From d69be2dd7e3040cbe1fcb02e06daab91a391fe8a Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 22 Apr 2015 15:03:39 -0400
Subject: [PATCH] Modernize job conf samples in docs a little.
They were remnants of LWR approach of one runner with many configuration options, use Pulsar specific runners which use better defaults and so require setting fewer options.
---
docs/files/job_conf_sample_mq.xml | 8 +-------
docs/files/job_conf_sample_remote_cluster.xml | 5 +----
2 files changed, 2 insertions(+), 11 deletions(-)
diff --git a/docs/files/job_conf_sample_mq.xml b/docs/files/job_conf_sample_mq.xml
index ebda5ac7..3978a32b 100644
--- a/docs/files/job_conf_sample_mq.xml
+++ b/docs/files/job_conf_sample_mq.xml
@@ -2,7 +2,7 @@
<job_conf>
<plugins>
<plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
- <plugin id="pulsar" type="runner" load="galaxy.jobs.runners.pulsar:PulsarLegacyJobRunner">
+ <plugin id="pulsar" type="runner" load="galaxy.jobs.runners.pulsar:PulsarMQJobRunner">
<!-- Must tell Pulsar where to send files. -->
<param id="galaxy_url">https://galaxyserver</param>
<!-- Message Queue Connection (should match message_queue_url in Pulsar's app.yml)
@@ -22,14 +22,8 @@
web server it can simply ask for this information.
-->
<param id="jobs_directory">/path/to/remote/pulsar/files/staging/</param>
- <!-- Invert file transfers - have Pulsar initiate downloads during preprocessing
- and uploads during postprocessing. -->
- <param id="default_file_action">remote_transfer</param>
-
<!-- Remaining parameters same as previous example -->
<param id="submit_native_specification">-P bignodes -R y -pe threads 16</param>
- <param id="dependency_resolution">remote</param>
- <param id="rewrite_parameters">True</param>
</destination>
</destinations>
<tools>
diff --git a/docs/files/job_conf_sample_remote_cluster.xml b/docs/files/job_conf_sample_remote_cluster.xml
index b6371428..52c5a146 100644
--- a/docs/files/job_conf_sample_remote_cluster.xml
+++ b/docs/files/job_conf_sample_remote_cluster.xml
@@ -2,7 +2,7 @@
<job_conf>
<plugins>
<plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
- <plugin id="pulsar" type="runner" load="galaxy.jobs.runners.pulsar:PulsarLegacyJobRunner"/>
+ <plugin id="pulsar" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner">
</plugins>
<handlers>
<handler id="main"/>
@@ -18,9 +18,6 @@
in the Pulsar app.yml file.
-->
<param id="dependency_resolution">remote</param>
- <!-- Use more correct parameter generation for *nix. Needs testing on Windows
- servers before this becomes default. -->
- <param id="rewrite_parameters">True</param>
</destination>
</destinations>
<tools>
--
GitLab