Merge pull request #82 from ARTbio/AG2023-01

Update of Analyse des génomes - édition 2023
ARTbio · Nov 13, 2023 · 96a7f3c · 96a7f3c
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diff --git a/docs/AnalyseGenomes_2022/Install_tools.md b/docs/AnalyseGenomes_2022/Install_tools.md
diff --git a/docs/AnalyseGenomes_2022/images/GalaxyStates-AG2022.png b/docs/AnalyseGenomes_2022/images/GalaxyStates-AG2022.png
diff --git a/docs/AnalyseGenomes_2022/manage_galaxy.md b/docs/AnalyseGenomes_2022/manage_galaxy.md
diff --git a/...alyseGenomes_2022/Google_cloud_Account.md → ...alyseGenomes_2023/Google_cloud_Account.md b/...alyseGenomes_2022/Google_cloud_Account.md → ...alyseGenomes_2023/Google_cloud_Account.md
diff --git a/docs/AnalyseGenomes_2023/Install_tools.md b/docs/AnalyseGenomes_2023/Install_tools.md
@@ -0,0 +1,30 @@
+## Go back to your Google ssh terminal
+
+- Run the following script using the bash interpreter:
+```
+source /root/.bashrc && \
+bash /root/AnalyseGenome/GalaxyServer/install_galaxy_tools.sh
+```
+You should now be asked for an API key:
+```
+please enter your admin API key: 
+```
+The next section explains how to generate and copy this API key to interact programmatically
+with the Galaxy server and be able to install tools
+
+## Go back to your Galaxy web window
+
+In the main menu `User` --> `Preferences`
+
+![user preferences](images/user_preferences.png){width="200"}
+
+Select `Manage API Key`, click `Create a new Key`, and copy the current API key
+
+## Paste the copied API key in the Google ssh terminal
+
+and press the ++return++ key
+
+The tool installation should start immediately and last for about 15 minutes (you should
+see tools installing one at a time)
+
+---
diff --git a/...yseGenomes_2022/Loading_data_in_galaxy.md → ...yseGenomes_2023/Loading_data_in_galaxy.md b/...yseGenomes_2022/Loading_data_in_galaxy.md → ...yseGenomes_2023/Loading_data_in_galaxy.md
diff --git a/...nalyseGenomes_2022/Preparing_reference.md → ...nalyseGenomes_2023/Preparing_reference.md b/...nalyseGenomes_2022/Preparing_reference.md → ...nalyseGenomes_2023/Preparing_reference.md
diff --git a/docs/AnalyseGenomes_2022/Run_workflow.md → docs/AnalyseGenomes_2023/Run_workflow.md b/docs/AnalyseGenomes_2022/Run_workflow.md → docs/AnalyseGenomes_2023/Run_workflow.md
diff --git a/docs/AnalyseGenomes_2022/admin_kit.md → docs/AnalyseGenomes_2023/admin_kit.md b/docs/AnalyseGenomes_2022/admin_kit.md → docs/AnalyseGenomes_2023/admin_kit.md
diff --git a/...AnalyseGenomes_2022/bare-galaxy-google.md → ...AnalyseGenomes_2023/bare-galaxy-google.md b/...AnalyseGenomes_2022/bare-galaxy-google.md → ...AnalyseGenomes_2023/bare-galaxy-google.md
diff --git a/docs/AnalyseGenomes_2022/bowtie_cli.md → docs/AnalyseGenomes_2023/bowtie_cli.md b/docs/AnalyseGenomes_2022/bowtie_cli.md → docs/AnalyseGenomes_2023/bowtie_cli.md
diff --git a/docs/AnalyseGenomes_2022/bowtie_galaxy.md → docs/AnalyseGenomes_2023/bowtie_galaxy.md b/docs/AnalyseGenomes_2022/bowtie_galaxy.md → docs/AnalyseGenomes_2023/bowtie_galaxy.md
diff --git a/...alyseGenomes_2022/deploy-galaxy-server.md → ...alyseGenomes_2023/deploy-galaxy-server.md b/...alyseGenomes_2022/deploy-galaxy-server.md → ...alyseGenomes_2023/deploy-galaxy-server.md
@@ -28,40 +28,51 @@ sh deploy_galaxy.sh
     This command runs the sh script
     [deploy_galaxy.sh](https://raw.githubusercontent.com/ARTbio/AnalyseGenome/main/GalaxyServer/deploy_galaxy.sh)
 
-  You should see an abundant log scrolling down. Don't worry !
+Running `deploy_galaxy.sh` shows abundant log scrolling down. The task being executed are:
 
-  - All Galaxy dependencies required for the Galaxy server instance are being downloaded and installed
-  - The Galaxy computing environment is automatically set up
-  - the Galaxy web server is installed and static pages are built
-  - The Galaxy database (sqlight) is automatically upgraded to its latest structure/model
+  - All python dependencies required for the Galaxy server instance are downloaded and installed
+  - The Galaxy computing environment (virtualenv) is automatically set up
+  - the Galaxy web server is installed (gunicorn) and static pages are built
+  - The Galaxy database (SQLite) is automatically upgraded to its latest structure/model
   - The package manager Conda, which is heavily used by Galaxy to install its tools is installed.
-  
-  After ~10 minutes, you should see the following log in the ssh console:
+
+
+This deployment process takes a while (~20 minutes with the release 23.1 of Galaxy), but
+this will happen only once.
+
+Naturally, the nextime you start Galaxy, the process will be quickly skipped.
+
+<center>
+
+![](images/coffee_time.png){width="200"}
+</center>
+
+When deployment is finished, you will see the following log in the console:
 
 ```{.bash title="Terminal"}
-Executing: galaxyctl start
-Registered galaxy config: /root/galaxy/config/galaxy.yml
-Creating or updating service gunicorn
-Creating or updating service celery
-Creating or updating service celery-beat
-celery: added process group
-celery-beat: added process group
-gunicorn: added process group
-celery                           STARTING  
-celery-beat                      STARTING  
-gunicorn                         STARTING  
-Log files are in /root/galaxy/database/gravity/log
+Adding systemd unit galaxy-gunicorn.service
+Adding systemd unit galaxy-celery.service
+Adding systemd unit galaxy-celery-beat.service
+Adding systemd unit galaxy.target
+Created symlink /etc/systemd/system/multi-user.target.wants/galaxy.target → /etc/systemd/system/galaxy.target.
+  UNIT                       LOAD   ACTIVE SUB     DESCRIPTION
+  galaxy-celery-beat.service loaded active running Galaxy celery-beat
+  galaxy-celery.service      loaded active running Galaxy celery
+  galaxy-gunicorn.service    loaded active running Galaxy gunicorn
+  galaxy.target              loaded active active  Galaxy
+
+LOAD   = Reflects whether the unit definition was properly loaded.
+ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
+SUB    = The low-level unit activation state, values depend on unit type.
+
+4 loaded units listed.
+To show all installed unit files use 'systemctl list-unit-files'.
 Galaxy is now running as a daemon in the background
+and is controlled by systemctl
 ```
 We will review in a section apart how to display the server activity, stop, start or restart
 it.
 
-??? bug "In case of band width issue only"
-    ```
-    wget https://raw.githubusercontent.com/ARTbio/AnalyseGenome/main/GalaxyServer/deploy_galaxy_B.sh && \
-    sh deploy_galaxy_B.sh
-    ```
-
 ### 2. Connect to your living Galaxy instance
 
 You should now be able to access to you Galaxy instance in a your web browser window.
@@ -79,7 +90,10 @@ You should now be able to access to you Galaxy instance in a your web browser wi
   ![register](images/register.png){ width="300" }
 
   and  **register** to your instance using the email address
-  `[email protected]` and the password of your choice (:warning: don't forget it)
+  ```
+  [email protected]
+  ```
+  and the password of your choice (:warning: don't forget it)
 
 - After login, you should see the admin tab in the top menu of the Galaxy interface.
 

diff --git a/docs/AnalyseGenomes_2022/emergency_image.md → docs/AnalyseGenomes_2023/emergency_image.md b/docs/AnalyseGenomes_2022/emergency_image.md → docs/AnalyseGenomes_2023/emergency_image.md
diff --git a/docs/AnalyseGenomes_2022/file_parsing_cli.md → docs/AnalyseGenomes_2023/file_parsing_cli.md b/docs/AnalyseGenomes_2022/file_parsing_cli.md → docs/AnalyseGenomes_2023/file_parsing_cli.md
diff --git a/...nalyseGenomes_2022/file_parsing_galaxy.md → ...nalyseGenomes_2023/file_parsing_galaxy.md b/...nalyseGenomes_2022/file_parsing_galaxy.md → ...nalyseGenomes_2023/file_parsing_galaxy.md
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diff --git a/docs/AnalyseGenomes_2022/images/suspend.png → docs/AnalyseGenomes_2023/images/suspend.png b/docs/AnalyseGenomes_2022/images/suspend.png → docs/AnalyseGenomes_2023/images/suspend.png
diff --git a/...nomes_2022/images/type_fastqsanger_gz.png → ...nomes_2023/images/type_fastqsanger_gz.png b/...nomes_2022/images/type_fastqsanger_gz.png → ...nomes_2023/images/type_fastqsanger_gz.png
diff --git a/...yseGenomes_2022/images/ubuntu_rainbio.png → ...yseGenomes_2023/images/ubuntu_rainbio.png b/...yseGenomes_2022/images/ubuntu_rainbio.png → ...yseGenomes_2023/images/ubuntu_rainbio.png
diff --git a/..._2022/images/uninstalled_dependencies.png → ..._2023/images/uninstalled_dependencies.png b/..._2022/images/uninstalled_dependencies.png → ..._2023/images/uninstalled_dependencies.png
diff --git a/...eGenomes_2022/images/user_preferences.png → ...eGenomes_2023/images/user_preferences.png b/...eGenomes_2022/images/user_preferences.png → ...eGenomes_2023/images/user_preferences.png
diff --git a/...seGenomes_2022/images/web_ssh_console.png → ...seGenomes_2023/images/web_ssh_console.png b/...seGenomes_2022/images/web_ssh_console.png → ...seGenomes_2023/images/web_ssh_console.png
diff --git a/docs/AnalyseGenomes_2022/images/wheel.png → docs/AnalyseGenomes_2023/images/wheel.png b/docs/AnalyseGenomes_2022/images/wheel.png → docs/AnalyseGenomes_2023/images/wheel.png
diff --git a/docs/AnalyseGenomes_2022/manage_VM.md → docs/AnalyseGenomes_2023/manage_VM.md b/docs/AnalyseGenomes_2022/manage_VM.md → docs/AnalyseGenomes_2023/manage_VM.md
@@ -4,19 +4,17 @@ If you read this, you have probably launched at least one time a Google Virtual
 
 A few rules to get your life easier during the rest of this training:
 
-- ==**Never** stop your VM, instead **suspend** it==
+- ==**Avoid** stopping your VM, instead **suspend** it==
 
   Stopping your VM is like stopping your PC or you laptop.
 
   You will stop everything and will have to literally reboot everything, including
-  the Galaxy server. It is not that difficult actually (see below). However, you have
-  many things to learn these days and it better not use your time and memory just to do
-  that.
+  the Galaxy server. It is not that difficult actually, but it takes a bit more time.
 
   Instead, **Suspending** your VM is like putting your PC in sleeping mode, or closing
   the lid of your laptop.
 
-  Thus, remember, at the end of the day or whenever you will not use your VM for a long
+  Thus, remember, at the end of the day or whenever you are not going to use your VM for a long
   time, use:
 
   ![suspend](images/suspend.png)

diff --git a/docs/AnalyseGenomes_2023/manage_galaxy.md b/docs/AnalyseGenomes_2023/manage_galaxy.md
@@ -0,0 +1,26 @@
+!!! info "Galaxy server commands, quick reminder"
+    Check that the server is running and see last logs
+    ```
+    systemctl status galaxy*.service
+
+    # the three services Galaxy celery-beat, celery and gunicorn must be
+    # active and running (green)
+    ```
+    Restart the server
+    ```
+    systemctl restart galaxy.target
+    ```
+    Start the Galaxy server, if for any reason it is down
+    ```
+    systemctl start galaxy.target
+    ```
+    Follow the activity of the web part only (gunicorn) of the Galaxy server:
+    ```
+    systemctl status galaxy-gunicorn.service
+    ```
+
+## A graphical view of the Galaxy server states and the commands to control them
+
+![Galaxy server states](images/GalaxyStates-AG2022.png){width="1200"}
+
+---
diff --git a/docs/AnalyseGenomes_2022/outline.md → docs/AnalyseGenomes_2023/outline.md b/docs/AnalyseGenomes_2022/outline.md → docs/AnalyseGenomes_2023/outline.md
diff --git a/docs/AnalyseGenomes_2022/spin_off_VM.md → docs/AnalyseGenomes_2023/spin_off_VM.md b/docs/AnalyseGenomes_2022/spin_off_VM.md → docs/AnalyseGenomes_2023/spin_off_VM.md
diff --git a/docs/AnalyseGenomes_2022/whyadmin.md → docs/AnalyseGenomes_2023/whyadmin.md b/docs/AnalyseGenomes_2022/whyadmin.md → docs/AnalyseGenomes_2023/whyadmin.md
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -115,25 +115,25 @@ nav:
 
   - Galaxy Trainings:
 
-    -  Analyse des Génomes (2022):
-        - PLAN: AnalyseGenomes_2022/outline.md
-        - START A VIRTUAL MACHINE IN GOOGLE CLOUD ENGINE : AnalyseGenomes_2022/bare-galaxy-google.md
-        - DEPLOY A GALAXY SERVER IN THE VM: AnalyseGenomes_2022/deploy-galaxy-server.md
-        - INSTALL GALAXY TOOLS: AnalyseGenomes_2022/Install_tools.md
-        - MANAGE YOUR GOOGLE VM: AnalyseGenomes_2022/manage_VM.md
-        - MANAGE YOUR GALAXY SERVER: AnalyseGenomes_2022/manage_galaxy.md
-        - BOWTIE ALIGNMENT USING COMMAND LINES: AnalyseGenomes_2022/bowtie_cli.md
-        - BOWTIE ALIGNMENT USING GALAXY: AnalyseGenomes_2022/bowtie_galaxy.md
-        - LOAD TRAINING DATA: AnalyseGenomes_2022/Loading_data_in_galaxy.md
-        - PREPARE A REFERENCE GENOME: AnalyseGenomes_2022/Preparing_reference.md
-        - Format conversion using command lines: AnalyseGenomes_2022/file_parsing_cli.md
-        - Format conversion using a galaxy tool: AnalyseGenomes_2022/file_parsing_galaxy.md
-        - Running a galaxy workflow: AnalyseGenomes_2022/Run_workflow.md
-        - Why administering galaxy ?: AnalyseGenomes_2022/whyadmin.md
-        - "Appendix 1: Getting a Google Cloud Engine Account": AnalyseGenomes_2022/Google_cloud_Account.md
-        - "Appendix 2: Start and stop a Google virtual machine": AnalyseGenomes_2022/spin_off_VM.md
-        - "Appendix 3: The ADMIN tool kit": AnalyseGenomes_2022/admin_kit.md
-        - "Appendix 4: EMERGENCY image!": AnalyseGenomes_2022/emergency_image.md
+    -  Analyse des Génomes (2023):
+        - PLAN: AnalyseGenomes_2023/outline.md
+        - START A VIRTUAL MACHINE IN GOOGLE CLOUD ENGINE : AnalyseGenomes_2023/bare-galaxy-google.md
+        - DEPLOY A GALAXY SERVER IN THE VM: AnalyseGenomes_2023/deploy-galaxy-server.md
+        - INSTALL GALAXY TOOLS: AnalyseGenomes_2023/Install_tools.md
+        - MANAGE YOUR GOOGLE VM: AnalyseGenomes_2023/manage_VM.md
+        - MANAGE YOUR GALAXY SERVER: AnalyseGenomes_2023/manage_galaxy.md
+        - BOWTIE ALIGNMENT USING COMMAND LINES: AnalyseGenomes_2023/bowtie_cli.md
+        - BOWTIE ALIGNMENT USING GALAXY: AnalyseGenomes_2023/bowtie_galaxy.md
+        - LOAD TRAINING DATA: AnalyseGenomes_2023/Loading_data_in_galaxy.md
+        - PREPARE A REFERENCE GENOME: AnalyseGenomes_2023/Preparing_reference.md
+        - Format conversion using command lines: AnalyseGenomes_2023/file_parsing_cli.md
+        - Format conversion using a galaxy tool: AnalyseGenomes_2023/file_parsing_galaxy.md
+        - Running a galaxy workflow: AnalyseGenomes_2023/Run_workflow.md
+        - Why administering galaxy ?: AnalyseGenomes_2023/whyadmin.md
+        - "Appendix 1: Getting a Google Cloud Engine Account": AnalyseGenomes_2023/Google_cloud_Account.md
+        - "Appendix 2: Start and stop a Google virtual machine": AnalyseGenomes_2023/spin_off_VM.md
+        - "Appendix 3: The ADMIN tool kit": AnalyseGenomes_2023/admin_kit.md
+        - "Appendix 4: EMERGENCY image!": AnalyseGenomes_2023/emergency_image.md
 
     -  Run your Galaxy server:
         - INTRODUCTION: Run-Galaxy/index.md