[Blends-commit] [Git][blends-team/med][master] 2 commits: https://lists.debian.org/debian-med/2020/03/msg00142.html - thanks to Ben Tris...

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
3e8075e3 by Andreas Tille at 2020-03-25T10:19:25+01:00
https://lists.debian.org/debian-med/2020/03/msg00142.html - thanks to Ben Tris <benattris at gezapig.nl> for the input

- - - - -
b0229eaf by Andreas Tille at 2020-03-25T10:22:50+01:00
Add extract of epi task

- - - - -


1 changed file:

- tasks/covid-19


Changes:

=====================================
tasks/covid-19
=====================================
@@ -16,9 +16,6 @@ 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: chime
-Remark: Needs streamlit (see below)
-
 Recommends: chip-seq
 
 Recommends: streamlit
@@ -46,6 +43,35 @@ X-Comment:  for further tools
 
 X-Mark:  </bio>
 
+X-Mark:  <epi>
+
+Recommends: epigrass
+
+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-Mark:  </epi>
+
 X-Mark:  <imaging>
 
 Recommends: aeskulap
@@ -91,3 +117,206 @@ Remark: Needs help from Debian Science team
  This is a machine learning framework which is required by chime.
 
 X-Mark:  </preconditions>
+
+X-Mark: <begin>https://lists.debian.org/debian-med/2020/03/msg00142.html
+Recommends: abyss
+
+Recommends: bbmap
+
+Recommends: bcalm
+
+Recommends: bcbio
+
+Recommends: biobambam2
+
+Recommends: biosig-tools
+
+Recommends: cimg-dev
+
+Recommends: clonalframeml
+
+Recommends: python3-cyvcf2
+
+Recommends: delly
+
+Recommends: diamond-aligner
+
+Recommends: discosnp
+
+Recommends: python3-drmaa
+
+Recommends: fasta3
+
+Recommends: fastqc
+
+Recommends: r-cran-foreign
+
+Recommends: genometools
+
+Recommends: gffread
+
+Recommends: gnumed-client
+
+Recommends: gnumed-server
+
+Recommends: gromacs
+
+Recommends: gubbins
+
+Recommends: libhtscodecs-dev
+
+Recommends: python3-htseq
+
+Recommends: kalign
+
+Recommends: kaptive
+
+Recommends: kleborate
+
+Recommends: kma
+
+Recommends: libbio-alignio-stockholm-perl
+
+Recommends: libbio-featureio-perl
+
+Recommends: libchipcard-dev
+
+Recommends: libdeflate-dev
+
+Recommends: libgclib-dev
+
+Recommends: libics-dev
+
+Recommends: libmaus2-dev
+
+Recommends: libmilib-java
+
+Recommends: mmseqs2
+
+Recommends: ncbi-blast+
+
+Recommends: odil
+
+Recommends: libopencv-dev
+
+Recommends: orthanc
+
+Recommends: orthanc-dicomweb
+
+Recommends: paleomix
+
+Recommends: plink1.9
+
+Recommends: plip
+
+Recommends: praat
+
+Recommends: prokka
+
+Recommends: proteinortho
+
+Recommends: psychopy
+
+Recommends: python3-pydicom
+
+Recommends: python-pynn
+
+Recommends: python3-biom-format
+
+Recommends: python3-bx
+
+Recommends: python3-cgecore
+
+Recommends: python3-cogent
+
+Recommends: python3-cutadapt
+
+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-treetime
+
+Recommends: python3-typed-ast
+
+Recommends: q2-cutadapt
+
+Recommends: q2-feature-table
+
+Recommends: q2-quality-filter
+
+Recommends: r-base
+
+Recommends: r-bioc-limma
+
+Recommends: r-cran-hms
+
+Recommends: r-cran-msm
+
+Recommends: r-cran-qtl
+
+Recommends: r-cran-stringi
+
+Recommends: r-cran-surveillance
+
+Recommends: ragout
+
+Recommends: rsem
+
+Recommends: ruby-bio
+
+Recommends: samblaster
+
+Recommends: libseqan3-dev
+
+Recommends: seqmagick
+
+Recommends: shapeit4
+
+Recommends: smrtanalysis
+
+Recommends: spaln
+
+Recommends: libspdlog-dev
+
+Recommends: staden-io-lib-utils
+
+Recommends: stringtie
+
+Recommends: sumaclust
+
+Recommends: texlive-science
+
+Recommends: thesias
+
+Recommends: tnseq-transit
+
+Recommends: toil
+
+Recommends: umis
+
+Recommends: vg
+
+Recommends: workrave
+
+X-Mark: <end>https://lists.debian.org/debian-med/2020/03/msg00142.html



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