[ARVADOS] updated: e86868d96caea7af41140e9d3e26f40b144a0ff6
git at public.curoverse.com
git at public.curoverse.com
Tue Mar 11 14:33:32 EDT 2014
Summary of changes:
doc/_layouts/default.html.liquid | 2 +-
...rial-gatk-variantfiltration.html.textile.liquid | 2 +-
doc/user/topics/tutorial-job1.html.textile.liquid | 2 +-
.../topics/tutorial-parallel.html.textile.liquid | 2 +-
.../tutorial-firstscript.html.textile.liquid | 4 ++--
5 files changed, 6 insertions(+), 6 deletions(-)
via e86868d96caea7af41140e9d3e26f40b144a0ff6 (commit)
from 9ab861b00881ea7a5737d89b90ad17ceb264c8da (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 e86868d96caea7af41140e9d3e26f40b144a0ff6
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Tue Mar 11 14:34:58 2014 -0400
Ran linkchecker and fixed links.
diff --git a/doc/_layouts/default.html.liquid b/doc/_layouts/default.html.liquid
index 3004974..987f525 100644
--- a/doc/_layouts/default.html.liquid
+++ b/doc/_layouts/default.html.liquid
@@ -58,7 +58,7 @@
margin-top: -61px;
}
</style>
- <link href="{{ site.baseurl }}/css/bootstrap-responsive.min.css" rel="stylesheet">
+
<!-- HTML5 shim, for IE6-8 support of HTML5 elements -->
<!--[if lt IE 9]>
<script src="../assets/js/html5shiv.js"></script>
diff --git a/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid b/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
index 4e9a1eb..f83c199 100644
--- a/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
+++ b/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
@@ -10,7 +10,7 @@ This tutorial demonstrates how to use the Genome Analysis Toolkit (GATK) with Ar
h2. Installing GATK
-Download the GATK binary tarball[1] -- e.g., @GenomeAnalysisTK-2.6-4.tar.bz2@ -- and "copy it to your Arvados VM":tutorial-keep.html.
+Download the GATK binary tarball[1] -- e.g., @GenomeAnalysisTK-2.6-4.tar.bz2@ -- and "copy it to your Arvados VM":{{site.baseurl}}/user/tutorials/tutorial-keep.html.
<notextile>
<pre><code>~$ <span class="userinput">arv keep put GenomeAnalysisTK-2.6-4.tar.bz2</span>
diff --git a/doc/user/topics/tutorial-job1.html.textile.liquid b/doc/user/topics/tutorial-job1.html.textile.liquid
index 0e90d9e..61eaa63 100644
--- a/doc/user/topics/tutorial-job1.html.textile.liquid
+++ b/doc/user/topics/tutorial-job1.html.textile.liquid
@@ -34,7 +34,7 @@ EOF
* @<<EOF@ tells the shell to direct the following lines into the standard input for @cat@ up until it sees the line @EOF@
* @>the_job@ redirects standard output to a file called @the_job@
* @"script"@ specifies the name of the script to run. The script is searched for in the "crunch_scripts/" subdirectory of the @git@ checkout specified by @"script_version"@.
-* @"script_version"@ specifies the version of the script that you wish to run. This can be in the form of an explicit @git@ revision hash, or in the form "repository:branch" (in which case it will take the HEAD of the specified branch). Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run. You can access a list of available @git@ repositories on the Arvados workbench under "Compute %(rarr)→% Code repositories":http://{{site.arvados_workbench_host}}/repositiories .
+* @"script_version"@ specifies the version of the script that you wish to run. This can be in the form of an explicit @git@ revision hash, or in the form "repository:branch" (in which case it will take the HEAD of the specified branch). Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run. You can access a list of available @git@ repositories on the Arvados workbench under "Compute %(rarr)→% Code repositories":http://{{site.arvados_workbench_host}}/repositories .
* @"script_parameters"@ are provided to the script. In this case, the input is the locator for the collection that we inspected in the previous section.
Use @arv job create@ to actually submit the job. It should print out a JSON object which describes the newly created job:
diff --git a/doc/user/topics/tutorial-parallel.html.textile.liquid b/doc/user/topics/tutorial-parallel.html.textile.liquid
index 21d9841..9d08b69 100644
--- a/doc/user/topics/tutorial-parallel.html.textile.liquid
+++ b/doc/user/topics/tutorial-parallel.html.textile.liquid
@@ -34,7 +34,7 @@ Next, add the file to @git@ staging, commit and push:
</code></pre>
</notextile>
-You should now be able to run your new script using Crunch, with "script" referring to our new "parallel-hash.py" script. We will use a different input from our previous examples. We will use @887cd41e9c613463eab2f0d885c6dd96+83@ which consists of three files, "alice.txt", "bob.txt" and "carol.txt" (the example collection used previously in "fetching data from Arvados using Keep":tutorial-keep.html).
+You should now be able to run your new script using Crunch, with "script" referring to our new "parallel-hash.py" script. We will use a different input from our previous examples. We will use @887cd41e9c613463eab2f0d885c6dd96+83@ which consists of three files, "alice.txt", "bob.txt" and "carol.txt" (the example collection used previously in "fetching data from Arvados using Keep":{{site.baseurl}}/user/tutorials/tutorial-keep.html#dir).
<notextile>
<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat >~/the_job <<EOF
diff --git a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
index 2e48833..97a7547 100644
--- a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
@@ -22,7 +22,7 @@ First, you should do some basic configuration for git (you only need to do this
~$ <span class="userinput">git config --global user.email <b>you</b>@example.com</span></code></pre>
</notextile>
-On the Arvados Workbench, navigate to "Compute %(rarr)→% Code repositories":http://{{site.arvados_workbench_host}}/repositiories . You should see a repository with your user name listed in the *name* column. Next to *name* is the column *push_url*. Copy the *push_url* value associated with your repository. This should look like <notextile><code>git at git.{{ site.arvados_api_host }}:<b>you</b>.git</code></notextile>.
+On the Arvados Workbench, navigate to "Compute %(rarr)→% Code repositories":http://{{site.arvados_workbench_host}}/repositories . You should see a repository with your user name listed in the *name* column. Next to *name* is the column *push_url*. Copy the *push_url* value associated with your repository. This should look like <notextile><code>git at git.{{ site.arvados_api_host }}:<b>you</b>.git</code></notextile>.
Next, on the Arvados virtual machine, clone your git repository:
@@ -125,7 +125,7 @@ EOF
* @"components"@ is a set of scripts that make up the pipeline
* The component is listed with a human-readable name (@"do_hash"@ in this example)
* @"script"@ specifies the name of the script to run. The script is searched for in the "crunch_scripts/" subdirectory of the @git@ checkout specified by @"script_version"@.
-* @"script_version"@ specifies the version of the script that you wish to run. This can be in the form of an explicit @git@ revision hash, or in the form "repository:branch" (in which case it will take the HEAD of the specified branch). Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run. You can access a list of available @git@ repositories on the Arvados workbench under "Compute %(rarr)→% Code repositories":http://{{site.arvados_workbench_host}}/repositiories .
+* @"script_version"@ specifies the version of the script that you wish to run. This can be in the form of an explicit @git@ revision hash, or in the form "repository:branch" (in which case it will take the HEAD of the specified branch). Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run. You can access a list of available @git@ repositories on the Arvados workbench under "Compute %(rarr)→% Code repositories":http://{{site.arvados_workbench_host}}//repositories .
* @"script_parameters"@ describes the parameters for the script. In this example, there is one parameter called @input@ which is @required@ and is a @Collection at .
Now, use @arv pipeline_template create@ tell Arvados about your pipeline template:
-----------------------------------------------------------------------
hooks/post-receive
--
More information about the arvados-commits
mailing list