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?
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
b) how shall we define the permissions for getData of the data directory?
Best,
Steffen
[1] http://wiki.debian.org/getData
[2] http://wiki.debian.org/BOINC/ServerGuide
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