Task: Covid-19
Metapackage: false
Description: This task exists only for tagging COVID-19 relevant cases
 The Debian Med team intends to take part at the
  COVID-19 Biohackathon (April 5-11, 2020)
 This task was created only for the purpose to list relevant packages.

X-Mark:  <bio>

Recommends: cwltool, snakemake

Suggests: python3-anndata

Recommends: arvados

Recommends: augur

Recommends: auspice
Remark: That's a nodejs package. Unfortunately lots of preconditions are missing
 Comments welcome whether it makes sense to package about 20 nodejs packages.
 A list can be found as "debian/TODO" or as comments in debian/control in Salsa.

Recommends: blat

Recommends: chip-seq

Recommends: fieldbioinformatics

Recommends: megahit

Recommends: python3-idseq-dag

Recommends: nextstrain-ncov
Remark: needs auspice

Recommends: parasail

Recommends: r-bioc-htsfilter

Recommends: r-bioc-mutationalpatterns

Recommends: r-bioc-rcpi

Recommends: r-bioc-rgsepd

Recommends: r-bioc-pwmenrich

Suggests: r-bioc-rsubread

Recommends: r-bioc-tcgabiolinks

Recommends: r-cran-kernelheaping

Recommends: r-cran-mediana

Recommends: r-cran-spp

Recommends: recan

Recommends: trinculo

Recommends: vadr

Recommends: wtdbg2

Recommends: pigx-rnaseq

X-Comment: <Jun_Aruga>
X-Comment: https://lists.debian.org/debian-med/2020/04/msg00235.html

Suggests: libsimde-dev

Recommends: bowtie2

Recommends: minimap2

Recommends: bwa

Recommends: nanoseq
Homepage: https://github.com/nf-core/nanoseq/blob/master/bin/scrape_software_versions.py

Recommends: guppy
Homepage: https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt
Remark: see https://lists.debian.org/debian-med/2020/04/msg00273.html

Recommends: chiron
Homepage: https://github.com/haotianteng/Chiron
Remark: Free alternative to non-free guppy

Recommends: qcat

Recommends: pycoqc

Recommends: nanoplot

Recommends: fastqc

Recommends: graphmap2

Recommends: samtools

Recommends: bedtools

Recommends: multiqc

Recommends: nf-core-artic

Recommends: viralrecon
Homepage: https://github.com/nf-core/viralrecon/blob/dev/bin/scrape_software_versions.py

Recommends: parallel-fastq-dump

Recommends: fastp

Recommends: picard-tools

Recommends: ivar

Recommends: varscan

Recommends: snpeff, snpsift

Recommends: bcftools

Recommends: cutadapt

Recommends: kraken2

Recommends: spades

Recommends: unicycler

Recommends: minia

Recommends: vg

Recommends: ncbi-blast+

Recommends: abacas

Recommends: quast

X-Comment: https://lists.debian.org/debian-med/2020/05/msg00093.html

Recommends: bustools

Recommends: kallisto

Recommends: salmon

Recommends: rna-star

Recommends: allelecount

Recommends: r-other-ascat

Recommends: r-other-fastbaps

Recommends: freebayes

Recommends: manta

Recommends: qualimap

Recommends: strelka

Recommends: tiddit

Recommends: umap-learn

Recommends: ensembl-vep

Recommends: busco

Recommends: cat-bat

Recommends: centrifuge

Recommends: dextractor

Recommends: drop-seq-tools

Recommends: filtlong

Recommends: mecat2

Recommends: metabat

Recommends: nanolyse

Recommends: porechop

Recommends: changeo

Recommends: muscle

Recommends: plasmidid

Recommends: pplacer

Recommends: presto

Recommends: python3-cooler, python3-pairix

Recommends: python3-scanpy

Recommends: r-cran-alakazam, r-cran-shazam, r-cran-tigger

Recommends: rosa

Recommends: sepp, tipp

Recommends: seqwish

Recommends: signalalign

Recommends: tombo

Recommends: vsearch

X-Comment: https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit?ts=5eb957ba#gid=543782716

Recommends: assembly-stats

Recommends: bamkit

Recommends: libbbhash-dev

Recommends: flappie

Recommends: flash

Recommends: flye

Recommends: lastz

Recommends: lighter

Recommends: lumpy-sv

Recommends: medaka

Recommends: ncbi-magicblast

Recommends: nanofilt

Recommends: python3-nanomath

Recommends: nanopolish

Recommends: nanook

Recommends: nanosv

Recommends: ngmlr

Recommends: oncofuse

Recommends: optitype

Recommends: pangolin

Recommends: python3-nanoget

Recommends: python3-pairtools

Recommends: python3-pauvre

Recommends: picopore

Recommends: pinfish

Recommends: pomoxis

Recommends: poretools

Recommends: prinseq-lite

Recommends: pybedtools-bin

Recommends: python3-pychopper

Recommends: pyomo

Recommends: python3-biopython

Suggests: python3-mmtf

Recommends: python3-vcf

Recommends: r-bioc-rsamtools

Recommends: readucks

Recommends: sailfish

Recommends: samclip

Recommends: scrappie

Recommends: python3-seqcluster

Recommends: seqkit

Recommends: shovill

Recommends: python3-streamz

Recommends: tophat-recondition

Recommends: vienna-rna

Recommends: vt

Recommends: python3-toolz, python3-tornado

Recommends: yanagiba

Recommends: yanosim

X-Comment: </Jun_Aruga>

X-Comment:  TODO: Check out
X-Comment:     https://www.bioinformatics.babraham.ac.uk/projects/index.html
X-Comment:  for further tools

Recommends: ufasta
X-Comment: Precondition for https://github.com/alekseyzimin/masurca

X-Mark:  </bio>

X-Mark:  <epi>

Recommends: epigrass

Recommends: r-cran-covid19

Recommends: r-cran-covid19us

Recommends: r-cran-epibasix

Recommends: r-cran-epitools

Recommends: r-cran-surveillance

Recommends: r-cran-epi

Recommends: r-cran-diagnosismed, r-cran-epicalc, r-cran-epir

Recommends: r-cran-seroincidence

Recommends: shiny-server

Recommends: r-cran-lexrankr

Recommends: r-cran-sf, r-cran-sjplot

Recommends: python3-treetime

Recommends: chime
Remark: Needs streamlit (see below)

X-Comment: Otto Kekäläinen <otto@kekalainen.net>
X-Comment:   -> https://gitlab.com/fevermap/fevermap
X-Comment:   Server API might be interesting.  Needs: uwsgi, mysqlclient, dataclasses

X-Mark:  </epi>

X-Mark:  <imaging>

Recommends: aeskulap

Recommends: conquest-common

Recommends: dcmtk

Recommends: ginkgocadx

Recommends: imagej

Recommends: libgdcm-tools

Recommends: orthanc

Recommends: orthanc-wsi

Recommends: orthanc-python

X-Mark:  </imaging>

X-Mark:  <tools>

X-Comment:  https://opensourceventilator.ie/
X-Comment:    -> https://gitlab.com/open-source-ventilator/OpenLung

X-Comment:  https://www.mikrocontroller.net/topic/491565
X-Comment:    -> https://github.com/jcl5m1/ventilator

X-Comment:  https://sormasorg.helmholtz-hzi.de/Open_source.html
X-Comment:    -> https://github.com/hzi-braunschweig/SORMAS-Project

X-Mark:  </tools>

X-Mark:  <preconditions>

Recommends: streamlit
Remark: Help is urgently needed - no idea how to package this :-(
 This is a machine learning framework which is required by chime.
 Needs python3-tensorflow

Recommends: libtensorflow-framework2
Remark: https://lists.debian.org/debian-devel/2019/10/msg00168.html
 The framework should also generate python3-tensorflow as predepencency
 for streamlit


X-Mark:  </preconditions>

X-Mark: <begin>https://lists.debian.org/debian-med/2020/03/msg00142.html
Recommends: abyss

Recommends: bamclipper

Recommends: bbmap

Recommends: bcalm

Recommends: bcbio

Recommends: biobambam2

Recommends: clonalframeml

Recommends: python3-cyvcf2

Recommends: covpipe

Recommends: delly

Recommends: diamond-aligner

Recommends: discosnp

Recommends: python3-drmaa

Recommends: fasta3

Recommends: fastani

Recommends: genometools

Recommends: gffread

Recommends: gnumed-client

Recommends: gnumed-server

Recommends: gromacs

Recommends: gubbins

Recommends: libhtscodecs-dev

Recommends: python3-htseq

Recommends: kalign

Recommends: libchipcard-dev

Recommends: libgclib-dev

Recommends: libics-dev

Recommends: libmaus2-dev

Recommends: libmilib-java

Recommends: mmseqs2

Recommends: nthash

Recommends: odil

Recommends: orthanc-dicomweb

Recommends: paleomix

Recommends: plink1.9, plink2

Recommends: plip

Recommends: prokka

Recommends: proteinortho

Recommends: python3-pydicom

Recommends: python3-pynn

Recommends: python3-biom-format

Recommends: python3-bx

Recommends: python3-cgecore

Recommends: python3-cogent3

Recommends: python3-depinfo

Recommends: python3-etelemetry

Recommends: python3-gffutils

Recommends: python3-pbcommand

Recommends: python3-pbcore

Recommends: python3-pyani

Recommends: python3-pyfaidx

Recommends: python3-pysam

Recommends: python3-questplus

Recommends: python3-scitrack

Recommends: python3-screed

Recommends: python3-tinyalign

Recommends: python3-typed-ast

Recommends: q2-cutadapt

Recommends: q2-feature-table

Recommends: q2-quality-filter

Recommends: r-bioc-limma

Recommends: r-cran-hms

Recommends: r-cran-msm

Recommends: r-cran-qtl

Recommends: r-cran-stringi

Recommends: ragout

Recommends: rsem

Recommends: ruby-bio

Recommends: samblaster

Recommends: libseqan3-dev

Recommends: seqmagick

Recommends: shapeit4

Recommends: smrtanalysis

Recommends: spaln

Recommends: staden-io-lib-utils

Recommends: stringtie

Recommends: sumaclust

Recommends: texlive-science

Recommends: thesias

Recommends: tnseq-transit

Recommends: toil

Recommends: uncalled

Recommends: umis

Recommends: workrave

X-Mark: <end>https://lists.debian.org/debian-med/2020/03/msg00142.html

Recommends: python3-torch

Recommends: nextflow

Recommends: quicktree

Recommends: r-cran-incidence, r-cran-epiestim

Recommends: python3-seirsplus

Recommends: mmb
