Skip to content

Commit

Permalink
Update: Databse info added
Browse files Browse the repository at this point in the history
  • Loading branch information
rhysnewell authored Apr 27, 2022
1 parent c9cbe1f commit 0c94e79
Showing 1 changed file with 14 additions and 0 deletions.
14 changes: 14 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -90,6 +90,20 @@ Initial requirements for aviary can be downloaded using the `aviary.yml`:
conda env create -n aviary -f aviary.yml
```

## Databases

Aviary uses programs which require access to locally stored databases. These databases can be quite large, as such we recommend setting up one instance of Aviary and these databases per machine or machine cluster.

The **required** databases are as follows:
* [GTDB](https://gtdb.ecogenomic.org/downloads) Required for taxonomic annotation

The **optional** databases are as follows:
* [EggNog](https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.7#setup) Will become required soon.
* [EnrichM](https://github.com/geronimp/enrichM)
* Busco

**If you do not have the optional databases installed, then when aviary asks you to specify these databse passes when configuring just press enter and specify no path.**

# Module details
|__method__ |__description__ |
| --- | --- |
Expand Down

0 comments on commit 0c94e79

Please sign in to comment.