I would advocate for a local copy (if missing) and an environment variable to override so that users can get a newer/different version.
I would also encourage upstream to find a way to embed a hash + download date in their logs and outputs, if possible.
We should also ask PDB to version their files. Do they keep old versions around?
--
Michael R. Crusoe
Hi all,
On 2021-07-19 10:24, Nilesh Patra wrote:
> On 19 July 2021 12:50:03 pm IST, Andrius Merkys <merkys@debian.org> wrote:
>> Currently I am looking into ProMod3 [3], which seems to be the engine
>> behind the great SWISS-MODEL service [4]. I seem to have figured out
>> the
>> dependencies, will go on to packaging next.
> Let us know if you need help with packaging the chain, in case you need helping hands :-)
So here I am asking for help/suggestions :)
Problem: OpenStructure, a dependency of ProMod3, requires PDB components
library, components.cif.gz, for some of its protein modeling routines.
This library is provided by the PDB at [1] and is itself freely
distributable (PDB discourages from modifying it though), but is updated
quite often and does not get a version number. Furthermore, people often
prefer to obtain the most up-to-date copy of components.cif.gz for their
research, thus providing it in a Debian package of its own would not be
very convenient.
I am aware of solutions to similar problems, for example, libcifpp
package, which keeps an up-to-date mmcif_pdbx_v50.dic.gz at
/var/cache/libcifpp/mmcif_pdbx_v50.dic.gz. This could work for
components.cif.gz as well, but my main concern is whether keeping
system-wide components.cif.gz up-to-date is what every user would want.
As a researcher I do my best to perform reproducible science. Thus I
want to know precise versions/timestamps/checksums of my input
databases, and have them suddenly change overnight is something akin to
a nightmare. What is more, there might be more than one user on a
machine wanting different versions of components.cif.gz.
Thus my candidate solution for providing components.cif.gz for
OpenStructure would be to talk to the upstream to implement an
environment variable allowing for greater flexibility. Or maybe there
are other solutions?
[1] ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
Best,
Andrius