ARBHOME not set (w/o wrapper script)

[epruesse]

When not using the wrapper script, e.g. installation via Bioconda, the ARBHOME environment variable may not be set causing arb_pt_server to fail.

Encode the path in the binary and try to find ARB at startup.

[epruesse]

fixed by 62239e37e5cf439598137e5f7b8344a6c3ab3759 ff

[mdehollander]

Still getting the same error with 1.3.4 installed from bioconda:

mattias@mattias-notebook:~$  conda activate sina-1.3.4
(sina-1.3.4) mattias@mattias-notebook:~$ printenv | grep ARB
ARBHOME=
ARBHOME_BACKUP=
(sina-1.3.4) mattias@mattias-notebook:~$ arb_pt_server
Fatal ERROR: Environment Variable ARBHOME not found !!!
   Please set 'ARBHOME' to the installation path of ARB
sum of above:  0 b
overall alloc: 0 b
(sina-1.3.4) mattias@mattias-notebook:~$ conda list | grep sina
# packages in environment at /home/mattias/miniconda3/envs/sina-1.3.4:
sina                      1.3.4                h4ef8376_2    bioconda

[epruesse]

@mdehollander Darn. Looking into it. Does the tarball from the releases work for you at least?

[epruesse]

Err. Wait. That's not an issue with SINA, but with the arb-bio package. In theory, there should be an activate script that sets ARBHOME when you activate the environment.

[epruesse]

Oh. Wait. Sigh. Need to update the arb-bio package yet again.

The activate script is part of arb-bio, but SINA installs only arb-bio-tools and libarbdb, so no activate script and hence no ARBHOME.

It is something of a corner case. SINA itself will set ARBHOME doing some hacky guesswork (using the memory address of ARB library calls to get the on-disk location of libARBDB and deducing ARBHOME from that). I don't think I want to add that kind of stuff to ARB itself.

[epruesse]

Updated the ARB package https://github.com/bioconda/bioconda-recipes/pull/10889

[mdehollander]

Perfect, I can confirm it works now. Thanks.