Re: Idea wanted: What is the most key open source projects to fight COVID-19?
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
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