<zimoun>civodul: I would enlarge HPC to «Scientific Context». The name GuixHPC is what it is. Something along this line «Users and developers of GNU Guix in scientific context and reproducible research»
<zimoun> civodul: do you know how to quickly reach GriCAD folks other than email?
<civodul>zimoun, efraim: yes, i think we should have something that people can start editing now
<zimoun>where do you all these answers? How birdsite works is really mysterious for me
<zimoun>I should be old because I find email threads much more easier to stay on touch :-)
<zimoun>As I wrote elsewhere, these “angry” arguments are implementation detail bikeshedding and miss the core point about why there is a “scientific reproducibility crisis” and how to move forward to fix it, IMHO. (At least fix what we can. :-))
<zimoun>in their Nature article, they write «They [workflow managers] simplify pipeline development, optimize resource usage, handle software installation and versions, and run on different compute platforms, enabling workflow portability and sharing»
<zimoun>To make a point, we should demonstrate that «handle software installation and versions, and run on different compute platforms, enabling workflow portability and sharing» is wrong for all the tools they use.
<zimoun>because these workflow managers are not connected to any package managers. Other said, their claim depends only on the underlying package manager. :-)
<rekado>if we want to show that this is not good enough we need to find a way to get our message across more succintly
<rekado>…and have a good answer to the question why in guix you can’t just say “use samtools version xyz” and have it DTRT
<rekado>I wonder: can we have a guixify-condaforge tool that provides an environment, builds a conda package, bundles it up, records references, and then lets you install it with Guix as any other guix package.
<rekado>slurp up all existing bioconda/condaforge packages out there
<zimoun>rekado, the message that I try to teach here is that “use samtools version xyz” is not enough because it says “use samtools source version xyz” and what about the binary version you run. Using the Milk and Yogurt analogy to explain binary. It works more or less… Bio people seems receptive, I guess.
<zimoun>Here some slides that I have to convert to text. :-)
<rekado>re the samtools recipes: conda has build.sh and meta.yml. For samtools they seem to have a bunch of different recipes for different versions, each in their own directories.
<rekado>I wonder if we can just reuse *their* tooling without complicated modifications, build in a base guix system, and then copy the results to a Guix output. (Then scan the output for references and make these things available when the package is installed.)
<rekado>PurpleSym: I fixed the rstudio-server-multi-version patches.
<rekado>I’m running the build with the guix-science package definition now and will then push my updated patches.
<rekado>previously, running rserver as root would break the multi-version feature as the wrong home directory was accessed (namely that of the user running "rserver", not the user account running "rsession").
<rekado>R versions can be specified globally (in /etc/rstudio/r-versions) or per user (e.g. /home/rekado/.local/share/rstudio/r-versions).
<rekado>every version that should be available in the GUI gets a record consisting of “Path: /tmp/r-test/.guix-profile” and “Label: whatever you want”.