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Update IT documentation

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mvdbeek
2022-03-02 14:15:46 +01:00
parent e896fdf7d9
commit 3a28fb07da
3 changed files with 80 additions and 86 deletions
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config/galaxy.yml.interactivetools
+12 -47
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@@ -1,54 +1,19 @@
uwsgi:
http: localhost:8080
threads: 8
http-raw-body: True
offload-threads: 8
master: true
module: galaxy.webapps.galaxy.buildapp:uwsgi_app()
interactivetools_map: database/interactivetools_map.sqlite
python-raw: scripts/interactivetools/key_type_token_mapping.py
route-host: ^([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)-([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.(interactivetool\.localhost:8080)$ goto:itdomain
route-run: goto:itdomainend
route-label: itdomain
route-host: ^([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)-([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.(interactivetool\.localhost:8080)$ rpcvar:TARGET_HOST rtt_key_type_token_mapper_cached $1 $3 $2 $4 $0 5
route-if-not: empty:${TARGET_HOST} httpdumb:${TARGET_HOST}
route: .* break:404 Not Found
route-label: itdomainend
# Path-based is currently less functional and less tested than domain-based
route: ^(/interactivetool/access/)([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)/([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)/([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)(()|(/.*)*)$ goto:itpath
route-run: goto:itpathend
route-label: itpath
route: ^/interactivetool/access/([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)/([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)/([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)(()|/.*)$ rpcvar:TARGET_HOST rtt_key_type_token_mapper_cached $2 $1 $3 $4 $0 5
route-if: empty:${TARGET_HOST} goto:itpathfail
route: ^/interactivetool/access/([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)/([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)/([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)((()|/.*)*)$ rewrite:$4
route-if: empty:${PATH_INFO} addvar:PATH_INFO=/
route-run: seturi:${PATH_INFO}
route-if-not: empty:${QUERY_STRING} seturi:${PATH_INFO}?${QUERY_STRING}
route-if-not: empty:${TARGET_HOST} httpdumb:${TARGET_HOST}
route-label: itpathfail
route: .* break:404 Not Found
route-label: itpathend
gravity:
gx_it_proxy:
enable: true
proxy_port: 4002
galaxy:
interactivetools_enable: true
# outputs_to_working_directory will provide you with a better level of isolation. It is highly recommended to set
# this parameter with InteractiveTools.
outputs_to_working_directory: true
interactivetools_prefix: interactivetool
interactivetools_map: database/interactivetools_map.sqlite
# If you develop InteractiveTools locally and do not have a full FQDN you can
# use an arbritrary one, e.g. 'my-hostname' here, if you set this hostname in your
# job_conf.xml as well (see the corresponding comment). If running mac OS X, do not match the
# "http://host.docker.internal:8080" used at galaxy_infrastructure_url in the galaxy.yml file,
# and use an arbitrary name here instead.
# Please make sure that in the local development case you use https://localhost:8080 to access
# your Galaxy. http://my-hostname:8080 will not work.
# galaxy_infrastructure_url: http://my-hostname:8080
# use an arbritrary one, e.g. 'host.docker.internal' here, if you set this hostname in your
# job_conf.xml as well (see the corresponding comment).
# In the local development case you should use http://localhost:8080 to access
# your Galaxy, so saving notebooks doesn't fail due to invalid certificates.
galaxy_infrastructure_url: http://localhost:8080
# Do not set the following 2 options if you are using an upstream proxy server like nginx
interactivetools_upstream_proxy: false
interactivetools_proxy_host: localhost:4002
config/job_conf.xml.interactivetools
+4 -10
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@@ -6,7 +6,6 @@
</plugins>
<destinations default="docker_dispatch">
<destination id="local" runner="local"/>
<destination id="docker_local" runner="local">
<param id="docker_enabled">true</param>
<!-- If you have not set 'outputs_to_working_directory: true' in galaxy.yml you can remove the docker_volumes setting. -->
@@ -21,21 +20,16 @@
If you develop interactive tools on your 'localhost' and don't have a proper domain name
you need to tell all Docker containers a hostname where Galaxy is running.
This can be done via the add-host parameter during the `docker run` command.
'my-hostname' here is an arbritrary hostname that matches the IP address of your
Galaxy host. Make sure this hostname ('my-hostname') is also set in your galaxy.yml file, e.g.
`galaxy_infrastructure_url: http://my-hostname:8080`.
Note: XML does not allow double hyphens in comments, hence the line below has them escaped as &#45;
'localhost' here is an arbritrary hostname that matches the IP address of your
Galaxy host. Make sure this hostname ('localhost') is also set in your galaxy.yml file, e.g.
`galaxy_infrastructure_url: http://localhost:8080`.
-->
<!-- <param id="docker_run_extra_arguments">&#45;&#45;add-host my-hostname:10.1.2.3</param> -->
<param id="docker_run_extra_arguments">--add-host localhost:host-gateway</param>
</destination>
<destination id="docker_dispatch" runner="dynamic">
<param id="type">docker_dispatch</param>
<param id="docker_destination_id">docker_local</param>
<param id="default_destination_id">local</param>
</destination>
</destinations>
</job_conf>
doc/source/admin/special_topics/interactivetools.rst
+64 -29
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@@ -42,52 +42,74 @@ Some important benefits of using Galaxy InteractiveTools
Server-side configuration of Galaxy InteractiveTools
----------------------------------------------------
For production deployments and additional considerations please see the `Galaxy Interactive Tools Tutorial <https://training.galaxyproject.org/training-material/topics/admin/tutorials/interactive-tools/tutorial.html>`__.
The ``galaxy.yml`` file will need to be populated as seen in
``config/galaxy.yml.interactivetools``.
Galaxy InteractiveTool routing relies on wildcard subdomain routes. For users
who manage their own DNS, you can set the appropriate A records to redirect
``*.interactivetool.yourdomain``, following format seen below.
Galaxy InteractiveTool routing relies on wildcard subdomain routes and a proxy server that forwards requests to a running container.
For users who manage their own DNS, you can set the appropriate A records to redirect
``*.interactivetool.yourdomain``.
It's not recommended for production, but for a quick local deployment
``localhost.blankenberglab.org`` is a domain record provided by Dan Blankenberg
(a Galaxy contributor and the architect of ITs) configured with the appropriate
wildcard redirect to 127.0.0.1, which you can use that in place of
``<server address>`` to resolve to your local machine.
`gravity` will automatically start the needed proxy server.
In the ``uwsgi:`` section:
The following configuration is only recommended for local testing, as users will directly connect to the InteractiveTool Proxy.
In a production setup an upstream proxy should route requests to the proxy via the ``*.interactivetool.yourdomain`` subdomain.
Set these values in `galaxy.yml`:
.. code-block:: yaml
http-raw-body: true
# master: true
interactivetools_map: database/interactivetools_map.sqlite
python-raw: scripts/interactivetools/key_type_token_mapping.py
route-host: ^([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)-([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.(interactivetool\.<server address>:8080)$ goto:interactivetool
route-run: goto:endendend
route-label: interactivetool
route-host: ^([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)-([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.(interactivetool\.<server address>:8080)$ rpcvar:TARGET_HOST rtt_key_type_token_mapper_cached $1 $3 $2 $4 $0 5
route-if-not: empty:${TARGET_HOST} httpdumb:${TARGET_HOST}
route: .* break:404 Not Found
route-label: endendend
gravity:
# ...
gx_it_proxy:
enable: true
proxy_port: 4002
galaxy:
# ...
interactivetools_enable: true
interactivetools_map: database/interactivetools_map.sqlite
galaxy_infrastructure_url: http://localhost:8080
# Do not set the following 2 options if you are using an upstream proxy server like nginx
interactivetools_upstream_proxy: false
interactivetools_proxy_host: localhost:4002
# ...
In the ``galaxy:`` section:
If you do want to use nginx as an upstream proxy server you can use the following server section to route requests to the InteractiveTool proxy:
.. code-block:: yaml
.. code-block:: nginx
interactivetools_enable: true
interactivetools_map: database/interactivetools_map.sqlite
galaxy_infrastructure_url: http://<server address>.org:8080
server {
# Listen on port 443
listen *:443 ssl;
# Match all requests for the interactive tools subdomain
server_name *.interactivetool.localhost;
# Proxy all requests to the GIE Proxy application
location / {
proxy_redirect off;
proxy_http_version 1.1;
proxy_set_header Host $host;
proxy_set_header X-Real-IP $remote_addr;
proxy_set_header Upgrade $http_upgrade;
proxy_set_header Connection "upgrade";
proxy_pass http://localhost:4002;
}
}
The admin should modify the ``route-host`` and ``interactivetools_prefix`` to match their preferred configuration.
Note that this nginx example uses https, so you need to have a wildcard certificate for your domain,
and you need to adjust ``galaxy_infrastructure_url`` as appropriate. You will most likely also want
to replace localhost with your server domain.
You will also need to enable a docker destination in the job_conf.xml file.
An example ``job_conf.xml`` file as seen in ``config/job_conf.xml.interactivetools``:
.. code-block:: xml
<?xml version="1.0"?>
<!-- A sample job config for InteractiveTools using local runner. -->
<job_conf>
<plugins>
<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
@@ -96,11 +118,23 @@ An example ``job_conf.xml`` file as seen in ``config/job_conf.xml.interactivetoo
<destination id="local" runner="local"/>
<destination id="docker_local" runner="local">
<param id="docker_enabled">true</param>
<!-- If you have not set 'outputs_to_working_directory: true' in galaxy.yml you can remove the docker_volumes setting. -->
<param id="docker_volumes">$galaxy_root:ro,$tool_directory:ro,$job_directory:rw,$working_directory:rw,$default_file_path:ro</param>
<param id="docker_sudo">false</param>
<param id="docker_net">bridge</param>
<param id="docker_auto_rm">true</param>
<param id="require_container">true</param>
<param id="container_monitor">true</param>
<param id="docker_set_user"></param>
<!-- InteractiveTools do need real hostnames or URLs to work - simply specifying IPs will not work.
If you develop interactive tools on your 'localhost' and don't have a proper domain name
you need to tell all Docker containers a hostname where Galaxy is running.
This can be done via the add-host parameter during the `docker run` command.
'localhost' here is an arbritrary hostname that matches the IP address of your
Galaxy host. Make sure this hostname ('localhost') is also set in your galaxy.yml file, e.g.
`galaxy_infrastructure_url: http://localhost:8080`.
-->
<param id="docker_run_extra_arguments">--add-host localhost:host-gateway</param>
</destination>
<destination id="docker_dispatch" runner="dynamic">
<param id="type">docker_dispatch</param>
@@ -108,10 +142,11 @@ An example ``job_conf.xml`` file as seen in ``config/job_conf.xml.interactivetoo
<param id="default_destination_id">local</param>
</destination>
</destinations>
</job_conf>
</job_conf>
Alternatively to the local job runner, InteractiveTools have been enabled for the condor job runner, e.g.:
InteractiveTools have been enabled for the Condor, Slurm, Pulsar and Kuberneters job runner.
A destination configuration for Condor may look like this:
.. code-block:: xml