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:
<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 \> '$(task.uuid).sam'</span>
0 stderr run-command: parallelizing on input0 with items [[u'/keep/d0136bc494c21f79fc1b6a390561e6cb+2778/HWI-ST1027_129_D0THKACXX.1_1.fastq.gz', u'/keep/d0136bc494c21f79fc1b6a390561e6cb+2778/HWI-ST1027_129_D0THKACXX.1_2.fastq.gz'], [u'/keep/d0136bc494c21f79fc1b6a390561e6cb+2778/HWI-ST1027_129_D0THKACXX.2_1.fastq.gz', u'/keep/d0136bc494c21f79fc1b6a390561e6cb+2778/HWI-ST1027_129_D0THKACXX.2_2.fastq.gz']]
[...]
1 stderr run-command: bwa mem /keep/3514b8e5da0e8d109946bc809b20a78a+5698/human_g1k_v37.fasta /keep/d0136bc494c21f79fc1b6a390561e6cb+2778/HWI-ST1027_129_D0THKACXX.1_1.fastq.gz /keep/d0136bc494c21f79fc1b6a390561e6cb+2778/HWI-ST1027_129_D0THKACXX.1_2.fastq.gz > qr1hi-ot0gb-a4bzzyqqz4ubair.sam
In the following examples, you can use "dry run mode" to determine the command line that @run-command@ will use without actually running the command. For example:
<notextile>
-<pre><code>~$ <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
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
* 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.
# 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*.
projects / arvados.git / commitdiff
