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docs: update readme (install seqrepo, uta/seqrepo test cmd, + submodu…
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…les) (#406)
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korikuzma committed May 3, 2024
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13 changes: 10 additions & 3 deletions README.md
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Expand Up @@ -82,9 +82,10 @@ First, you must install a local [SeqRepo](https://github.com/biocommons/biocommo
```shell
pip install seqrepo
export SEQREPO_VERSION=2021-01-29 # or newer if available -- check `seqrepo list-remote-instances`
sudo mkdir /usr/local/share/seqrepo
sudo mkdir -p /usr/local/share/seqrepo
sudo chown $USER /usr/local/share/seqrepo
seqrepo pull -i $SEQREPO_VERSION
seqrepo update-latest
```

If you encounter a permission error similar to the one below:
Expand Down Expand Up @@ -138,8 +139,8 @@ nearly instantaneous.
You can test UTA and seqrepo installations like so:

```shell
$ psql -XAt postgres://anonymous@localhost/uta -c 'select count(*) from transcript'
249909
$ psql -XAt postgres://anonymous@localhost/uta -c 'select count(*) from uta_20210129b.transcript'
314227
```

##### It doesn't work
Expand Down Expand Up @@ -200,6 +201,12 @@ make devready
source venv/3.10/bin/activate
```

If you already cloned the repo, but forgot to include `--recurse-submodules` you can run:

```shell
git submodule update --init --recursive
```

#### Submodules

vrs-python embeds vrs as a submodule, only for testing purposes. When checking out vrs-python and switching
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