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Add instructions for installing w/new shell dependency
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Reece Hart committed Jul 5, 2024
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Expand Up @@ -111,17 +111,17 @@ tested. Patches to get other systems working would be welcomed.

### OS X

$ brew install python libpq
brew install python libpq

### Ubuntu

$ sudo apt install -y python3-dev gcc zlib1g-dev tabix
sudo apt install -y python3-dev gcc zlib1g-dev tabix

### All platforms

$ python -m venv venv
$ source venv/bin/activate
$ pip install seqrepo
$ pip install biocommons.seqrepo
$ sudo mkdir -p /usr/local/share/seqrepo
$ sudo chown $USER /usr/local/share/seqrepo
$ seqrepo pull -i 2018-11-26
Expand All @@ -138,7 +138,9 @@ tested. Patches to get other systems working would be welcomed.
>> sr["NC_000001.11"][780000:780020]
'TGGTGGCACGCGCTTGTAGT'

# Or, use the seqrepo shell for even easier access
# Optional: Install with the `shell` dependency group
# (i.e., `pip install biocommons.seqrepo[shell]`)
# and use the seqrepo shell
$ seqrepo start-shell -i 2018-11-26
In [1]: sr["NC_000001.11"][780000:780020]
Out[1]: 'TGGTGGCACGCGCTTGTAGT'
Expand Down Expand Up @@ -198,7 +200,7 @@ Install pre-commit hook:

## Building a docker image

Docker images are available at https://hub.docker.com/r/biocommons/seqrepo.
Docker images are available at <https://hub.docker.com/r/biocommons/seqrepo>.
Tags correspond to the version of data, not the version of seqrepo, because the
intent is to make it easy to depend on a local version of seqrepo *files*. Each
docker image is an installation of seqrepo that downloads the corresponding
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