[Blends-commit] [Git][blends-team/med][master] 2 commits: python3-h5py was added to...
Andreas Tille
gitlab at salsa.debian.org
Tue May 26 14:04:01 BST 2020
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
685d9fbb by Andreas Tille at 2020-05-26T13:45:28+02:00
python3-h5py was added to https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit?ts=5eb957ba#gid=543782716
- - - - -
fe04995e by Andreas Tille at 2020-05-26T15:03:29+02:00
Updated list of packages according to https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit?ts=5eb957ba#gid=543782716
- - - - -
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
=====================================
@@ -71,7 +71,10 @@ INSERT INTO covid19_packages VALUES
('nf-core'),
('abacas'),
('allelecount'),
+('python3-anndata'),
('r-other-ascat'),
+('augustus'),
+('bandage'),
('bcftools'),
('bedtools'),
('python3-biopython'),
@@ -93,18 +96,25 @@ INSERT INTO covid19_packages VALUES
('flash'),
('freebayes'),
('gatk'),
+('tigr-glimmer'),
('graphmap2'),
('bio-guppy'),
+('python3-h5py'),
('libhts-dev'),
('python3-htseq'),
('ivar'),
('kallisto'),
+('kmc'),
('kraken2'),
('radiant'), -- == krona - Debian had to change the name
+('lighter'),
('lumpy'),
+('magicblast'),
('manta'),
+('mash'),
('megahit'),
('metabat'),
+('metaspades'),
('minia'),
('minimap2'),
('multiqc'),
@@ -115,8 +125,11 @@ INSERT INTO covid19_packages VALUES
('python3-pandas'),
('parallel-fastq-dump'),
('picard-tools'),
+('pilon'),
('porechop'),
+('pplacer'),
('presto'),
+('prinseq-lite'),
('prodigal'),
('pycoqc'),
('qcat'),
@@ -127,6 +140,7 @@ INSERT INTO covid19_packages VALUES
('r-cran-rmarkdown'),
('r-cran-shazam'),
('r-cran-tigger'),
+/*
('r-cran-locfit'),
('r-bioc-deseq2'),
('r-bioc-tximport'),
@@ -144,8 +158,14 @@ INSERT INTO covid19_packages VALUES
('r-bioc-summarizedexperiment'),
('r-bioc-rtracklayer'),
('r-cran-rjson'),
+*/
('salmon'),
+('samclip'),
('samtools'),
+('sepp'),
+('seqtk'),
+('seqwish'),
+('skesa'),
('snpeff'),
('snpsift'),
('spades'),
@@ -154,12 +174,15 @@ INSERT INTO covid19_packages VALUES
('strelka'),
('tiddit'),
('trim-galore'),
+('trimmomatic'),
('umap-learn'),
('unicycler'),
('varscan'),
('vcftools'),
+('velvet'),
('vep'),
-('vg')
+('vg'),
+('vsearch')
;
SELECT co.package, architectures, s.section,
=====================================
covid-19_doc/bio_covid-19_dependencies_result
=====================================
@@ -1,98 +1,104 @@
-Last-Update: Mon, 25 May 2020 17:17:42 +0200
+Last-Update: Tue, 26 May 2020 15:02:54 +0200
- package | architectures | section | releases | conda | bio.tools
------------------------------+---------------------+----------+---------------------------------------------+--------------------------+--------------
- abacas | all | main | buster,bullseye,sid | |
- allelecount | amd64,arm64,ppc64el | main | bullseye,sid | cancerit-allelecount |
- 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 | | | new | 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 | | | new | 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 |
- 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 | | | new | 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 | manta |
- megahit | | | new | megahit |
- metabat | | | | |
- 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
- porechop | amd64,arm64,ppc64el | main | buster,bullseye,sid | porechop |
- presto | | | | |
- prodigal | amd64,arm64,ppc64el | main | buster,bullseye,sid | prodigal |
- pycoqc | all | main | bullseye,sid | pycoqc |
- 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 | 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-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
- r-other-ascat | | | new | ascat |
- 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 | 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 | | | | |
- 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 | vg |
-(92 Zeilen)
+ package | architectures | section | releases | conda | bio.tools
+---------------------+---------------------+----------+---------------------------------------------+----------------------+--------------
+ abacas | all | main | buster,bullseye,sid | |
+ allelecount | amd64,arm64,ppc64el | main | 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 | sid | busco |
+ bustools | amd64,arm64,ppc64el | main | bullseye,sid | bustools | BUStools
+ bwa | amd64,arm64,ppc64el | main | buster,bullseye,sid | bwa | BWA
+ cat-bat | | | new | 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 | | | new | 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 | | | | |
+ 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 | | | new | 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 | | | | |
+ magicblast | | | | |
+ manta | | | https://salsa.debian.org/med-team/manta | manta |
+ mash | amd64,arm64,ppc64el | main | buster,bullseye,sid | mash |
+ megahit | | | new | |
+ metabat | | | | |
+ metaspades | | | | |
+ 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 | | | https://salsa.debian.org/med-team/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 | 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 | |
+ pplacer | | | https://salsa.debian.org/med-team/pplacer | pplacer |
+ presto | | | | |
+ prinseq-lite | all | main | bullseye,sid | |
+ prodigal | amd64,arm64,ppc64el | main | buster,bullseye,sid | |
+ pycoqc | all | main | bullseye,sid | |
+ python3-anndata | | | https://salsa.debian.org/med-team/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
+ 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-cran-alakazam | amd64,arm64,ppc64el | main | buster,bullseye,sid | |
+ r-cran-ggplot2 | all | main | buster,bullseye,sid | |
+ r-cran-rmarkdown | 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
+ r-other-ascat | | | new | ascat |
+ salmon | amd64 | main | buster,bullseye,sid | salmon | salmon
+ samclip | | | | |
+ samtools | amd64,arm64,ppc64el | main | buster,bullseye,sid | samtools | samtools
+ sepp | | | | |
+ seqtk | amd64,arm64,ppc64el | main | buster,bullseye,sid | seqtk | seqtk
+ 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 | | | | |
+ 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 | | | | |
+ 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 | |
+ vsearch | amd64,ppc64el | main | buster,bullseye,sid | vsearch | vsearch
+(98 Zeilen)
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/e9fcb6dbfb3cf5a63d542c2ae16e47fbe04446d5...fe04995eeaf955f56542434bfeb76ff051f9a4ed
--
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/e9fcb6dbfb3cf5a63d542c2ae16e47fbe04446d5...fe04995eeaf955f56542434bfeb76ff051f9a4ed
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