[ARVADOS] created: aa6f07c9687670ee98e15d9afa2bd47416839dc6

Mon Nov 17 16:44:09 EST 2014

at  aa6f07c9687670ee98e15d9afa2bd47416839dc6 (commit)


commit aa6f07c9687670ee98e15d9afa2bd47416839dc6
Author: radhika <radhika at curoverse.com>
Date:   Mon Nov 17 16:42:12 2014 -0500

    4250: update user guide to reflect current code.

diff --git a/doc/_includes/_ssh_addkey.liquid b/doc/_includes/_ssh_addkey.liquid
index 412ae67..3770635 100644
--- a/doc/_includes/_ssh_addkey.liquid
+++ b/doc/_includes/_ssh_addkey.liquid
@@ -11,7 +11,7 @@ h3. Alternate way to add SSH keys
 
 Click on the link with your _email address_ in the upper right corner to access the user settings menu, and click on the menu item *Manage account* to go to the account management page.
 
-On the *Manage account* page, click on the button <span class="btn btn-primary">Add new SSH key</span> button in the upper right corner of the page in the SSH Keys panel.
+On the *Manage account* page, click on the button <span class="btn btn-primary">*+* Add new SSH key</span> button in the upper right corner of the page in the SSH Keys panel.
 
 This will open a popup as shown in this screenshot:
 
diff --git a/doc/images/workbench-move-selected.png b/doc/images/workbench-move-selected.png
index cae64d0..5ed1ef5 100644
Binary files a/doc/images/workbench-move-selected.png and b/doc/images/workbench-move-selected.png differ
diff --git a/doc/user/topics/arv-run.html.textile.liquid b/doc/user/topics/arv-run.html.textile.liquid
index 91c49c8..69195d8 100644
--- a/doc/user/topics/arv-run.html.textile.liquid
+++ b/doc/user/topics/arv-run.html.textile.liquid
@@ -157,7 +157,7 @@ h2. Putting it all together: bwa mem
 <notextile>
 <pre>
 $ <span class="userinput">cd ~/keep/by_id/d0136bc494c21f79fc1b6a390561e6cb+2778</span>
-$ <span class="userinput">arv-run --docker-image arvados/jobs-java-bwa-samtools --repository peter --script-version 3609-arv-run  bwa mem ../3514b8e5da0e8d109946bc809b20a78a+5698/human_g1k_v37.fasta -- --batch-size 2 *.fastq.gz \> '$(task.uuid).sam'</span>
+$ <span class="userinput">arv-run --docker-image arvados/jobs-java-bwa-samtools --script-version 3609-arv-run bwa mem ../3514b8e5da0e8d109946bc809b20a78a+5698/human_g1k_v37.fasta -- --batch-size 2 *.fastq.gz \> '$(task.uuid).sam'</span>
  0 stderr run-command: parallelizing on input0 with items [[u'/keep/d0136bc494c21f79fc1b6a390561e6cb+2778/HWI-ST1027_129_D0THKACXX.1_1.fastq.gz', u'/keep/d0136bc494c21f79fc1b6a390561e6cb+2778/HWI-ST1027_129_D0THKACXX.1_2.fastq.gz'], [u'/keep/d0136bc494c21f79fc1b6a390561e6cb+2778/HWI-ST1027_129_D0THKACXX.2_1.fastq.gz', u'/keep/d0136bc494c21f79fc1b6a390561e6cb+2778/HWI-ST1027_129_D0THKACXX.2_2.fastq.gz']]
 [...]
  1 stderr run-command: bwa mem /keep/3514b8e5da0e8d109946bc809b20a78a+5698/human_g1k_v37.fasta /keep/d0136bc494c21f79fc1b6a390561e6cb+2778/HWI-ST1027_129_D0THKACXX.1_1.fastq.gz /keep/d0136bc494c21f79fc1b6a390561e6cb+2778/HWI-ST1027_129_D0THKACXX.1_2.fastq.gz > qr1hi-ot0gb-a4bzzyqqz4ubair.sam
diff --git a/doc/user/topics/run-command.html.textile.liquid b/doc/user/topics/run-command.html.textile.liquid
index 78f1c84..ca0045b 100644
--- a/doc/user/topics/run-command.html.textile.liquid
+++ b/doc/user/topics/run-command.html.textile.liquid
@@ -18,7 +18,8 @@ The basic @run-command@ process evaluates its inputs and builds a command line,
 In the following examples, you can use "dry run mode" to determine the command line that @run-command@ will use without actually running the command.  For example:
 
 <notextile>
-<pre><code>~$ <span class="userinput">./run-command --dry-run --script-parameters '{
+<pre><code>~$ <span class="userinput">cd $HOME/arvados/crunch_scripts</span>
+~$ <span class="userinput">./run-command --dry-run --script-parameters '{
   "command": ["echo", "hello world"]
 }'</span>
 run-command: echo hello world
diff --git a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
index d59275d..b8b90ca 100644
--- a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
@@ -54,7 +54,7 @@ You can now run your script on your local workstation or VM using @arv-crunch-jo
 2014-08-06_15:16:22 qr1hi-8i9sb-qyrat80ef927lam 14473  node localhost - 1 slots
 2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473  start
 2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473  script hash.py
-2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473  script_version /home/peter/peter
+2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473  script_version $HOME/tutorial
 2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473  script_parameters {"input":"c1bad4b39ca5a924e481008009d94e32+210"}
 2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473  runtime_constraints {"max_tasks_per_node":0}
 2014-08-06_15:16:23 qr1hi-8i9sb-qyrat80ef927lam 14473  start level 0
diff --git a/doc/user/tutorials/tutorial-keep.html.textile.liquid b/doc/user/tutorials/tutorial-keep.html.textile.liquid
index 74319fd..359c4a2 100644
--- a/doc/user/tutorials/tutorial-keep.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-keep.html.textile.liquid
@@ -28,11 +28,11 @@ c1bad4b39ca5a924e481008009d94e32+210
 
 * The output value @c1bad4b39ca5a924e481008009d94e32+210@ is the Arvados collection locator that uniquely describes this file.
 
-Now visit the Workbench *Dashboard*.  In the *My projects* pane, select your *Home* project.  Your newly uploaded collection should appear near the top of the *Data collections* tab.  The collection locator printed by @arv-put@ will appear under the *name* column.  To move the collection to a different project, check the box at the left of the collection row.  Pull down the *Selection...* menu near the top of the page tab, and select *Move selected*.
+Now visit the Workbench *Dashboard*.  Click on *Projects*<span class="caret"></span> dropdown menu in the top navigation menu, select your *Home* project.  Your newly uploaded collection should appear near the top of the *Data collections* tab.  The collection locator printed by @arv-put@ will appear under the *name* column.
 
-!{{ site.baseurl }}/images/workbench-move-selected.png!
+To move the collection to a different project, check the box at the left of the collection row.  Pull down the *Selection...*<span class="caret"></span> menu near the top of the page tab, and select *Move selected*. This will open a dialog box where you can select a destination project for the collection.  Click a project, then finally the <span class="btn btn-sm btn-primary">Move</span> button.
 
-This will open a dialog box where you can select a destination project for the collection.  Click a project, then finally the <span class="btn btn-sm btn-primary">Move</span> button.
+!{{ site.baseurl }}/images/workbench-move-selected.png!
 
 Click on the *<i class="fa fa-fw fa-archive"></i> Show* button next to the collection's listing on a project page to go to the Workbench page for your collection.  On this page, you can see the collection's contents, download individual files, and set sharing options.
 
diff --git a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
index 3640880..8dad6ab 100644
--- a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
@@ -17,7 +17,7 @@ notextile. <div class="spaced-out">
 # Start from the *Workbench Dashboard*.  You can access the Dashboard by clicking on *<i class="fa fa-lg fa-fw fa-dashboard"></i> Dashboard* in the upper left corner of any Workbench page.
 # Click on the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a pipeline...</span> button.  This will open a dialog box titled *Choose a pipeline to run*.
 # Click to open the *All projects <span class="caret"></span>* menu.  Under the *Projects shared with me* header, select *<i class="fa fa-fw fa-share-alt"></i> Arvados Tutorial*.
-# Select *<i class="fa fa-fw fa-gear"></i> Tutorial align using bwa mem* and click the <span class="btn btn-sm btn-primary" >Next: choose inputs <i class="fa fa-fw fa-arrow-circle-right"></i></span> button.  This will load a new page where you will supply the inputs for the pipeline.
+# Select *<i class="fa fa-fw fa-gear"></i> Tutorial align using bwa mem* and click the <span class="btn btn-sm btn-primary" >Next: choose inputs <i class="fa fa-fw fa-arrow-circle-right"></i></span> button.  This will create a new pipeline in your *Home* project and will open it. You can now supply the inputs for the pipeline.
 # The first input parameter to the pipeline is *Reference genoma (fasta)*.  Click the <span class="btn btn-sm btn-primary">Choose</span> button beneath that header.  This will open a dialog box titled *Choose a dataset for Reference genome (fasta)*.
 # Once again, open the *All projects <span class="caret"></span>* menu and select *<i class="fa fa-fw fa-share-alt"></i> Arvados Tutorial*.  Select *<i class="fa fa-fw fa-archive"></i> Tutorial chromosome 19 reference* and click the <span class="btn btn-sm btn-primary" >OK</span> button.
 # Repeat the previous two steps to set the *Input genome (fastq)* parameter to *<i class="fa fa-fw fa-archive"></i> Tutorial sample exome*.

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


hooks/post-receive
-- 


