[ARVADOS] updated: 5d26f7e8bf84d5ed055dc1e88996a25c4db80e85

[git at public.curoverse.com]

Summary of changes:
 doc/user/tutorials/running-external-program.html.textile.liquid | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

       via  5d26f7e8bf84d5ed055dc1e88996a25c4db80e85 (commit)
      from  9b44bba316583b68f326920d378fbbc77b4567a2 (commit)

Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.


commit 5d26f7e8bf84d5ed055dc1e88996a25c4db80e85
Author: Brett Smith <brett at curoverse.com>
Date:   Thu May 21 16:06:16 2015 -0400

    Update tutorial pipeline page to match new definition.
    
    No issue #.

diff --git a/doc/user/tutorials/running-external-program.html.textile.liquid b/doc/user/tutorials/running-external-program.html.textile.liquid
index 18f5f7d..6e29613 100644
--- a/doc/user/tutorials/running-external-program.html.textile.liquid
+++ b/doc/user/tutorials/running-external-program.html.textile.liquid
@@ -21,12 +21,13 @@ This will open the template record in an interactive text editor (as specified b
 * @"name"@ is a human-readable name for the pipeline.
 * @"components"@ is a set of scripts or commands that make up the pipeline.  Each component is given an identifier (@"bwa-mem"@ and @"SortSam"@) in this example).
 ** Each entry in components @"components"@ is an Arvados job submission.  For more information about individual jobs, see the "job object reference":{{site.baseurl}}/api/schema/Job.html and "job create method.":{{site.baseurl}}/api/methods/jobs.html#create
-* @"repository"@, @"script_version"@, and @"script"@ indicate that we intend to use the external @"run-command"@ tool wrapper that is part of the Arvados.  These parameters are described in more detail in "Writing a script":tutorial-firstscript.html
+* @"repository"@, @"script_version"@, and @"script"@ indicate that we intend to use the external @"run-command"@ tool wrapper that is part of the Arvados.  These parameters are described in more detail in "Writing a script":tutorial-firstscript.html.
 * @"runtime_constraints"@ describes runtime resource requirements for the component.
-** @"docker_image"@ specifies the "Docker":https://www.docker.com/ runtime environment in which to run the job.  The Docker image @"arvados/jobs-java-bwa-samtools"@ supplied here has the Arvados SDK, Java runtime environment, bwa, and samtools installed.
+** @"docker_image"@ specifies the "Docker":https://www.docker.com/ runtime environment in which to run the job.  The Docker image @"bcosc/arv-base-java"@ supplied here has the Java runtime environment, bwa, and samtools installed.
+** @"arvados_sdk_version"@ specifies a version of the Arvados SDK to load alongside the job's script.
 * @"script_parameters"@ describes the component parameters.
 ** @"command"@ is the actual command line to invoke the @bwa@ and then @SortSam at .  The notation @$()@ denotes macro substitution commands evaluated by the run-command tool wrapper.
-** @"stdout"@ indicates that the output of this command should be captured to a file.
+** @"task.stdout"@ indicates that the output of this command should be captured to a file.
 ** @$(node.cores)@ evaluates to the number of cores available on the compute node at time the command is run.
 ** @$(tmpdir)@ evaluates to the local path for temporary directory the command should use for scratch data.
 ** @$(reference_collection)@ evaluates to the script_parameter @"reference_collection"@
@@ -34,7 +35,7 @@ This will open the template record in an interactive text editor (as specified b
 ** @$(file $(...))@ constructs a local path to a given file within the supplied Arvados collection.
 ** @$(glob $(...))@ searches the specified path based on a file glob pattern and evalutes to the first result.
 ** @$(basename $(...))@ evaluates to the supplied path with leading path portion and trailing filename extensions stripped
-** @"output_of"@ indicates that the @output@ of the @bwa-mem@ component should be used as the @"input"@ of @SortSam at .  Arvados uses these dependencies between components to automatically determine the correct order to run them.
+* @"output_of"@ indicates that the @output@ of the @bwa-mem@ component should be used as the @"input"@ script parameter of @SortSam at .  Arvados uses these dependencies between components to automatically determine the correct order to run them.
 
 When using @run-command@, the tool should write its output to the current working directory.  The output will be automatically uploaded to Keep when the job completes.
 

-----------------------------------------------------------------------


hooks/post-receive
--