mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-01 15:37:32 +08:00
Drop remaining references to uWSGI
This commit is contained in:
mvdbeek
+1
-1
@@ -191,4 +191,4 @@ ENV GALAXY_CONFIG_CONDA_AUTO_INIT=False
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ENTRYPOINT ["tini", "--"]
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# [optional] to run:
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CMD uwsgi --yaml config/galaxy.yml
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CMD galaxy
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@@ -1,45 +0,0 @@
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# This is a sample supervisor config file.
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# In this configuration, 2 handlers and 1 uwsgi (uwsgi is more performant than the default Paste) instance with 2 processes and 2 threads will be started.
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# In order for this to work, you will need to have a [uwsgi] section in galaxy.ini, as such:
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#
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# [uwsgi]
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# master = True
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#
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# Further, this assumes uwsgi has been installed through pip into a virtualenv (/home/galaxy/galaxy/.venv/, in this example).
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# If this is not the case, adjust the path to uwsgi accordingly.
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# If uwsgi was not installed through pip, include "--plugin python" in the uwsgi command.
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# This configuration has been tested with galaxy release_16.01 and uWSGI==2.0.12.
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# This assumes galaxy is installed in /home/galaxy/galaxy, so change occurences of /home/galaxy/galaxy accordingly.
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# If you want to run galaxy under a different username, change "user = galaxy" to "user = <your user>".
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# You will probably want to proxy uwsgi (you can't connect with a browser to uwsgi port 4001) with nginx or apache,
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# see https://galaxyproject.org/admin/config/performance/scaling/#apache
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# or https://galaxyproject.org/admin/config/performance/scaling/#nginx
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[program:galaxy_web]
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command = /home/galaxy/galaxy/.venv/bin/uwsgi --virtualenv /home/galaxy/galaxy/.venv --ini-paste /home/galaxy/galaxy/config/galaxy.ini --logdate --master --processes 2 --threads 2 --logto /home/galaxy/galaxy/uwsgi.log --socket 127.0.0.1:4001 --pythonpath lib --stats 127.0.0.1:9191
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directory = /home/galaxy/galaxy
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umask = 022
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autostart = true
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autorestart = true
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startsecs = 20
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user = galaxy
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environment = PATH=/home/galaxy/galaxy/.venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin,PYTHONHOME=/home/galaxy/galaxy/.venv
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numprocs = 1
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stopsignal = INT
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startretries = 15
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[program:handler]
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command = /home/galaxy/galaxy/.venv/bin/python ./lib/galaxy/main.py -c /home/galaxy/galaxy/config/galaxy.ini --server-name=handler%(process_num)s --log-file=/home/galaxy/galaxy/handler%(process_num)s.log
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directory = /home/galaxy/galaxy
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process_name = handler%(process_num)s
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numprocs = 2
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umask = 022
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autostart = true
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autorestart = true
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startsecs = 20
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user = galaxy
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environment = PYTHONHOME=/home/galaxy/galaxy/.venv
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startretries = 15
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[group:galaxy]
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programs = handler, galaxy_web
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@@ -50,18 +50,10 @@ Advanced Configuration
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----------------------------
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For more useful and manageable logging when running Galaxy with forking application stacks where multiple
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Galaxy server processes are forked after the Galaxy application is loaded, some extensions to standard Python
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:mod:`logging` are available in Galaxy:
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- Two custom fields (aka Python :class:`logging.LogRecord` attributes) identifying the uWSGI worker ID and mule ID can
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be added to log messages: ``%(worker_id)s`` and ``%(mule_id)s``. These fields aid in associating log messages with the
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Galaxy server processes that emitted them. They are included in the default log format (found in
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:data:`galaxy.web.stack.UWSGIApplicationStack.log_format`) when using uWSGI and are available for use in custom log
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formats.
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- A custom ``filename_template`` config option is available to :class:`logging.FileHandler` (or derivative class) log
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handler definitions so that multiple file logging is possible. Without this custom option, all forked Galaxy server
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processes would only be able to log to a single combined log file, which can be very difficult to work with.
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Galaxy server processes are forked after the Galaxy application is loaded, a custom ``filename_template`` config option
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is available to :class:`logging.FileHandler` (or derivative class) log handler definitions so that multiple file logging is possible.
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Without this custom option, all forked Galaxy server processes would only be able to log to a single combined log file,
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which can be very difficult to work with.
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YAML
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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@@ -2,7 +2,8 @@
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## Why do we migrate away from uWSGI
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Starting with Galaxy release 22.01 the default application webserver is [Gunicorn](https://gunicorn.org/), which replaces [uWSGI](https://uwsgi-docs.readthedocs.io/en/latest/). We will remove support for running Galaxy under uWSGI in Galaxy release 22.05.
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Starting with Galaxy release 22.01 the default application webserver is [Gunicorn](https://gunicorn.org/), which replaces [uWSGI](https://uwsgi-docs.readthedocs.io/en/latest/).
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We have removed support for running Galaxy under uWSGI in Galaxy release 22.05.
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We have made this move because uWSGI support for newer Python versions has been problematic and because
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we have modernized the API portion of our backend. The Galaxy web application is now an ASGI application
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driven by [FastAPI](https://fastapi.tiangolo.com/) and [Starlette](https://www.starlette.io/).
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@@ -89,7 +89,7 @@ without enclosing them in any sort of block:
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.. code-block:: nginx
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uwsgi_read_timeout 180;
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proxy_read_timeout 180;
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client_max_body_size 10g;
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ssl_certificate /etc/nginx/ssl/server.crt;
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ssl_certificate_key /etc/nginx/ssl/server.key;
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@@ -34,7 +34,6 @@ Some important benefits of using Galaxy InteractiveTools
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- If you accidentally close the **InteractiveTool browser window**, you can **regain access** by selecting from a **list of active InteractiveTools**
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- A single **InteractiveTool** can **grant access** to **multiple running applications, servers, and interfaces**
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- **InteractiveTools** can be **added to** Galaxy **Workflows**
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- **Native, out-of-the box support for InteractiveTools** in Galaxy via uWSGI proxying
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- **InteractiveTools** are **bonafide Galaxy Tools**; just specify **tool_type as "interactive"** and list the ports you want to expose
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- **InteractiveTools** can be **added** to and **installed from the ToolShed**.
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- **R Shiny apps**, **Javascript-based VNC** access to desktop environments, **genome-browsers-in-a-box**, **interactive notebook environments**, etc, are all possible with **InteractiveTools**
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@@ -113,7 +113,7 @@
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scratch directory available on compute). -->
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<!-- Specify a complete description of the Pulsar app
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to create. If this configuration defines more than
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one manager - you can specify the manager name
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one manager - you can specify the manager name
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using the "manager" destination parameter. For more
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information on configuring a Pulsar app see:
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@@ -208,7 +208,7 @@
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<!-- Comma separated list of Persistent Volume Claim (PVC) to container mount point mappings, in the format
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PVC:mount point
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Typical mount paths are extra mounts that are expected to be mounted for all jobs, such as
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Typical mount paths are extra mounts that are expected to be mounted for all jobs, such as
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tool scripts, the CVMFS, and all library paths set in galaxy.yml (or equivalent general galaxy config file). -->
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<!-- <param id="k8s_namespace">default</param> -->
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@@ -390,7 +390,7 @@
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- `assign_with` - How jobs should be assigned to handlers. The value can be a single method or a
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comma-separated list that will be tried in order. The default depends on whether any handlers and a job
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handler "pool" (such as uWSGI mules in a `job-handlers` farm) are configured. Valid methods are
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handler "pool" are configured. Valid methods are
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explained in detail in the documentation referenced above and have the values:
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- `mem-self` - In-memory Self Assignment
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@@ -549,7 +549,7 @@
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command.
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-->
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<!-- <param id="docker_auto_rm">true</param> -->
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<!-- Override which user to launch Docker container as - defaults to
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<!-- Override which user to launch Docker container as - defaults to
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Galaxy's user id. For remote job execution (e.g. Pulsar) set to
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remote job user. Leave empty to not use the -u argument with
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Docker. -->
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@@ -901,8 +901,8 @@
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<param id="job_memory">16000</param>
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<param id="job_cores">8</param>
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<param id="job_project">BigMem</param>
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<!-- Exclude hosts in the LSF cluster from receiving the job.
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Useful for avoiding nodes with temporal issues.
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<!-- Exclude hosts in the LSF cluster from receiving the job.
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Useful for avoiding nodes with temporal issues.
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-->
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<param id="job_excluded_hosts">/path/to/file/with/hosts/to/be/excluded/one_per_line.txt</param>
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</destination>
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@@ -927,8 +927,8 @@
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<container type="docker">bgruening/galaxy-stable</container>
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</requirements>
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Unless the job destination specifies an override
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with docker_container_id_override. If neither of
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Unless the job destination specifies an override
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with docker_container_id_override. If neither of
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these is set a default container can be specified
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with docker_default_container_id. The resolved
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container ID will be passed along to condor as
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@@ -962,7 +962,7 @@
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handler will be reused for the resubmitted job. The ``destination`` attriubte
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is optional, if not present the job's original destination will be reused for the
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re-submission. The ``delay`` attribute is optional, if present it will cause the job to
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delay for that number of seconds before being re-submitted.
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delay for that number of seconds before being re-submitted.
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-->
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<destination id="short_fast" runner="slurm">
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<param id="nativeSpecification">--time=00:05:00 --nodes=1</param>
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@@ -1090,12 +1090,12 @@
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<param id="docker_default_container_id">centos:latest</param>
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<!-- Specify the image on which the jobs have to be executed -->
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<param id="godocker_volumes"></param>
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<!-- Mount the godocker volumes
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<!-- Mount the godocker volumes
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volumes must be separated by commas.
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eg: <param id="godocker_volumes">home,galaxy</param>
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-->
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<param id="virtualenv">false</param>
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<!-- If a tool execution in container requires galaxy virtualenv,
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<!-- If a tool execution in container requires galaxy virtualenv,
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then enable it by setting the value to true.
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Disable venv by setting the value to false.
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-->
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@@ -85,7 +85,6 @@ pysam = "*"
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python = ">=3.7,<4"
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python-dateutil = "*"
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python-multipart = "*" # required to support form parsing in FastAPI/Starlette
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pyuwsgi = "*"
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PyYAML = "*"
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refgenconf = ">=0.12.0"
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requests = "*"
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