[Blends-commit] [Git][blends-team/med][master] Update bio_covid-19 list, added libbbhash-dev
Andreas Tille
gitlab at salsa.debian.org
Thu Jun 4 08:19:08 BST 2020
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
c6f8ef30 by Andreas Tille at 2020-06-04T09:18:55+02:00
Update bio_covid-19 list, added libbbhash-dev
- - - - -
4 changed files:
- covid-19_doc/bio_covid-19_dependencies_query
- covid-19_doc/bio_covid-19_dependencies_result
- tasks/bio-dev
- tasks/covid-19
Changes:
=====================================
covid-19_doc/bio_covid-19_dependencies_query
=====================================
@@ -67,12 +67,24 @@ BEGIN;
CREATE TEMPORARY TABLE covid19_packages ( package text ) ;
INSERT INTO covid19_packages VALUES
('nextflow'),
+('capsule'),
('snakemake'),
+('artic'),
+('bcbio'),
+('pigx-rnaseq'),
+('scrnaseq'),
+('shovill'),
+('smartseq2'),
+('viralcon'),
('nf-core'),
('abacas'),
('allelecount'),
('python3-anndata'),
+('args'),
+('argparser'),
+('arvados'),
('r-other-ascat'),
+('atomicbitvector'),
('augustus'),
('bandage'),
('libbbhash-dev'),
@@ -101,6 +113,7 @@ INSERT INTO covid19_packages VALUES
('graphmap2'),
('bio-guppy'),
('python3-h5py'),
+('r-bioc-htsfilter'),
('libhts-dev'),
('python3-htseq'),
('ivar'),
@@ -118,6 +131,9 @@ INSERT INTO covid19_packages VALUES
('metaspades'),
('minia'),
('minimap2'),
+('mmap_allocator'),
+('mmmulti'),
+('mosdepth'),
('multiqc'),
('muscle'),
('nanolyse'),
@@ -183,7 +199,8 @@ INSERT INTO covid19_packages VALUES
('velvet'),
('ensembl-vep'),
('vg'),
-('vsearch')
+('vsearch'),
+('wham-align')
;
SELECT co.package, architectures, s.section,
=====================================
covid-19_doc/bio_covid-19_dependencies_result
=====================================
@@ -1,105 +1,122 @@
-Last-Update: Wed, 03 Jun 2020 14:13:24 +0200
+Last-Update: Thu, 04 Jun 2020 09:08:22 +0200
- 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 | 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 | autopkgtest
- diamond-aligner | amd64,arm64,ppc64el | main | buster,bullseye,sid | diamond | Diamond |
- drop-seq-tools | all | main | sid | dropseq_tools | |
- ensembl-vep | | | https://salsa.debian.org/med-team/ensembl-vep | ensembl-vep | |
- 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 | bullseye,sid | flash | |
- freebayes | amd64,arm64,ppc64el | main | buster,bullseye,sid | freebayes | freebayes | autopkgtest
- gatk | | | https://salsa.debian.org/med-team/gatk | gatk4 | |
- graphmap2 | | | https://salsa.debian.org/med-team/graphmap2 | graphmap | |
- 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
- libbbhash-dev | | | | | |
- libhts-dev | amd64,arm64,ppc64el | main | buster,bullseye,sid | htslib | | autopkgtest
- lighter | | | new | 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 | | | new | metabat2 | |
- 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 | | | 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 | |
- 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 | | | new | 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 | | | 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
- vg | amd64 | main | bullseye,sid | vg | | autopkgtest
- vsearch | amd64,ppc64el | main | buster,bullseye,sid | vsearch | vsearch |
-(99 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
+ argparser | | | | | |
+ args | | | | | |
+ artic | | | | | |
+ arvados | | | https://salsa.debian.org/med-team/arvados | | |
+ atomicbitvector | | | | | |
+ augustus | amd64,arm64,ppc64el | main | buster,bullseye,sid | augustus | AUGUSTUS | autopkgtest
+ bandage | amd64,arm64,ppc64el | main | buster,bullseye,sid | bandage | bandage |
+ bcbio | all | main | buster,bullseye,sid | bcbio-nextgen | bcbio-nextgen | autopkgtest-pkg-python
+ 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
+ capsule | | | | | |
+ 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 | autopkgtest
+ diamond-aligner | amd64,arm64,ppc64el | main | buster,bullseye,sid | diamond | Diamond |
+ drop-seq-tools | all | main | sid | dropseq_tools | |
+ ensembl-vep | | | https://salsa.debian.org/med-team/ensembl-vep | ensembl-vep | |
+ 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 | bullseye,sid | flash | |
+ freebayes | amd64,arm64,ppc64el | main | buster,bullseye,sid | freebayes | freebayes | autopkgtest
+ gatk | | | https://salsa.debian.org/med-team/gatk | gatk4 | |
+ graphmap2 | | | https://salsa.debian.org/med-team/graphmap2 | graphmap | |
+ 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
+ libbbhash-dev | | | | | |
+ libhts-dev | amd64,arm64,ppc64el | main | buster,bullseye,sid | htslib | | autopkgtest
+ lighter | | | new | 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 | | | new | metabat2 | |
+ metaspades | | | | | |
+ minia | amd64,arm64,ppc64el | main | buster,bullseye,sid | minia | minia | autopkgtest
+ minimap2 | amd64,arm64,ppc64el | main | buster,bullseye,sid | minimap2 | | autopkgtest
+ mmap_allocator | | | | | |
+ 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 | |
+ 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
+ pigx-rnaseq | | | https://salsa.debian.org/med-team/pigx-rnaseq | | |
+ 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-bioc-htsfilter | all | main | bullseye,sid | | | autopkgtest, autopkgtest-pkg-r
+ 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 | | | new | samclip | |
+ samtools | amd64,arm64,ppc64el | main | buster,bullseye,sid | samtools | samtools | autopkgtest
+ scrnaseq | | | | | |
+ 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 | |
+ shovill | | | | | |
+ skesa | amd64 | main | bullseye,sid | skesa | |
+ smartseq2 | | | | | |
+ 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 | | | new | 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 | | | 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
+ vg | amd64 | main | bullseye,sid | vg | | autopkgtest
+ viralcon | | | | | |
+ vsearch | amd64,ppc64el | main | buster,bullseye,sid | vsearch | vsearch |
+ wham-align | amd64 | main | bullseye,sid | wham | wham |
+(116 Zeilen)
=====================================
tasks/bio-dev
=====================================
@@ -553,3 +553,5 @@ Recommends: libhtscodecs-dev
Recommends: python3-torch
Recommends: python3-anndata
+
+Suggests: libbbhash-dev
=====================================
tasks/covid-19
=====================================
@@ -205,6 +205,8 @@ Recommends: vsearch
X-Comment: https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit?ts=5eb957ba#gid=543782716
+Recommends: libbbhash-dev
+
Recommends: flash
Recommends: lighter
View it on GitLab: https://salsa.debian.org/blends-team/med/-/commit/c6f8ef308a6a9422e1dd90f0238ffb5b42ec8c8b
--
View it on GitLab: https://salsa.debian.org/blends-team/med/-/commit/c6f8ef308a6a9422e1dd90f0238ffb5b42ec8c8b
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