On Mon, May 11, 2020 at 03:39:41PM +0200, Andreas Tille wrote: > Hi Jun, > > thanks a lot for your input which is extremely helpful. > > On Sat, May 09, 2020 at 10:10:33PM +0200, Jun Aruga wrote: > > Hi Andreas, > > > > The 3 pipelines nf-core/nanoseq, nf-core/artic, nf-core/viralrecon I > > shared are the most applicable (= the highest priority) to COVID-19 > > analysis. [1]. > > Now I share the additional 5 pipelines that are certainly relevant (= > > the 2nd highest priority). [2] > > This is the result of my interview in the nf-core Slack channel. > > Thanks for doing this. > > > Could you check the packages situations in Debian? > > Done below. Every package without a remark is in Debian. I gave > upstream URLs for those packages that are not yet touched and URLs on > salsa.debian.org for preliminary packaging stuff. Sometimes I had > some additional comments from previous experience. > > > Sorry I knew information about the 5 pipelines a few weeks ago. But I > > took a time to summarize the list of the packages and email it. > > That's fine. We found other work to do meanwhile. ;-) > > > * nf-core/scrnaseq (single cell) > > * nf-core/smartseq2 (single cell) > > * nf-core/sarek (whole-genome sequencing) > > * nf-core/mag (meta-genomics) > > * nf-core/bcellmagic (immune response) > > > > https://github.com/nf-core/scrnaseq/blob/master/bin/scrape_software_versions.py > > bustools
Ahh, that's packaged as well. :-) > > kallisto > > multiqc > > salmon > > star > In Debian named rna-star > > > https://github.com/nf-core/smartseq2/blob/master/bin/scrape_software_versions.py > > fastqc > > multiqc > > > > https://github.com/nf-core/sarek/blob/master/bin/scrape_software_versions.py > > allelecount > > -> https://github.com/cancerit/alleleCount Now in https://salsa.debian.org/med-team/allelecount featuring the build of the C code build. I'll ask the Perl team for hints how to install the Perl code. Kind regards Andreas. > > ascat > > -> https://github.com/Crick-CancerGenomics/ascat > > > bcftools > > bwa > > fastqc > > freebayes > > gatk > > -> https://salsa.debian.org/med-team/gatk > > > htslib > > manta > > -> https://salsa.debian.org/med-team/manta > > May be somebody volunteers to ping upstream about a Python3 port here > https://github.com/Illumina/manta/issues/180 > We can not get it into Debian before this is solved. > > > multiqc > > qualimap > > -> https://salsa.debian.org/med-team/qualimap > I once was pretty close to package this. However it contains some binary > JARs named bioinfo-commons-0.10.1.jar, bioinfo-ngs-0.1.0.jar, ... > where the source just seems to be "lost". See my discussion on the > mailing list: > > > https://groups.google.com/forum/#!msg/qualimap/KVJ8m5ZsAhU/O30pHTkADAAJ;context-place=searchin/qualimap/org.bioinfo > > If anybody has some idea where to find those sources that would be really > helpful! > > > r > > samtools > > snpeff > > -> https://salsa.debian.org/med-team/snpeff > > > strelka > > -> https://github.com/Illumina/strelka/ > > > tiddit > > -> https://github.com/SciLifeLab/TIDDIT > > > vcftools > > vep > > Please confirm that you mean > https://github.com/Ensembl/ensembl-vep > > > > https://github.com/nf-core/mag/blob/master/bin/scrape_software_versions.py > > busco > > -> https://gitlab.com/ezlab/busco > > > cat > > -> https://github.com/dutilh/CAT > BTW, its not a good idea to name a tool like a pretty generid UNIX command > > > centrifuge > > fastp > > fastqc > > filtlong > > kraken2 > > megahit > > -> https://ftp-master.debian.org/new/megahit_1.2.9-1.html > (just uploaded to new) > > > metabat > > -> https://bitbucket.org/berkeleylab/metabat > > > multiqc > > nanolyse > > -> https://pypi.org/project/NanoLyse/1.1.0/ (with version tag) > -> Asked for release tags on https://github.com/wdecoster/nanolyse/issues/6 > > > nanoplot > > -> https://salsa.debian.org/med-team/nanoplot > > > porechop > > quast > > -> https://salsa.debian.org/med-team/quast > As I wrote in some other mail this itself has a lot of predepends > that are included as binaries. > > > spades > > > > https://github.com/nf-core/bcellmagic/blob/master/bin/scrape_software_versions.py > > changeo > > fastqc > > multiqc > > muscle > > presto > > Binary package name is python3-presto > > > r > > r-alakazam > > Binary package name is r-cran-alakazam > > > r-shazam > > Binary package name is r-cran-shazam > > > r-tigger > > Binary package name is r-cran-tigger > > > vsearch > > > If anybody wants to work on one of the packages its probably helpful to > announce it here. > > Kind regards and thanks again for your very helpful contribution > > Andreas. > > > > [1] nf-core Slack #covid19 channel > > https://nfcore.slack.com/archives/C0105J0J9T8/p1587480925053900 > > > The pipelines you listed are the ones that are/will be most > > applicable to COVID-19 analysis. > > [2] nf-core Slack #covid19 channel > > https://nfcore.slack.com/archives/C0105J0J9T8/p1587498948095200 > > > But the single cell pipelines could certainly be relevant. Also > > sarek for whole-genome sequencing analysis, mag for metagenomics > > analysis and bcellmagic for investigations into the immune response.. > > > > Thanks & Cheers, > > Jun > > > > -- > > Jun | He - His - Him > > > > > > -- > http://fam-tille.de > > -- http://fam-tille.de
