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abretaud committed Oct 25, 2018
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4 changes: 2 additions & 2 deletions Makefile
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Expand Up @@ -2,10 +2,10 @@ RELEASE=$(shell cat Dockerfile| grep chado-schema-builder | grep -o 'download\/.
PG_VERS=$(shell head -n 1 Dockerfile | sed 's/FROM postgres://g')

run:
docker run -it -e INSTALL_YEAST_DATA=1 -p 5432:5432 erasche/chado
docker run -it -e INSTALL_YEAST_DATA=1 -p 5432:5432 quay.io/galaxy-genome-annotation/chado

run_persist:
docker run -it -e INSTALL_YEAST_DATA=1 -v $(shell pwd)/.pgdata:/var/lib/postgresql/data/ -p 5432:5432 erasche/chado
docker run -it -e INSTALL_YEAST_DATA=1 -v $(shell pwd)/.pgdata:/var/lib/postgresql/data/ -p 5432:5432 quay.io/galaxy-genome-annotation/chado

release:
git tag -s -a -m "Automated release" $(RELEASE)-pg$(PG_VERS)
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16 changes: 8 additions & 8 deletions README.md
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@@ -1,4 +1,4 @@
# Docker Chado Container [![Docker Automated buil](https://img.shields.io/docker/automated/erasche/chado.svg)](https://hub.docker.com/r/erasche/chado/)
# Docker Chado Container [![Docker Repository on Quay](https://quay.io/repository/galaxy-genome-annotation/chado/status "Docker Repository on Quay")](https://quay.io/repository/galaxy-genome-annotation/chado)

[![DOI](https://zenodo.org/badge/10899/erasche/docker-chado.svg)](https://zenodo.org/badge/latestdoi/10899/erasche/docker-chado)

Expand All @@ -10,14 +10,14 @@ The Chado container is very simple to start, as simple as a regular postgres
container:

```console
docker run -d --name chado erasche/chado:latest
docker run -d --name chado quay.io/galaxy-genome-annotation/chado:latest
```

The Chado schema in this container will not persist across restarts, to allow
for that, supply a volume with `-v` like so:

```console
docker run -d --name chado -v /path/to/storage:/var/lib/postgresql/data/ erasche/chado
docker run -d --name chado -v /path/to/storage:/var/lib/postgresql/data/ quay.io/galaxy-genome-annotation/chado
```

The schema and five default ontologies are installed upon launch, if no chado
Expand All @@ -28,7 +28,7 @@ instance is detected.
If you haven't exposed a port with the `-p/-P` options, you can connect to your chado container via a linked container:

```console
docker run -i -t --link chado:db erasche/chado bash
docker run -i -t --link chado:db quay.io/galaxy-genome-annotation/chado bash
root@0069babbd55f:/# psql -h db -U postgres postgres
# Password is postgres
```
Expand All @@ -39,7 +39,7 @@ If you do not wish to have the schema automatically installed upon launch,
simply set the environment variable `INSTALL_CHADO_SCHEMA` to `0`:

```console
docker run -d --name chado-tools -e INSTALL_CHADO_SCHEMA=0 erasche/chado
docker run -d --name chado-tools -e INSTALL_CHADO_SCHEMA=0 quay.io/galaxy-genome-annotation/chado
```

This will let you use all the GMOD tools without needing to wait for the chado
Expand All @@ -51,17 +51,17 @@ If you would like some default yeast data installed for you, you can supply the
environment variable `INSTALL_YEAST_DATA=1`. This requires that you leave `INSTALL_CHADO_SCHEMA=1`:

```console
docker run -d --name chado-yeast -e INSTALL_YEAST_DATA=1 erasche/chado
docker run -d --name chado-yeast -e INSTALL_YEAST_DATA=1 quay.io/galaxy-genome-annotation/chado
```

## Using the Container in `docker-compose.yml`

It is strongly, strongly recommended that you pin your images to a [specific tag](https://hub.docker.com/r/erasche/chado/tags/) of this repository. I have intentionally and unintentionally broken the `:latest` images before.
It is strongly, strongly recommended that you pin your images to a [specific tag](https://quay.io/repository/galaxy-genome-annotation/chado?tab=tags) of this repository. I have intentionally and unintentionally broken the `:latest` images before.

E.g.

```
image: erasche/chado:1.31-jenkins97-pg9.5
image: quay.io/galaxy-genome-annotation/chado:1.31-jenkins97-pg9.5
```

Given that I as the developer have no easy way to communicate to you as the end user that breaking changes have been made (and keeping backwards compatability is prohibitve for a 1-person team..., sorry!), it is best to pin and read the changelog before upgrading.
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