[Blends-commit] [Git][blends-team/med][master] Analyse package mentioned at...
Andreas Tille
gitlab at salsa.debian.org
Mon May 11 20:50:56 BST 2020
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
c17b641c by Andreas Tille at 2020-05-11T21:50:46+02:00
Analyse package mentioned at https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit?ts=5eb957ba#gid=543782716
- - - - -
3 changed files:
- + covid-19_doc/bio_covid-19_dependencies
- + covid-19_doc/bio_covid-19_dependencies_query
- + covid-19_doc/bio_covid-19_dependencies_result
Changes:
=====================================
covid-19_doc/bio_covid-19_dependencies
=====================================
@@ -0,0 +1,100 @@
+# Packages column of https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit?ts=5eb957ba#gid=543782716
+## resolved: "20 dependencies on R packages for pigx-rnaseq would need to go here"
+## todo: 20 dependencies on R packages for pigx-scrnaseq would need to go here
+## Fixme: pigx-rnaseq and pigx-scrnaseq are missing in this list
+
+
+nextflow
+snakemake
+nf-core
+abacas
+allelecount
+ascat
+bcftools
+bedtools
+biopython
+blast
+bowtie2
+busco
+bustools
+bwa
+cat
+centrifuge
+changeo
+cutadapt
+diamond
+deeptools
+drop-seq-tools
+fastp
+fastqc
+filtlong
+freebayes
+gatk
+graphmap2
+guppy
+htslib
+htseq
+ivar
+java
+kallisto
+kraken2
+krona
+lumpy
+manta
+megahit
+metabat
+minia
+minimap2
+multiqc
+muscle
+nanolyse
+nanoplot
+numpy
+pandas
+parallel-fastq-dump
+picard
+porechop
+presto
+prodigal
+pycoqc
+python
+qcat
+qualimap
+quast
+r-cran-alakazam
+r-cran-ggplot2
+r-cran-rmarkdown
+r-cran-shazam
+r-cran-tigger
+r-cran-locfit
+r-bioc-deseq2
+r-bioc-tximport
+r-cran-data.table
+r-cran-rlang
+r-cran-ggrepel
+r-cran-dt
+r-cran-pheatmap
+r-cran-corrplot
+r-cran-reshape2
+r-cran-plotly
+r-cran-scales
+r-cran-crosstalk
+r-cran-gprofiler
+r-bioc-summarizedexperiment
+r-bioc-rtracklayer
+r-cran-rjson
+salmon
+samtools
+snpeff
+snpsift
+spades
+sra-toolkit
+rna-star
+strelka
+tiddit
+trim-galore
+unicycler
+varscan2
+vcftools
+vep
+vg
=====================================
covid-19_doc/bio_covid-19_dependencies_query
=====================================
@@ -0,0 +1,172 @@
+#!/bin/sh
+# query packages mentioned at
+# Packages column of https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit?ts=5eb957ba#gid=543782716
+#
+
+usage() {
+cat >/dev/stderr <<EOT
+Usage: $0
+ -h this help screen
+ -m forcing public mirror over local one
+
+Description:
+ Query UDD for packages belonging to a task of a specified blend.
+ The output is sorted according to usage statistics and contains
+ information about existence of an autopkgtest as well whether the
+ interface might require X11 or not.
+EOT
+}
+
+if [ ! $(which psql) ] ; then
+ cat <<EOT
+No PostgreSQL client providing /usr/bin/psql installed.
+On a Debian system please
+ sudo apt-get install postgresql-client-common
+EOT
+ exit 1
+fi
+
+SERVICE="service=udd"
+#if there is a local UDD clone just use this
+if psql $PORT -l 2>/dev/null | grep -qw udd ; then
+ SERVICE=udd
+fi
+
+# Check UDD connection
+if ! psql $PORT $SERVICE -c "" 2>/dev/null ; then
+ echo "No local UDD found, use public mirror."
+ export PGPASSWORD="public-udd-mirror"
+ SERVICE="--host=public-udd-mirror.xvm.mit.edu --port=5432 --username=public-udd-mirror udd"
+fi
+
+while getopts "hjm" o; do
+ case "${o}" in
+ h)
+ usage
+ exit 0
+ ;;
+ m)
+ export PGPASSWORD="public-udd-mirror"
+ SERVICE="--host=public-udd-mirror.xvm.mit.edu --port=5432 --username=public-udd-mirror udd"
+ ;;
+ *)
+ usage
+ exit 1
+ ;;
+ esac
+done
+
+output="bio_covid-19_dependencies_result"
+
+if which psql-public-udd >/dev/null ; then
+ RUNPSQL=psql-public-udd
+else
+ RUNPSQL="psql $SERVICE"
+fi
+
+echo "Last-Update: `date -R`" > "$output"
+echo >> "$output"
+
+$RUNPSQL >>"$output" <<EOT
+SELECT package, string_agg(architecture, ',') as architectures FROM (
+ SELECT DISTINCT package, architecture FROM packages WHERE
+ architecture in ('all', 'amd64', 'arm64', 'ppc64el' ) and
+ package in (
+'nextflow',
+'snakemake',
+'nf-core',
+'abacas',
+'allelecount',
+'ascat',
+'bcftools',
+'bedtools',
+'biopython',
+'blast',
+'bowtie2',
+'busco',
+'bustools',
+'bwa',
+'cat',
+'centrifuge',
+'changeo',
+'cutadapt',
+'diamond',
+'deeptools',
+'drop-seq-tools',
+'fastp',
+'fastqc',
+'filtlong',
+'freebayes',
+'gatk',
+'graphmap2',
+'guppy',
+'htslib',
+'htseq',
+'ivar',
+'java',
+'kallisto',
+'kraken2',
+'krona',
+'lumpy',
+'manta',
+'megahit',
+'metabat',
+'minia',
+'minimap2',
+'multiqc',
+'muscle',
+'nanolyse',
+'nanoplot',
+'numpy',
+'pandas',
+'parallel-fastq-dump',
+'picard',
+'porechop',
+'presto',
+'prodigal',
+'pycoqc',
+'qcat',
+'qualimap',
+'quast',
+'r-cran-alakazam',
+'r-cran-ggplot2',
+'r-cran-rmarkdown',
+'r-cran-shazam',
+'r-cran-tigger',
+'r-cran-locfit',
+'r-bioc-deseq2',
+'r-bioc-tximport',
+'r-cran-data.table',
+'r-cran-rlang',
+'r-cran-ggrepel',
+'r-cran-dt',
+'r-cran-pheatmap',
+'r-cran-corrplot',
+'r-cran-reshape2',
+'r-cran-plotly',
+'r-cran-scales',
+'r-cran-crosstalk',
+'r-cran-gprofiler',
+'r-bioc-summarizedexperiment',
+'r-bioc-rtracklayer',
+'r-cran-rjson',
+'salmon',
+'samtools',
+'snpeff',
+'snpsift',
+'spades',
+'sra-toolkit',
+'rna-star',
+'strelka',
+'tiddit',
+'trim-galore',
+'unicycler',
+'varscan2',
+'vcftools',
+'vep',
+'vg'
+)
+ ORDER BY package, architecture
+) tmp GROUP by package ORDER BY package
+ ;
+EOT
=====================================
covid-19_doc/bio_covid-19_dependencies_result
=====================================
@@ -0,0 +1,63 @@
+Last-Update: Mon, 11 May 2020 21:48:13 +0200
+
+ package | architectures
+-----------------------------+-------------------------
+ abacas | all
+ bcftools | amd64,arm64,ppc64el
+ bedtools | amd64,arm64,ppc64el
+ blast | amd64
+ bowtie2 | amd64,arm64,ppc64el
+ bustools | amd64
+ bwa | amd64,arm64,ppc64el
+ centrifuge | amd64
+ changeo | all
+ cutadapt | all
+ diamond | all
+ fastp | amd64,arm64,ppc64el
+ fastqc | all
+ freebayes | amd64,arm64,ppc64el
+ kallisto | amd64,arm64,ppc64el
+ kraken2 | amd64,arm64,ppc64el
+ minia | amd64,arm64,ppc64el
+ minimap2 | amd64,arm64,ppc64el
+ multiqc | all
+ muscle | amd64,arm64,ppc64el
+ picard | amd64,arm64,ppc64el
+ porechop | amd64,arm64,ppc64el
+ prodigal | amd64,arm64,ppc64el
+ pycoqc | all
+ qcat | all
+ r-bioc-deseq2 | amd64,arm64,ppc64el
+ r-bioc-rtracklayer | amd64,arm64,ppc64el
+ r-bioc-summarizedexperiment | all
+ r-bioc-tximport | all
+ r-cran-alakazam | amd64,arm64,ppc64el
+ r-cran-corrplot | all
+ r-cran-crosstalk | all
+ r-cran-data.table | amd64,arm64,ppc64el
+ r-cran-dt | all
+ r-cran-ggplot2 | all
+ r-cran-ggrepel | amd64,arm64,ppc64el
+ r-cran-gprofiler | all
+ r-cran-locfit | amd64,arm64,ppc64el
+ r-cran-pheatmap | all
+ r-cran-plotly | all
+ r-cran-reshape2 | all,amd64,arm64,ppc64el
+ r-cran-rjson | amd64,arm64,ppc64el
+ r-cran-rlang | amd64,arm64,ppc64el
+ r-cran-rmarkdown | all
+ r-cran-scales | all,amd64,arm64,ppc64el
+ r-cran-shazam | all
+ r-cran-tigger | all
+ rna-star | amd64,arm64,ppc64el
+ salmon | amd64
+ samtools | amd64,arm64,ppc64el
+ snakemake | all
+ spades | amd64
+ sra-toolkit | amd64
+ trim-galore | all
+ unicycler | amd64
+ vcftools | amd64,arm64,ppc64el
+ vg | amd64
+(57 Zeilen)
+
View it on GitLab: https://salsa.debian.org/blends-team/med/-/commit/c17b641c9d622cd9f2da37c4ced4cfce93d20265
--
View it on GitLab: https://salsa.debian.org/blends-team/med/-/commit/c17b641c9d622cd9f2da37c4ced4cfce93d20265
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