removed quay.io support from instructions

docker-files/my-example.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
-#docker run -it -v /opt/apollo/:/data -v /Users/nathandunn/PGDATA/:/var/lib/postgresql -p 8888:8080 quay.io/gmod/docker-apollo:neat-expermint-v3
-#docker run -it -v /opt/apollo/:/data -p 8888:8080 quay.io/gmod/docker-apollo:neat-expermint-v3
-#docker run -it -v /opt/apollo/:/data -p 8888:8080 quay.io/gmod/docker-apollo:latest
-#docker run -it -v /opt/apollo/:/data -p 8888:8080 quay.io/gmod/docker-apollo:latest
+#docker run -it -v /opt/apollo/:/data -v /Users/nathandunn/PGDATA/:/var/lib/postgresql -p 8888:8080 gmod/docker-apollo:neat-expermint-v3
+#docker run -it -v /opt/apollo/:/data -p 8888:8080 gmod/docker-apollo:neat-experemint-v3
+#docker run -it -v /opt/apollo/:/data -p 8888:8080 gmod/docker-apollo:latest
+#docker run -it -v /opt/apollo/:/data -p 8888:8080 gmod/docker-apollo:latest
 #docker run -it -v /opt/apollo/:/data -p 8888:8080 d50c1cd918e3
-docker run -it --env-file=env.list -v /opt/apollo/:/data -p 8888:8080 quay.io/gmod/docker-apollo:latest
+docker run -it --env-file=env.list -v /opt/apollo/:/data -p 8888:8080 gmod/docker-apollo:latest

docs/Docker.md

@@ -16,7 +16,7 @@ Note: data is not guaranteed to be saved in this manner, but data is `/jbrowse/r
 ## Production
 
 To **run in production** against **persistent** JBrowse data and a **persistent** database you should:
-- `docker pull gmod/apollo` (or `docker pull quay.io/gmod/apollo` if using quay.io)  if running `latest` build to guarantee you are using the latest build (not necessary for point releases).
+- `docker pull gmod/apollo` if running `latest` build to guarantee you are using the latest build (not necessary for point releases).
 - Create an empty directory for database data, e.g. `/postgres/data/directory` if you want to save data if the image goes down.
 - If you want to upload tracks and genomes directories, create an empty directory for that, e.g., `/jbrowse/root/apollo_data`
 - Put JBrowse data in a directory, e.g. `/jbrowse/root/directory/`.
@@ -29,7 +29,7 @@ To **run in production** against **persistent** JBrowse data and a **persistent*
     -v /jbrowse/root/apollo_data:/data/temporary/apollo_data \
     -e APOLLO_ADMIN_EMAIL=adminuser \
     -e APOLLO_ADMIN_PASSWORD=superdupersecretpassword \
-    -p 8888:8080 quay.io/gmod/apollo:latest
+    -p 8888:8080 gmod/apollo:latest
 ```    
 
 - As above, open [http://localhost:8888](http://localhost:8888) in a browser to begin [setting up Apollo](UsersGuide.md).
@@ -40,7 +40,7 @@ See [docker run instructions](https://docs.docker.com/engine/reference/run/) to
 
 Additional options could be to set memory (required for running production off a mac) ` --memory=4g`, running a docker daemon `d` or adding debugging to the server ` -e "WEBAPOLLO_DEBUG=true"`.  For example (after creating the local `apollo_shared_dir`): 
 
-    docker run --memory=4g -d -it -p 8888:8080 -v `pwd`/apollo_shared_dir/:`pwd`/apollo_shared_dir/ -e "WEBAPOLLO_DEBUG=true"  -v /postgres/data/directory:/var/lib/postgresql quay.io/gmod/apollo:latest 
+    docker run --memory=4g -d -it -p 8888:8080 -v `pwd`/apollo_shared_dir/:`pwd`/apollo_shared_dir/ -e "WEBAPOLLO_DEBUG=true"  -v /postgres/data/directory:/var/lib/postgresql gmod/apollo:latest 
 
 You can configure additional options by setting environmental variables for [docker apollo-config.groovy](https://github.com/GMOD/Apollo/blob/develop/docker-files/docker-apollo-config.groovy) by passing 
 through via [multiple `-e` parameters](https://vsupalov.com/docker-arg-env-variable-guide/).
@@ -57,17 +57,17 @@ or [set appropriate environment variables](https://docs.docker.com/engine/refere
 
 ### Notes on releases and availability
 
-The image is available on [docker hub](https://hub.docker.com/r/gmod/apollo) and [quay.io](https://quay.io/repository/gmod/apollo?tab=builds).
+The image is available on [docker hub](https://hub.docker.com/r/gmod/apollo).
 
-On docker hub you always pull from `gmod/apollo:release-<version>` and from quay.io you pull from `quay.io/apollo:<version>` where version is something like 2.6.2.
+On docker hub you always pull from `gmod/apollo:release-<version>` where version is something like 2.6.2.
 
 #### Versions
 
 On docker hub versions are `stable` is the `master` branch or the latest stable release  (e.g., 2.6.0), `latest` is the checkin, which has not necessarily been thoroughly tested and `release-X.Y.Z` represents the release of the tag `X.Y.Z` (e.g., `release-2.6.0`).   
 
-quay.io mirrors tags and all branches directly.  So `master` is `master` and `X.Y.Z` is the same.  So `quay.io/gmod/apollo:2.6.0` is the same as `gmod/apollo:release-2.6.0`
+quay.io mirrors tags and all branches directly.  So `master` is `master` and `X.Y.Z` is the same.  So `quay.io/<user or orgname>/apollo:2.6.0` is the same as `<user or org name>/apollo:release-2.6.0`, but you'll have to fork your own version
 
-See what is avaiable for [docker hub builds](https://hub.docker.com/r/gmod/apollo/tags)  or [quay.io builds](https://quay.io/repository/gmod/apollo?tab=builds).
+See what is avaiable for [docker hub builds](https://hub.docker.com/r/gmod/apollo/tags).
 
 
 ### Logging In
@@ -85,7 +85,7 @@ The default credentials in this image are:
 
 1. Make the following directories somewhere with write permissions: `postgres-data` and `jbrowse-data`. 
 1. Copy your jbrowse data into `jbrowse-data`.  We provide [working sample data](http://genomearchitect.readthedocs.io/en/latest/Apollo2Build.html#adding-sample-data).
-1. Run the docker-command:  `docker run -it -v /absolute/path/to/jbrowse-data:/data -v /absolute/path/to/postgres-data:/var/lib/postgresql -p 8888:8080 quay.io/gmod/apollo:latest`
+1. Run the docker-command:  `docker run -it -v /absolute/path/to/jbrowse-data:/data -v /absolute/path/to/postgres-data:/var/lib/postgresql -p 8888:8080 gmod/apollo:latest`
 1. Login to the server at `http://localhost:8888/`
 1. Add an organism per the [instructions under Figure 2](http://genomearchitect.readthedocs.io/en/latest/Apollo2Build.html#login-to-the-web-interface).   Using yeast as an example, if you copy the data into `jbrowse-data/yeast` then on the server 
 you'll add the directory: `/data/yeast`. 

docs/Release.md

@@ -10,7 +10,7 @@
 
 - Update servers / images:
     - Update demo, download new release and build.
-    - Confirm docker images are updated automatically on [quay.io](https://quay.io/repository/gmod/apollo?tab=builds) and [docker hub](https://hub.docker.com/r/gmod/apollo/tags).  With docker hub, will need to pull and tag and push stable and release number.
+    - Confirm docker images are updated automatically on [docker hub](https://hub.docker.com/r/gmod/apollo/tags).  With docker hub, will need to pull and tag and push stable and release number.
     - (1) Update AWS empty images and data image, (2)  create newer versions of the images from the running instances, (3) test, (4) distribute to N. Virginia and N. California.
 
 Zenodo:     

docs/TestScript.md

@@ -350,11 +350,11 @@ boundary using the arrows in the display.  Modify a number explicitly and click
 
 ### F) Test Docker load
 
-17.0) Run against docker built on quay.io and/or Docker hub
+17.0) Run against docker built on Docker hub
 
 17.1) Load docker with a sample files directory and database: 
 
-    docker run -it -v /jbrowse/root/directory/:/data -v /postgres/data/directory:/var/lib/postgresql -p 8888:8080 quay.io/gmod/apollo:latest
+    docker run -it -v /jbrowse/root/directory/:/data -v /postgres/data/directory:/var/lib/postgresql -p 8888:8080 gmod/apollo:latest
 
 17.2) Confirm that we can load a genome and tracks from the existing directory (e.g,. Honeybee)