Famli

Increment FAMLI to v1.1 -- includes a new flag (`--output-aln`) which will write out a file with the filtered set of alignments.

Taxonomic analysis via `diamond-tax.py`, a standalone script in the PATH.

This release updated DIAMOND to v0.9.22. That means that this version will not work with any databases built with the prior version of FAMLI. All databases must be rebuilt in order to use this updated version.

Add the bucket_command_wrapper, a small utility that enables easier execution within larger sciluigi workflows

This release represents the version of FAMLI that is described in the first published description.

The best way to run FAMLI is using the Docker image `quay.io/fhcrc-microbiome/famli:v1.0`.

Alternatively, FAMLI can be installed via `pip install famli`. However, it is then necessary to include a working copy of [DIAMOND](https://github.com/bbuchfink/diamond) in the path. For that reason we suggest that it is easiest to use the Docker image that is provided.

Using Aspera for downloads (the previous release) did not work for all SRA accessions, as the FTP path indicated by the NCBI documentation is not always correct.

Instead, to get around the issue of writing large files to the root directory I am creating a cache folder within the `temp_folder` for each run, and symlinking `/root/public/ncbi/sra` to that folder.

This release has no changes in the outputs from the previous one -- it should just work on more SRA accessions.