[Blends-commit] [Git][blends-team/med][master] Add all software mentioned here...

[Andreas Tille]

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


Commits:
a3fbb705 by Andreas Tille at 2020-04-22T16:14:32+02:00
Add all software mentioned here https://lists.debian.org/debian-med/2020/04/msg00235.html to the covid-19 task

- - - - -


1 changed file:

- tasks/covid-19


Changes:

=====================================
tasks/covid-19
=====================================
@@ -22,8 +22,6 @@ Recommends: blat
 
 Recommends: chip-seq
 
-Recommends: fastqc
-
 Recommends: fieldbioinformatics
 
 Recommends: idseq-dag
@@ -33,10 +31,6 @@ Remark: needs auspice
 
 Recommends: parasail
 
-Recommends: pycoqc
-
-Recommends: qcat
-
 Recommends: r-bioc-htsfilter
 
 Recommends: r-bioc-mutationalpatterns
@@ -61,6 +55,78 @@ Recommends: vadr
 
 Recommends: wtdbg2
 
+X-Comment: <Jun_Aruga>
+X-Comment: https://lists.debian.org/debian-med/2020/04/msg00235.html
+
+Recommends: simde
+
+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://staff.aist.go.jp/yutaka.ueno/guppy/
+X-FIXME: Is this correct?
+
+Recommends: qcat
+
+Recommends: pycoqc
+
+Recommends: nanoplot
+Homepage: https://github.com/wdecoster/NanoPlot
+
+Recommends: fastqc
+
+Recommends: graphmap2
+Homepage: https://github.com/lbcb-sci/graphmap2
+
+Recommends: samtools
+
+Recommends: bedtools
+
+Recommends: multiqc
+
+Recommends: parallel-fastq-dump
+Homepage: https://github.com/rvalieris/parallel-fastq-dump
+
+Recommends: fastp
+
+Recommends: picard-tools
+
+Recommends: ivar
+Homepage: https://github.com/andersen-lab/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: </Jun_Aruga>
+
 X-Comment:  TODO: Check out
 X-Comment:     https://www.bioinformatics.babraham.ac.uk/projects/index.html
 X-Comment:  for further tools
@@ -182,8 +248,6 @@ Recommends: python3-drmaa
 
 Recommends: fasta3
 
-Recommends: fastqc
-
 Recommends: genometools
 
 Recommends: gffread
@@ -214,8 +278,6 @@ Recommends: libmilib-java
 
 Recommends: mmseqs2
 
-Recommends: ncbi-blast+
-
 Recommends: odil
 
 Recommends: orthanc
@@ -244,8 +306,6 @@ Recommends: python3-cgecore
 
 Recommends: python3-cogent
 
-Recommends: python3-cutadapt
-
 Recommends: python3-depinfo
 
 Recommends: python3-etelemetry
@@ -326,7 +386,6 @@ Recommends: toil
 
 Recommends: umis
 
-Recommends: vg
 
 Recommends: workrave
 



View it on GitLab: https://salsa.debian.org/blends-team/med/-/commit/a3fbb7055d702dba787aae6383499e6db33527f5

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