Hi Ben, On Tue, Mar 24, 2020 at 10:51:07PM +0100, Ben Tris wrote: > I have put up a list with recent updated Debian Med packages.
Could you please explain on what basis you assembled this list. To give only two examples that make me wondering about this: kleborate - tool to screen Klebsiella genome assemblies Well, I injected this package since it helps my colleagues and its a useful package, thought. However, I fail to see the connection between Klebsiella and COVID-19. libspdlog-dev - Very fast, header only or compiled, C++ logging library (source: spdlog mentioned in your list) Well, sure this is used in some of our Debian Med packages. But adding this to such a list opens the question why you leave out libc and linux kernel. IMHO we need to track issues inside these packages via dependencies. I plan to enhance our Blends QA tools by a page which lists testing migration issues that are showing issues inside dependant packages. Similarly with libopencv-dev (source opencv). We have lots of packages that might be more relevant currently on our med-bio list[1] (which you hopefully consulted when you assembled your list). > Also inviting to update or add entries to the Free Software Directory. > > https://www.gezapig.nl/debianmedcovid.html In your list you are naming source packages. The Blends framework is based on binary packages so I will translate this to the probably most relevant binary package. Regarding debian-science I admit I do not really know what exactly you might have in mind. Debian-Science contains *a huge amount* of packages. Do you consider some specific metapackage more relevant? In any case I have added the extract of your list[2] to the covid-19 task. I admit if you want changes here I'd really appreciate merge requests (or simply send me a diff to the list I attached to this mail: sourcepkg.list is basically column three of your web page above and pkg.list is my translation to binary packages). > Debian Meds r-cran-surveillance relates to predicting outbreaks? . Well, probably I could cut-n-paste the whole med-epi task. So I did in my latest commit[3]. Rendering the web pages will take say one hour after pushing the new data. As a first work item: I remember that I failed to solve bug #813821 (of source package pynn - see my bug log). > May be interesting: > > https://www.eff.org/deeplinks/2020/03/embracing-open-science-medical-crisis-0 > > With these mentioned links > > https://nextstrain.org/ https://www.gisaid.org/ https://openpcr.org/ I just inspected nextstrain.org. All those tools are requiring https://blends.debian.org/med/tasks/covid-19#auspice This in turn needs about 20 nodejs packages. Do we want to tackle these in a COVID-19 web tools effort? Looking at gisaid.org I think that's just a data exchange. If you find some software tool we could package it would be great if we could help. Openpcr.org does not really look like Open Source: OpenPCR Software The OpenPCR application runs on both Windows and Mac OS X platforms using Adobe Air. For sure we could use the COVID-19 crisis as a chance to ask software authors to free their code - but we have other work to do now IMHO. Thanks a lot for all your input Andreas. [1] > >> https://blends.debian.org/med/tasks/bio > >> https://blends.debian.org/med/tasks/bio-dev > >> https://blends.debian.org/med/tasks/epi > >> ??? [2] https://salsa.debian.org/blends-team/med/-/commit/3e8075e331a90c494fbf1dfaa4bb6acc2cdd1815 [3] https://salsa.debian.org/blends-team/med/-/commit/b0229eafc61f9a32fa892fc2847b0a818dfb9aa3 -- http://fam-tille.de
abyss bbmap bcalm bcbio biobambam2 biosig4c++ cimg clonalframeml cyvcf2 debian-science delly diamond-aligner discosnp drmaa fasta3 fastqc foreign genometools gffread gnumed-client gnumed-server gromacs gubbins htscodecs htseq kalign kaptive kleborate kma libbio-alignio-stockholm-perl libbio-featureio-perl libchipcard libdeflate libgclib libics libmaus2 milib mmseqs2 ncbi-blast+ odil opencv orthanc orthanc-dicomweb paleomix plink1.9 plip praat prokka proteinortho psychopy pydicom pynn python-biom-format python-bx python-cgecore python-cogent python-cutadapt python-depinfo python-etelemetry python-gffutils python-pbcommand python-pbcore python-pyani python-pyfaidx python-pysam python-questplus python-scitrack python-screed python-tinyalign python-treetime python3-typed-ast q2-cutadapt q2-feature-table q2-quality-filter r-base r-bioc-limma r-cran-hms r-cran-msm r-cran-qtl r-cran-stringi r-cran-surveillance ragout rsem ruby-bio samblaster seqan3 seqmagick shapeit4 smrtanalysis spaln spdlog staden-io-lib stringtie sumaclust texlive-extra thesias tnseq-transit toil umis vg workrave
abyss bbmap bcalm bcbio biobambam2 biosig-tools cimg-dev clonalframeml python3-cyvcf2 delly diamond-aligner discosnp python3-drmaa fasta3 fastqc r-cran-foreign genometools gffread gnumed-client gnumed-server gromacs gubbins libhtscodecs-dev python3-htseq kalign kaptive kleborate kma libbio-alignio-stockholm-perl libbio-featureio-perl libchipcard-dev libdeflate-dev libgclib-dev libics-dev libmaus2-dev libmilib-java mmseqs2 ncbi-blast+ odil libopencv-dev orthanc orthanc-dicomweb paleomix plink1.9 plip praat prokka proteinortho psychopy python3-pydicom python-pynn python3-biom-format python3-bx python3-cgecore python3-cogent python3-cutadapt python3-depinfo python3-etelemetry python3-gffutils python3-pbcommand python3-pbcore python3-pyani python3-pyfaidx python3-pysam python3-questplus python3-scitrack python3-screed python3-tinyalign python3-treetime python3-typed-ast q2-cutadapt q2-feature-table q2-quality-filter r-base r-bioc-limma r-cran-hms r-cran-msm r-cran-qtl r-cran-stringi r-cran-surveillance ragout rsem ruby-bio samblaster libseqan3-dev seqmagick shapeit4 smrtanalysis spaln libspdlog-dev staden-io-lib-utils stringtie sumaclust texlive-science thesias tnseq-transit toil umis vg workrave
