Configurable libraries path #378
Description
For the use of repeatmasker in Galaxy (where it seems to be used quite a bit) we use containers. Which makes it difficult (/impossible) to add any files to the installation directory.
Currently repeatmasker assumes a writable directory Libraries/famdb which is a problem in multiuser environments and in environments where the installation dir is not writable.
This seems also a good idea in terms of reproducibility because we could use different dfam versions.
Would it be possible to
- make the library path configurable (e.g. with an environment variable).
- in a discussion at bioconda it seemed that repeatmasker might write to the library directory (unsure if this is actually the case). Can this be avoided, e.g. by providing the complete dfam? Ideally all writes would go only to the working directory / a tmp directory.
The only workaround that I could think of so far would be to copy the whole installation directory (or at least the binary and the Libraries dir .. such that their paths are in the correct relation) for each job.