jun 2020 20:27:29 +0200
- package | architectures | section | releases | conda | bio.tools | testsuite
-------------------------+---------------------+----------+-----------------------------------------------+----------------------+---------------+-------------------------------------
- nextflow | | | https://salsa.debian.org/med-team/nextflow | | |
- capsule | | | | | |
- snakemake | all | main | buster,bullseye,sid | snakemake | snakemake | autopkgtest
- artic | | | | | |
- bcbio | all | main | buster,bullseye,sid | bcbio-nextgen | bcbio-nextgen | autopkgtest-pkg-python
- pigx-rnaseq | | | https://salsa.debian.org/med-team/pigx-rnaseq | | |
- scrnaseq | | | | | |
- shovill | | | | | |
- smartseq2 | | | | | |
- viralcon | | | | | |
- nf-core | | | | | |
- abacas | all | main | buster,bullseye,sid | | |
- allelecount | amd64,arm64,ppc64el | main | bullseye,sid | cancerit-allelecount | | autopkgtest-pkg-perl
- python3-anndata | | | new | anndata | |
- libargs-dev | | | new | | |
- arvados | | | https://salsa.debian.org/med-team/arvados | | |
- r-other-ascat | all | main | sid | ascat | | autopkgtest-pkg-r
- libatomicbitvector-dev | | | new | | |
- augustus | amd64,arm64,ppc64el | main | buster,bullseye,sid | augustus | AUGUSTUS | autopkgtest
- bandage | amd64,arm64,ppc64el | main | buster,bullseye,sid | bandage | bandage |
- libbbhash-dev | | | new | | |
- bcftools | amd64,arm64,ppc64el | main | buster,bullseye,sid | bcftools | bcftools | autopkgtest
- bedtools | amd64,arm64,ppc64el | main | buster,bullseye,sid | biotools | bedtools | autopkgtest
- python3-biopython | amd64,arm64,ppc64el | main | buster,bullseye,sid | | Biopython | autopkgtest
- ncbi-blast+ | amd64,arm64,ppc64el | main | buster,bullseye,sid | blast | blast | autopkgtest
- 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 | bullseye,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 |
- diamond-aligner | amd64,arm64,ppc64el | main | buster,bullseye,sid | diamond | Diamond | autopkgtest
- python3-deeptools | all | main | bullseye,sid | deeptools | deeptools | autopkgtest, autopkgtest-pkg-python
- 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
- flappie | | | | | |
- flash | amd64,arm64,ppc64el | main | bullseye,sid | flash | |
- flye | | | | | |
- freebayes | amd64,arm64,ppc64el | main | buster,bullseye,sid | freebayes | freebayes | autopkgtest
- gatk | | | https://salsa.debian.org/med-team/gatk | gatk4 | |
- tigr-glimmer | amd64,arm64,ppc64el | main | buster,bullseye,sid | glimmer | glimmer | autopkgtest
- graphmap2 | | | https://salsa.debian.org/med-team/graphmap2 | graphmap | |
- bio-guppy | | | | | |
- python3-h5py | all | main | buster,bullseye,sid | | | autopkgtest
- r-bioc-htsfilter | all | main | bullseye,sid | | | autopkgtest, autopkgtest-pkg-r
- libhts-dev | amd64,arm64,ppc64el | main | buster,bullseye,sid | htslib | | autopkgtest
- python3-htseq | amd64,arm64,ppc64el | main | buster,bullseye,sid | htseq | htseq | autopkgtest
- iitii | | | | | |
- ivar | amd64,arm64 | main | bullseye,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
- radiant | all | main | buster,bullseye,sid | | krona |
- lighter | | | new | lighter | |
- lumpy-sv | | | new | lumpy-sv | |
- magicblast | | | | | |
- manta | | | https://salsa.debian.org/med-team/manta | manta | |
- mash | amd64,arm64,ppc64el | main | buster,bullseye,sid | mash | | autopkgtest
- masurca | | | | | |
- mcaller | | | | | |
- mecat2 | | | | | |
- medaka | | | | | |
- megahit | | | new | megahit | |
- megalodon | | | | | |
- metabat | | | new | metabat2 | |
- metaspades | | | | | |
- minia | amd64,arm64,ppc64el | main | buster,bullseye,sid | minia | minia | autopkgtest
- minimap2 | amd64,arm64,ppc64el | main | buster,bullseye,sid | minimap2 | | autopkgtest
- minitour | | | | | |
- libmmap-allocator-dev | | | | | |
- mmmulti | | | | | |
- mosdepth | | | https://salsa.debian.org/med-team/mosdepth | mosdepth | |
- 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 | |
- 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
- 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 | |
- 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 | |
- 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
- salmon | amd64 | main | buster,bullseye,sid | salmon | salmon |
- samclip | | | new | 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 | |
- 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
- rna-star | amd64,arm64,ppc64el | main | buster,bullseye,sid | star | star | autopkgtest
- strelka | | | https://salsa.debian.org/med-team/strelka | strelka | |
- tiddit | | | new | tiddit | |
- trim-galore | all | main | bullseye,sid | trim-galore | | autopkgtest
- trimmomatic | all | main | buster,bullseye,sid | trimmomatic | Trimmomatic | autopkgtest
- umap-learn | | | new | | |
- 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
- ensembl-vep | | | https://salsa.debian.org/med-team/ensembl-vep | ensembl-vep | |
- vg | amd64 | main | bullseye,sid | vg | | autopkgtest
- vsearch | amd64,ppc64el | main | buster,bullseye,sid | vsearch | vsearch |
- vt | | | | | |
- wham-align | amd64 | main | bullseye,sid | wham | wham |
-(125 Zeilen)
+ package | architectures | section | releases | conda | bio.tools | testsuite
+------------------------+---------------------+----------+-----------------------------------------------------+----------------------+---------------+-------------------------------------
+ nextflow | | | https://salsa.debian.org/med-team/nextflow | | |
+ capsule | | | | | |
+ snakemake | all | main | buster,bullseye,sid | snakemake | snakemake | autopkgtest
+ artic | | | | | |
+ bcbio | all | main | buster,bullseye,sid | bcbio-nextgen | bcbio-nextgen | autopkgtest-pkg-python
+ pigx-rnaseq | | | https://salsa.debian.org/med-team/pigx-rnaseq | | |
+ scrnaseq | | | | | |
+ shovill | | | | | |
+ smartseq2 | | | | | |
+ viralcon | | | | | |
+ nf-core | | | | | |
+ abacas | all | main | buster,bullseye,sid | | |
+ allelecount | amd64,arm64,ppc64el | main | bullseye,sid | cancerit-allelecount | | autopkgtest-pkg-perl
+ python3-anndata | | | new | anndata | |
+ libargs-dev | | | new | | |
+ arvados | | | https://salsa.debian.org/med-team/arvados | | |
+ r-other-ascat | all | main | sid | ascat | | autopkgtest-pkg-r
+ libatomicbitvector-dev | | | new | | |
+ augustus | amd64,arm64,ppc64el | main | buster,bullseye,sid | augustus | AUGUSTUS | autopkgtest
+ bandage | amd64,arm64,ppc64el | main | buster,bullseye,sid | bandage | bandage |
+ libbbhash-dev | | | new | | |
+ bcftools | amd64,arm64,ppc64el | main | buster,bullseye,sid | bcftools | bcftools | autopkgtest
+ bedtools | amd64,arm64,ppc64el | main | buster,bullseye,sid | biotools | bedtools | autopkgtest
+ python3-biopython | amd64,arm64,ppc64el | main | buster,bullseye,sid | | Biopython | autopkgtest
+ ncbi-blast+ | amd64,arm64,ppc64el | main | buster,bullseye,sid | blast | blast | autopkgtest
+ 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 | bullseye,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 |
+ diamond-aligner | amd64,arm64,ppc64el | main | buster,bullseye,sid | diamond | Diamond | autopkgtest
+ python3-deeptools | all | main | bullseye,sid | deeptools | deeptools | autopkgtest, autopkgtest-pkg-python
+ drop-seq-tools | all | main | bullseye,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
+ flappie | | | https://salsa.debian.org/med-team/flappie | | |
+ flash | amd64,arm64,ppc64el | main | bullseye,sid | flash | |
+ flye | | | https://salsa.debian.org/med-team/flye | flye | |
+ freebayes | amd64,arm64,ppc64el | main | buster,bullseye,sid | freebayes | freebayes | autopkgtest
+ gatk | | | https://salsa.debian.org/med-team/gatk | gatk4 | |
+ tigr-glimmer | amd64,arm64,ppc64el | main | buster,bullseye,sid | glimmer | glimmer | autopkgtest
+ graphmap2 | | | https://salsa.debian.org/med-team/graphmap2 | graphmap | |
+ bio-guppy | | | | | |
+ python3-h5py | all | main | buster,bullseye,sid | | | autopkgtest
+ r-bioc-htsfilter | all | main | bullseye,sid | | | autopkgtest, autopkgtest-pkg-r
+ libhts-dev | amd64,arm64,ppc64el | main | buster,bullseye,sid | htslib | | autopkgtest
+ python3-htseq | amd64,arm64,ppc64el | main | buster,bullseye,sid | htseq | htseq | autopkgtest
+ iitii | | | https://salsa.debian.org/med-team/iitii | | |
+ ivar | amd64,arm64 | main | bullseye,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
+ radiant | all | main | buster,bullseye,sid | | krona |
+ lighter | | | new | lighter | |
+ lumpy-sv | | | new | lumpy-sv | |
+ magicblast | | | | | |
+ manta | | | https://salsa.debian.org/med-team/manta | manta | |
+ mash | amd64,arm64,ppc64el | main | buster,bullseye,sid | mash | | autopkgtest
+ masurca | | | | | |
+ mcaller | | | | | |
+ mecat2 | | | | | |
+ medaka | | | | | |
+ megahit | | | new | megahit | |
+ megalodon | | | | | |
+ metabat | | | new | metabat2 | |
+ metaspades | | | | | |
+ minia | amd64,arm64,ppc64el | main | buster,bullseye,sid | minia | minia | autopkgtest
+ minimap2 | amd64,arm64,ppc64el | main | buster,bullseye,sid | minimap2 | | autopkgtest
+ minitour | | | | | |
+ libmmap-allocator-dev | | | new | | |
+ mmmulti | | | | | |
+ mosdepth | | | https://salsa.debian.org/med-team/mosdepth | mosdepth | |
+ multiqc | all | main | bullseye,sid | multiqc | multiqc |
+ muscle | amd64,arm64,ppc64el | main | buster,bullseye,sid | muscle | MUSCLE | autopkgtest
+ nanofilt | | | | | |
+ nanolyse | | | https://salsa.debian.org/med-team/nanolyse | nanolyse | |
+ python3-nanomath | | | new | | |
+ nanopolish | amd64,arm64 | main | buster,bullseye,sid | nanopolish | nanopolish | autopkgtest
+ nanook | all | main | buster,bullseye,sid | | NanoOK |
+ nanoraw | | | | | |
+ nanosv | | | | | |
+ ngmlr | | | | | |
+ oncofuse | | | https://salsa.debian.org/med-team/oncofuse | | |
+ optitype | | | https://salsa.debian.org/med-team/optitype | | |
+ nanoplot | | | https://salsa.debian.org/med-team/nanoplot | nanoplot | |
+ parallel-fastq-dump | all | main | sid | parallel-fastq-dump | |
+ python3-pauvre | | | new | | |
+ picopore | | | | | |
+ pinfish | | | | | |
+ plasmidid | | | https://salsa.debian.org/med-team/plasmidid | plasmidid | |
+ picard-tools | amd64 | main | buster,bullseye,sid | picard | Picard_tools | autopkgtest
+ pilon | all | main | buster,bullseye,sid | pilon | pilon |
+ pomoxis | | | | | |
+ pore | | | | | |
+ pore-c | | | | | |
+ porechop | amd64,arm64,ppc64el | main | buster,bullseye,sid | porechop | | autopkgtest
+ porejuicer | | | | | |
+ poretools | all | main | buster,bullseye,sid | poretools | | 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
+ pybedtools-bin | all | main | buster,bullseye,sid | pybedtools | pybedtools | autopkgtest-pkg-python
+ pychopper | | | | | |
+ pycoqc | all | main | bullseye,sid | pycoqc | |
+ pyomo | | | | | |
+ python3-pysam | amd64,arm64,ppc64el | main | buster,bullseye,sid | pysam | pysam | autopkgtest, autopkgtest-pkg-python
+ python3-vcf | amd64,arm64,ppc64el | main | bullseye,sid | pyvcf | | autopkgtest, autopkgtest-pkg-python
+ qcat | all | main | bullseye,sid | qcat | | autopkgtest
+ qsignature | | | | | |
+ qualimap | | | https://salsa.debian.org/med-team/qualimap | qualimap | |
+ quast | | | https://salsa.debian.org/med-team/quast | quast | |
+ 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
+ r-bioc-rsamtools | amd64,arm64,ppc64el | main | buster,bullseye,sid | | | autopkgtest, autopkgtest-pkg-r
+ sailfish | | | https://salsa.debian.org/med-team/sailfish | | |
+ salmon | amd64 | main | buster,bullseye,sid | salmon | salmon |
+ samblaster | amd64,arm64,ppc64el | main | buster,bullseye,sid | samblaster | SAMBLASTER |
+ samclip | | | new | samclip | |
+ samtools | amd64,arm64,ppc64el | main | buster,bullseye,sid | samtools | samtools | autopkgtest
+ scrappie | | | | | |
+ sepp | | | https://salsa.debian.org/med-team/sepp | sepp | |
+ python3-seqcluster | | | https://salsa.debian.org/med-team/python-seqcluster | | |
+ seqlib | | | | | |
+ seqkit | | | | | |
+ 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 | |
+ 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
+ rna-star | amd64,arm64,ppc64el | main | buster,bullseye,sid | star | star | autopkgtest
+ streamformatics | | | | | |
+ strelka | | | https://salsa.debian.org/med-team/strelka | strelka | |
+ tiddit | | | new | tiddit | |
+ tombo | | | | | |
+ tophat-recondition | all | main | sid | | |
+ tornado | | | | | |
+ trim-galore | all | main | bullseye,sid | trim-galore | | autopkgtest
+ trimmomatic | all | main | buster,bullseye,sid | trimmomatic | Trimmomatic | autopkgtest
+ tulip | | | | | |
+ umap-learn | | | new | | |
+ 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
+ ensembl-vep | | | https://salsa.debian.org/med-team/ensembl-vep | ensembl-vep | |
+ vg | amd64 | main | bullseye,sid | vg | | autopkgtest
+ viennarna | | | | | |
+ vsearch | amd64,ppc64el | main | buster,bullseye,sid | vsearch | vsearch |
+ vt | | | | | |
+ wham-align | amd64 | main | bullseye,sid | wham | wham |
+ yanagiba | | | | | |
+ yanosim | | | | | |
+ 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
+ python3-toolz | all | main | buster,bullseye,sid | | | autopkgtest
+ python3-tornado | amd64,arm64,ppc64el | main | buster,bullseye,sid | | | autopkgtest
+(166 Zeilen)
=====================================
tasks/covid-19
=====================================
@@ -215,8 +215,48 @@ Recommends: lighter
Recommends: lumpy-sv
+Recommends: nanofilt
+
+Recommends: python3-nanomath
+
+Recommends: nanopolish
+
+Recommends: nanook
+
+Recommends: oncofuse
+
+Recommends: optitype
+
+Recommends: python3-pauvre
+
+Recommends: picopore
+
+Recommends: poretools
+
+Recommends: pybedtools-bin
+
+Recommends: pyomo
+
+Recommends: python3-vcf
+
+Recommends: r-bioc-rsamtools
+
+Recommends: sailfish
+
Recommends: samclip
+Recommends: scrappie
+
+Recommends: python3-seqcluster
+
+Recommends: seqkit
+
+Recommends: tophat-recondition
+
+Recommends: viennarna
+
+Recommends: python3-toolz, python3-tornado
+
X-Comment: </Jun_Aruga>
X-Comment: TODO: Check out
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/f3dca1abdd2f7613bf523a0dea9640c6ec2d0698...c71441afaec9129c6298257ba97dd5345eb8601b
--
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/f3dca1abdd2f7613bf523a0dea9640c6ec2d0698...c71441afaec9129c6298257ba97dd5345eb8601b
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