Advanced Database Handling

Several of these databases are quite large. Understandably, you probably don't want to download or prepare them again if you already have. There are a few scenarios you might run in to.

You already have the databases, and they're all in one place and properly named.
Excellent! This is the easiest. You can make use of dammit's --database-dir flag to tell it where to look. When running with --install, it will find the existing files and prep them if necessary.:
```
dammit databases --database-dir <my_database_dir> --install
```
Same as above, but they have different names.
dammit expects the databases to be "properly" named -- that is, named the same as their original forms. If your databases aren\'t named the same, you'll need to fix them. But that's okay! We can just soft link them. Let's say you have Pfam-A already, but for some reason its named all-the-models.hmm. You can link them to the proper name like so:
```
cd <my_database_dir>
ln -s all-the-models.hmm Pfam-A.hmm
```
If you already formatted it with hmmpress, you can avoid repeating that step as well:
```
ln -s all-the-models.hmm.h3f Pfam-A.hmm.h3f
ln -s all-the-models.hmm.h3i Pfam-A.hmm.h3i
ln -s all-the-models.hmm.h3m Pfam-A.hmm.h3m
ln -s all-the-models.hmm.h3p Pfam-A.hmm.h3p
```
For a complete listing of the expected names, just run the databases command:
```
dammit databases
```
You have the databases, but they're scattered to the virtual winds.
The fix here is similar to the above. This time, however, we'll soft link all the databases to one location. If you've run dammit databases, a new directory will have been created at \$HOME/.dammit/databases. This is where they are stored by default, so we might as well use it! For example:
```
cd $HOME/.dammit/databases
ln -s /path/to/all-the-models.hmm Pfam-A.hmm
```
And repeat for all the databases. Now, in the future, you will be able to run dammit without the --database-dir flag.

Alternatively, if this all seems like too much of a hassle and you have lots of hard drive space, you can just say "to hell with it!" and reinstall everything with:

dammit databases --install