Re: Debian Med Covid special?
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
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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
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