Don't put databases in the bin/ folder

[tseemann]

% amrfinder_update
Running amrfinder_update
Dowloading AMRFinder database version 2019-07-10.1 into
   /home/miniconda3/envs/ncbi-amrfinderplus_env/bin/data/2019-07-10.1/
Indexing

It is bad form to put non-executables in the bin/ folder.
Could you use /share/data instead?

[evolarjun]

You're absolutely right. That is in the plans for the next release, which should be "beta" and put things in the right places.

[evolarjun]

So this should be resolved in a relatively quick-n-dirty way with the newest release 3.1.1b with an option to make "DEFAULT_DB_DIR=/wherever/you/want/it" which hard-codes the default database directory in the source code. We also altered the bioconda build script to make this go in a sensible place there. $PREFIX/share/amrfinderplus/data.

(Note this bugged me and I wanted to fix it before we finally finish our testing, so the current 3.1.1b release is still not fully tested to our satisfaction)

Our plan is to set this via a configuration file.

[tseemann]

@evolarjun has this bug regressed?
latest conda putting it in bin/ again?

/opt/miniconda3/envs/amrfinderplus_env/bin/data/
0 drwxr-sr-x 2 torsten punim0401 193486110 Nov  7 09:27 2019-10-30.1

I can see in bioconda

build.sh
#!/bin/bash

make CXX="$CXX $LDFLAGS" CPPFLAGS="$CXXFLAGS" PREFIX="$PREFIX" DEFAULT_DB_DIR="$PREFIX/share/amrfinderplus/data"
make install

but maybe it isn't honouring DEFAULT_DB_DIR properly?

https://github.com/ncbi/amr/search?q=DEFAULT_DB_DIR&unscoped_q=DEFAULT_DB_DIR