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Improvements to structure of docs in job_conf advanced sample.

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This commit is contained in:
John Chilton
2019-05-03 11:01:18 -04:00
parent 72919beba0
commit a8734f5cb4
1 changed files with 21 additions and 19 deletions
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config/job_conf.xml.sample_advanced
+21 -19
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@@ -51,7 +51,7 @@
<param id="amqp_url">amqp://guest:guest@localhost:5672//</param>
<!-- URL remote Pulsar apps should transfer files to this Galaxy
instance to/from. This can be unspecified/empty if
galaxy_infrastructure_url is set in galaxy.ini.
galaxy_infrastructure_url is set in galaxy.yml.
-->
<param id="galaxy_url">http://localhost:8080</param>
<!-- AMQP does not guarantee that a published message is received by
@@ -141,7 +141,7 @@
server: 192.168.64.1
The path (nfs:path: in the example) set needs to be a parent directory of the directories used for
variables “file_path” and “new_file_path” on the galaxy.ini files. Clearly, for this particular example
variables “file_path” and “new_file_path” on the galaxy.yml files. Clearly, for this particular example
to work, there needs to be a NFS server serving that directory on that ip. Please make sure that you
use reasonable storage size for your set up (possibly larger that the 10Gi written).
An example of the volume claim should be (this needs to be followed more closely) (pv_claim.yaml):
@@ -303,7 +303,7 @@
This runner requires a shared file system where the directories of
`job_working_directory`, `file_path` and `new_file_path` settings defined on
the `galaxy.ini` file are shared amongst the Mesos agents (i.e. nodes which
the `galaxy.yml` file are shared amongst the Mesos agents (i.e. nodes which
actually run the jobs).
-->
<param id="chronos">`chronos_host`</param>
@@ -415,7 +415,7 @@
This configuration allows any docker instance to write to any Galaxy
file - for greater isolation set outputs_to_working_directory in
galaxy.ini. This will cause $defaults to allow writing to much
galaxy.yml. This will cause $defaults to allow writing to much
less. It will then expand as follows:
$galaxy_root:ro,$tool_directory:ro,$job_directory:ro,$working_directory:rw,$default_file_path:ro
@@ -580,16 +580,18 @@
<!-- Define parameters that are native to the job runner plugin. -->
<param id="Resource_List">walltime=72:00:00</param>
</destination>
<destination id="remote_cluster" runner="drmaa" tags="longjobs"/>
<destination id="java_cluster" runner="drmaa">
<!-- Allow users that are not mapped to any real users to run jobs
as a Galaxy (fallback). Default is False.
-->
<param id="allow_guests">True</param>
<destination id="remote_cluster" runner="drmaa" tags="longjobs">
<!-- Set to False if cluster nodes don't shared Galaxy library,
it will perform metadata calculation locally after the job finishes.
-->
<param id="embed_metadata_in_job">True</param>
<!-- If jobs are configured to run as the real user, this option allows
users that are not mapped to any real users to run jobs
as a Galaxy (fallback). Default is False.
-->
<param id="allow_guests">True</param>
</destination>
<destination id="java_cluster" runner="drmaa">
<!-- set arbitrary environment variables at runtime. General
dependencies for tools should be configured via
tool_dependency_dir and package options and these
@@ -623,7 +625,7 @@
<param id="tmp_dir">$(mktemp -d /mnt/scratch/fastest/gxyjobXXXXXXXXXXX)</param>
</destination>
<destination id="real_user_cluster" runner="drmaa">
<!-- Make sure to setup 3 real user parameters in galaxy.ini. -->
<!-- Make sure to setup 3 real user parameters in galaxy.yml. -->
</destination>
<destination id="dynamic" runner="dynamic">
<!-- A destination that represents a method in the dynamic runner.
@@ -896,7 +898,7 @@
<resubmit condition="unknown_error and attempt &lt;= 5" delay="attempt * 30" />
</destination>
<!-- Any tag param in this file can be set using an environment variable or using
values from galaxy.ini using the from_environ and from_config attributes
values from galaxy.yml using the from_environ and from_config attributes
repectively. The text of the param will still be used if that environment variable
or config value isn't set.
-->
@@ -1012,19 +1014,19 @@
a tag, a handler or destination that matches that tag will be
chosen at random.
-->
<tool id="foo" handler="trackster_handler">
<param id="source">trackster</param>
<tool id="bwa" handler="handler0">
</tool>
<tool id="bowtie" handler="handler1">
</tool>
<tool id="bar" destination="dynamic"/>
<!-- Next example defines resource group to insert into tool interface
and pass to dynamic destination (as resource_params argument). -->
<tool id="longbar" destination="dynamic" resources="all" />
<!-- Pick a handler randomly from those declaring this tag. -->
<tool id="baz" handler="special_handlers" destination="bigmem"/>
<!-- Finally for Kubernetes runner, the following connects a particular tool to be executed with
the container of choice in Kubernetes.
-->
<tool id="my-tool" destination="my-tool-container"/>
<tool id="foo" handler="handler0">
<param id="source">trackster</param>
</tool>
</tools>
<limits>
<!-- Certain limits can be defined. The 'concurrent_jobs' limits all