Refgenie

Changed
- `--genome-server` can now be called multiple times to add additional refgenieservers
- `listr` will check each available refgenieserver and display assets
- `pull` will check each available refgenieserver and take the first matching asset found

Added
- possibility to list **multiple** selected genomes in `refgenie list/listr -g`

Added
- `import_igenome` command line tool for iGenomes integration with Refgenie
- `--genome/tag-description` arguments to the `refgenie build` command
- `-r`/`--requirements` argument to the `refgenie build` command recipe requirements to display required inputs and required assets for a particular recipe
- config manipulation support in multi-user contexts, it's racefree, uses file locks
- `dbNSFP` asset recipe
- assets tagging
- `refgenie tag` command that assigns a tag to an assets (re-tags it)
- `refgenie getseq` command that retrieves sequence ranges from a genome
- `seek_keys`, which provide control over files within an asset
- `asset_digests`, which are calculated after asset building and used to assure asset provenance
- asset relationships recording (`asset_children`, `asset_parents` fields)

Changed
- assets can be referred to by registry paths: `genome/asset.seek_key:tag`
- config v0.3 is required
- `refgenie pull` uses `refgenieserver` API v2

Added
- `list` and `listr` subcommand results can be restricted to a specific genome with `-g/--genome` options
- `remove` subcommand will remove an asset from disk and config
- Added recipes for new assets: `ensembl_gtf` and `feat_annotation`
- `build` now populates the `asset_description` field in the config with corresponding value from the recipe

Changed
- changed some asset locations; `tss_annotation` is now named `refgene_tss` or `ensembl_tss` and is built by the `refgene_anno` or `ensembl_gtf` assets. Renamed `gene_anno` to `refgene_anno`.

Changed
- `refgenie build` uses dict-like recipes for build instructions
- Major genome configuration file format changes
- Added `config_version` entry
- Added `assets` section in `genomes` section

- recipes can now include container images

Added
- `genomes` can have attributes, like description
- Added recipes for new assets `salmon`, `bwa`, `star`, `gene_anno`, and `tss_annotation`.

Added
- `add` subcommand

Changed
- Build process now builds individual assets