tutorial.md

layout	title	questions	objectives	time_estimation	key_points	contributors	subtopic	tags	requirements
tutorial_hands_on	Distributed Object Storage	How does Galaxy locate data? How can I have Galaxy use multiple storage locations?	Setup Galaxy with both the Hierarachical and Distributed Object Storages	30m	The distributed object store configuration allows you to easily expand that storage that is attached to your Galaxy. You can move data around without affecting users.	natefoo hexylena	features	storage	type topic_name tutorials internal admin ansible ansible-galaxy

Expanding Storage

{:.no_toc}

You may find that your Galaxy files directory has run out of space, but you don't want to move all of the files from one filesystem to another. One solution to this problem is to use Galaxy's hierarchical object store to add an additional file space for Galaxy.

Alternatively, you may wish to write new datasets to more than one filesystem. For this, you can use Galaxy's distributed object store.

This tutorial assumes you have done the "Ansible for installing Galaxy" tutorial, it references the base configuration set up in that tutorial in numerous places.

Agenda

1. TOC {:toc}

{: .agenda}

Hierarchical Object Store

First, note that your Galaxy datasets have been created thus far in the directory /data, due to galaxy_config: galaxy: file_path. In some cases, we run out of storage in a particular location. Galaxy allows us to add additional storage locations where it will create new datasets, while still looking in the old locations for old datasets. You will not have to migrate any of your datasets, and can just "plug and play" with new storage pools.

{% icon hands_on %} Hands-on: Adding Hierarchical Storage

1. Open your group variables file and set the object_store_config_file variable:

   galaxy_config:
     galaxy:
       object_store_config_file: {% raw %}"{{ galaxy_config_dir }}/object_store_conf.xml"{% endraw %}

2. In your group variables file, add it to the galaxy_config_templates section:

   galaxy_config_templates:
     - src: templates/galaxy/config/object_store_conf.xml
       dest: {% raw %}"{{ galaxy_config.galaxy.object_store_config_file }}"{% endraw %}

3. Create and edit templates/galaxy/config/object_store_conf.xml with the following contents:

   <?xml version="1.0"?>
   <object_store type="hierarchical">
       <backends>
           <backend id="newdata" type="disk" order="0">
               <files_dir path="/data2" />
               <extra_dir type="job_work" path="/data2/job_work_dir" />
           </backend>
           <backend id="olddata" type="disk" order="1">
               <files_dir path="/data" />
               <extra_dir type="job_work" path="/data/job_work_dir" />
           </backend>
       </backends>
   </object_store>

4. Add a pre_task to create the /data2 folder using the file module.

       - name: Create the second storage directory
         file:
           owner: galaxy
           group: galaxy
           path: /data2
           state: directory
           mode: '0755'
   

   We've hardcoded the user/group because creating a storage directory is unusual. In normal practice someone provides you with an NFS mount and you will simply point your Galaxy there.

5. Run the playbook and restart Galaxy

6. Run a couple of jobs after Galaxy has restarted, run a couple of jobs.

   {% icon question %} Question

   Where is the data now stored?

   {% icon solution %} Solution

   You should see /data2 in the Full Path, if not, something went wrong. Check that your "order" is correct

   {: .solution }

   {: .question}

{: .hands_on}

Distributed Object Store

Rather than searching a hierarchy of object stores until the dataset is found, Galaxy can store the ID (in the database) of the object store in which a dataset is located when the dataset is created. This allows Galaxy to write to more than one object store for new datasets.

{% icon hands_on %} Hands-on: Distributed Object Store

1. Edit your templates/galaxy/config/object_store_conf.xml file and replace the contents with:

   <?xml version="1.0"?>
   <object_store type="distributed">
       <backends>
           <backend id="newdata" type="disk" weight="1">
               <files_dir path="/data2"/>
               <extra_dir type="job_work" path="/data2/job_work_dir"/>
           </backend>
           <backend id="olddata" type="disk" weight="1">
               <files_dir path="/data"/>
               <extra_dir type="job_work" path="/data/job_work_dir"/>
           </backend>
       </backends>
   </object_store>

2. Run the playbook, restart Galaxy

3. Run 4 or so jobs, and check where the output appear. You should see that they are split relatively evenly between the two data directories.

{: .hands_on}

Sites like UseGalaxy.eu use the distributed object store in order to balance dataset storage across 10 different storage pools.

{% icon details %} More documentation

More information can be found in the sample file.

{: .details}

{% icon warning %} Warning: switching object store types will cause issues

We have switched between two different object stores here, but this is not supported. If you need to do this, you will need to update datasets in Galaxy's database. Any datasets that were created as hierarchical will lack the object_store_id, and you will need to supply the correct one. Do not just blindly copy these instructions, please understand what they do before running them and talk to us on Gitter for more help

1. Move the datasets to their new location: sudo -u galaxy rsync -avr /hierarchical/000/ /distributed/000/

2. Update the database: sudo -Hu galaxy psql galaxy -c "UPDATE dataset SET object_store_id='data';"

3. Restart your Galaxy

{: .warning}

S3 Object Store

Many sites have access to an S3 service (either public AWS, or something private like Swift or Ceph), and you can take advantage of this for data storage.

we will set up a local S3-compatible object store, and then talk to the API of this service.

{% icon hands_on %} Hands-on: Setting up an S3-compatible Object Store

1. Edit your requirements.yml file and add:

   - src: atosatto.minio
     version: v1.1.0

2. ansible-galaxy install -p roles -r requirements.yml

3. Edit your group variables to configure the object store:

   minio_server_datadirs: ["/minio-test"]
   minio_access_key: "my-access-key"
   minio_secret_key: "my-super-extra-top-secret-key"
   

4. Edit your playbook and add the minio role before galaxyproject.galaxy:

       - atosatto.minio
   

   Galaxy will need to use the bucket, and will want it to be there when it boots, so we need to setup the object store first.

5. Edit the templates/galaxy/config/object_store_conf.xml, and configure the object store as one of the hierarchical backends. The object store does not play nicely with the distributed backend during training preparation. Additionally, reset the orders of the disk backends to be higher than the order of the swift backend.

   {% raw %}

   @@ -1,13 +1,21 @@
    <?xml version="1.0"?>
   - <object_store type="distributed">
   + <object_store type="hierarchical">
        <backends>
   -        <backend id="newdata" type="disk" weight="1">
   +        <backend id="newdata" type="disk" order="1">
                <files_dir path="/data2"/>
                <extra_dir type="job_work" path="/data2/job_work_dir"/>
            </backend>
   -        <backend id="olddata" type="disk" weight="1">
   +        <backend id="olddata" type="disk" order="2">
                <files_dir path="/data"/>
                <extra_dir type="job_work" path="/data/job_work_dir"/>
            </backend>
   +        <object_store id="swifty" type="swift" order="0">
   +            <auth access_key="{{ minio_access_key }}" secret_key="{{ minio_secret_key }}" />
   +            <bucket name="galaxy" use_reduced_redundancy="False" max_chunk_size="250"/>
   +            <connection host="127.0.0.1" port="9091" is_secure="False" conn_path="" multipart="True"/>
   +            <cache path="{{ galaxy_mutable_data_dir }}/database/object_store_cache" size="1000" />
   +            <extra_dir type="job_work" path="{{ galaxy_mutable_data_dir }}/database/job_working_directory_swift"/>
   +            <extra_dir type="temp" path="{{ galaxy_mutable_data_dir }}/database/tmp_swift"/>
   +        </object_store>
        </backends>
    </object_store>

   {% endraw %}

6. Run the playbook.

7. Galaxy should now be configure to use the object store!

8. When the playbook is done, upload a dataset to Galaxy, and check if it shows up in the bucket:

   $ sudo ls /minio-test/galaxy/000/
   dataset_24.dat
   

{: .hands_on}