Re: getData and a new upload of autodocksuite
----- Mail original -----
> De: "Steffen Möller" <steffen_moeller@gmx.de>
> À: "Debian Med Project List" <debian-med@lists.debian.org>
> Envoyé: Dimanche 4 Septembre 2011 15:25:47
> Objet: getData and a new upload of autodocksuite
> Hello,
>
> this very early morning I had prepared getData [1] configs to download
> the descriptions of ligands for docking with autodock. It
> was motivated as a followup to that Google Summer of Code project to
> prepare explicit instructions for setting up a BOINC server
> with Debian for molecular docking [2]. Then, I did not really know
> where to put it, so I had come up with the idea to prepare a
> separate (binary) package for it and have it shipped with the
> autodocksuite source package.
>
> It was good to see all the work that Charles has already put into it
> all for some genomes. And I like his idea to come up with
> shared Makefiles. I should possibly have done so, too.
>
> foreach $n (("asinex", "chembridge_buildingblocks_pdbqt_1000split",
> "drugbank_nutraceutics",
> "drugbank_smallmol", "fda_approved",
> "human_metabolome_pdbqt_1000split", "otava",
> "zinc_natural_products")) {
>
> $toBeMirrored{"zinc.pdbqt.$n"}={
> "name" => "ZINC - PDBQT formatted – $n",
> "tags" => ["pdbqt","compounds"],
> "source" => "wget $sharedWgetOptions
> http://zinc.docking.org/pdbqt/$n.tar.gz";,
> "post-download" => "tar --no-same-owner --exclude prepare_lig.log
> --exclude mol2 -xzvf $n.tar.gz && chmod -R go+r . && find .
> -type d
> -exec chmod +x {} \\; "
> };
> }
>
> My basic question to you guys now would be
> 0) do you share the vision that the packages should come with
> instructions how to get the data, not the getData package itself?
This is a difficult point. Data location/format may change in time, and impacts the software package in this case (let's http location change), and all packages needing it.... But, post download processes is specific to each package so....
> a) how can we have something that both BioMaj (because it is nice) and
> getData (because it is easy for me at least) can work with
Biomaj takes in charge the download etc... so setting direct commands will not work directly.
However, biomaj could parse this kind of data. The impact is data package will not use all biomaj features.
One nice point however would be to set the source without the wget etc..., only the URL (or to separate those in "source" and "download" for example)
Biomaj use mainly URLs and regexp to know what need to be downloaded, however a description need to be generic e.g. tool agnostic (to be able to use any tool and ease tools changes).
Regarding Biomaj/Getdata/other, what would be required I think is a generic tool name and to use system alternatives. User would set in Depends either the generic name (for any) or a specific tool name. In postinst he would exec the data download/update task with the generic tool name.
> b) how shall we define the permissions for getData of the data
> directory?
Well, a specific data directory must be used for all "data" (/var/lib/med/data?, or whatever...). It should be read-only for other users. This directory should be used for data access but should not be modified, I think, by the user.
Olivier
>
> Best,
>
> Steffen
>
> [1] http://wiki.debian.org/getData
> [2] http://wiki.debian.org/BOINC/ServerGuide
>
>
> --
> To UNSUBSCRIBE, email to debian-med-REQUEST@lists.debian.org
> with a subject of "unsubscribe". Trouble? Contact
> listmaster@lists.debian.org
> Archive: [🔎] 4E637C5B.90800@gmx.de">http://lists.debian.org/[🔎] 4E637C5B.90800@gmx.de
Reply to: