Deployment docs fix url

docs/deployment/Dockerfile

@@ -3,6 +3,7 @@ ARG JBROWSE_VERSION
 ARG APOLLO_VERSION
 ARG FORWARD_HOSTNAME
 ARG FORWARD_PORT
+ARG URL
 COPY <<EOF /usr/local/apache2/conf/httpd.conf.append
 LoadModule proxy_module modules/mod_proxy.so
 LoadModule proxy_http_module modules/mod_proxy_http.so
@@ -50,9 +51,9 @@ COPY <<EOF /usr/local/apache2/htdocs/config.json
       "name": "My Apollo Server",
       "description": "A server for my annotations",
       "domains": [
-        "${FORWARD_HOSTNAME}"
+        "${URL}"
       ],
-      "baseURL": "${FORWARD_HOSTNAME}"
+      "baseURL": "${URL}"
     }
   ]
 }

docs/deployment/compose.yml

@@ -26,6 +26,7 @@ services:
         JBROWSE_VERSION: 2.10.3
         FORWARD_HOSTNAME: apollo-collaboration-server
         FORWARD_PORT: 3999
+        URL: http://my-apollo-site.org
       context: .
     depends_on:
       - apollo-collaboration-server

docs/deployment/deployment.md

@@ -2,6 +2,21 @@ Apollo 3 Deployment
 
 ## Full deployment with collaboration server
 
+<!-- vim-markdown-toc GFM -->
+
+* [Basic components](#basic-components)
+* [Deploying with Docker](#deploying-with-docker)
+    * [Name](#name)
+    * [Volumes](#volumes)
+    * [Services](#services)
+        * [Client](#client)
+        * [Apollo Collaboration Server](#apollo-collaboration-server)
+        * [MongoDB](#mongodb)
+* [Starting everything](#starting-everything)
+* [Deploying](#deploying)
+
+<!-- vim-markdown-toc -->
+
 Apollo can be used in some cases on local files with no need to set up a server,
 but this guide will focus on deploying Apollo with all the components needed for
 a hosted server that allows collaborative annotation.
@@ -109,17 +124,18 @@ compose file:
 
 ```yml
 client:
-  build:
-    args:
-      APOLLO_VERSION: 0.1.0
-      JBROWSE_VERSION: 2.10.3
-      FORWARD_HOSTNAME: apollo-collaboration-server
-      FORWARD_PORT: 3999
-    context: .
-  depends_on:
-    - apollo-collaboration-server
-  ports:
-    - '80:80'
+build:
+  args:
+    APOLLO_VERSION: 0.1.0
+    JBROWSE_VERSION: 2.10.3
+    FORWARD_HOSTNAME: apollo-collaboration-server
+    FORWARD_PORT: 3999
+    URL: http://my-apollo-site.org
+  context: .
+depends_on:
+  - apollo-collaboration-server
+ports:
+  - '80:80'
 ```
 
 This service will be a static file server that serves the JBrowse and Apollo
@@ -180,24 +196,27 @@ before starting the collaboration server, and defines which port the app is
 exposed on.
 
 The collaboration server is configured with environment variables, often in a
-`.env` file. However, we use the `environment` option to set a couple variables
-whose value depends on other places in the compose file, to try to keep the
-related options all in one place. These two variables are `MONGODB_URI` and
-`FILE_UPLOAD_FOLDER`. The example URI is
+`.env` file. However, we use the `environment` option to set a couple of
+variables whose value depends on other places in the compose file, to try to
+keep the related options all in one place. These two variables are
+`MONGODB_URI` and `FILE_UPLOAD_FOLDER`. The example URI is
 `mongodb://mongo-node-1:27017,mongo-node-2:27018/apolloDb?replicaSet=rs0`. If
 you change the names of either of the MongoDB services, their ports, or add or
 remove a MongoDB service, be sure to update this value. The value of
 `FILE_UPLOAD_FOLDER` should match what's on the right side of the colon in the
 `volumes` section (e.g. `/data/uploads`).
 
 There are a few other variables that need to be configured for the Apollo
-Collaboration Server to work. They are `URL`, `JWT_SECRET`, and `SESSION_SECRET`
-variables. `URL` is the URL of the server that's hosting Apollo. We'll discuss
-this more in a later section when talking about authentication. You can think of
-`JWT_SECRET` and `SESSION_SECRET` as kind of like passwords. They need to be a
-random string, but should be the same each time you run the server so that user
-sessions are not invalidated (unless you want to intentionally invalidate user
-sessions). You can use a password generator to create them.
+Collaboration Server to work. They are `URL`, `JWT_SECRET`, and
+`SESSION_SECRET` variables. `URL` is the URL of the server that's hosting
+Apollo. Note that the `URL` option set in the `.env` file or in the
+corresponding entry in `apollo-collaboration-server` should match the `URL` entry
+under `client` section.  We'll discuss this more in a later section when
+talking about authentication. You can think of `JWT_SECRET` and
+`SESSION_SECRET` as kind of like passwords. They need to be a random string,
+but should be the same each time you run the server so that user sessions are
+not invalidated (unless you want to intentionally invalidate user sessions).
+You can use a password generator to create them.
 
 You can put these variables in the `environment` section, or you can put them in
 a `.env` file, which has a format that looks like this
@@ -208,7 +227,8 @@ URL=https://my-apollo-site.org
 
 There are several other options you can configure. You can see [this](.env)
 sample `.env` file for a description of the other configuration options. For
-now, we will set `ALLOW_GUEST_USER` to be true to simplify testing.
+now, we will set `ALLOW_GUEST_USER` to be true to simplify testing. Options set
+in `compose.yml` take precedence over the options in the `.env` file.
 
 ##### MongoDB
 

docs/deployment/localhost.md

@@ -0,0 +1,114 @@
+<!-- vim-markdown-toc GFM -->
+
+* [Deployment on local machine for single users](#deployment-on-local-machine-for-single-users)
+    * [Full installation including the collaboration server](#full-installation-including-the-collaboration-server)
+    * [Installation using JBrowse Desktop](#installation-using-jbrowse-desktop)
+        * [Download and start Apollo plugin](#download-and-start-apollo-plugin)
+        * [Download and start JBrowse Desktop](#download-and-start-jbrowse-desktop)
+        * [Load Apollo plugin](#load-apollo-plugin)
+
+<!-- vim-markdown-toc -->
+
+# Deployment on local machine for single users
+
+## Full installation including the collaboration server
+
+This is a quick guide for users willing to install Apollo on their local
+machine and with the intention of being the only user. This installation
+requires docker, for further details see the [full installation
+guide](deployment.md).
+
+```
+mkdir -p apollo # Or any directory of your choice
+cd apollo
+
+## MEMO: Edit URL once branch is merged
+
+curl -O https://raw.githubusercontent.com/GMOD/Apollo3/deployment_docs_fix_url/docs/deployment/compose.yml
+curl -O https://raw.githubusercontent.com/GMOD/Apollo3/deployment_docs_fix_url/docs/deployment/Dockerfile
+curl -O https://raw.githubusercontent.com/GMOD/Apollo3/deployment_docs_fix_url/docs/deployment/.env
+```
+
+Since we deploy on localhost for a single user, we give the *guest* user full
+permission (NB: the `sed` commands edit the target files *in place*):
+
+```
+sed -i'' 's|#* *GUEST_USER_ROLE=.*|GUEST_USER_ROLE=admin|' .env
+
+# Allow root user and set its username and password
+sed -i'' 's|#* *ALLOW_ROOT_USER=.*|ALLOW_ROOT_USER=true|' .env
+sed -i'' 's|#* *ROOT_USER_NAME=.*|ROOT_USER_NAME=admin|' .env
+sed -i'' 's|#* *ROOT_USER_PASSWORD=.*|ROOT_USER_PASSWORD=pass|' .env
+
+sed -i'' 's| ALLOW_GUEST_USER:.*| ALLOW_GUEST_USER: true|' compose.yml
+sed -i'' 's| URL: .*| URL: http://localhost|' compose.yml
+```
+
+Note that you can set options in either `compose.yml` or `.env`. `compose.yml` takes precedence over `.env`.
+
+
+Start Apollo:
+
+```
+docker compose up
+```
+
+Open a web browser, navigate to [localhost](http://localhost), start a new
+session, and login as guest. You may need to refresh the page for the full list
+of options to appear under the Apollo menu.
+
+## Installation using JBrowse Desktop
+
+### Download and start Apollo plugin
+
+```
+git clone https://github.com/GMOD/Apollo3
+cd Apollo3/packages/jbrowse-plugin-apollo 
+yarn
+yarn build
+yarn start
+```
+
+### Download and start JBrowse Desktop
+
+To run the latest code of JBrowse:
+
+```
+git clone https://github.com/GMOD/jbrowse-components
+cd jbrowse-components
+yarn
+```
+
+The in one terminal window:
+
+```
+cd products/jbrowse-desktop
+yarn start
+```
+
+and in another terminal window (still in `products/jbrowse-desktop`):
+
+```
+yarn electron
+```
+
+This last may give an error window which you close and continue (close only
+that window not the all JBrowse application)
+
+### Load Apollo plugin
+
+In JBrowse:
+
+* Select one of the available genomes just for starting jbrowse, e.g. hg19 then `GO`. 
+
+* Then: `TOOLS -> Plugin store -> ADD CUSTOM PLUGIN`, give a name to *Plugin
+name*, e.g. Apollo, and in *Plugin URL* use
+`http://localhost:9000/dist/jbrowse-plugin-apollo.umd.development.js`
+
+The menu APOLLO should be active now and you can load a local GFF file. Gff files must include the fasta sequence of the respective genome. If you have gff (`features.gff`) and genome (`genome.fasta`) as separate files concatenate them with, e.g.:
+
+```
+cp features.gff features.fasta.gff
+echo '## FASTA' >> features.fasta.gff
+cat genome.fasta >> features.fasta.gff
+```