6093: some more doc updates.

diff --git a/doc/user/reference/api-tokens.html.textile.liquid b/doc/user/reference/api-tokens.html.textile.liquid
index 768c7d1c266a2d137bc76ed1a86b0b91b7f3ca10..a30209a2be42026aa232bb2e8fa588531bc4e669 100644 (file)
--- a/doc/user/reference/api-tokens.html.textile.liquid
+++ b/doc/user/reference/api-tokens.html.textile.liquid
@@ -10,7 +10,7 @@ Access the Arvados Workbench using this link: "https://{{ site.arvados_workbench
 
 Open a shell on the system where you want to use the Arvados client. This may be your local workstation, or an Arvados virtual machine accessed with SSH (instructions for "Unix":{{site.baseurl}}/user/getting_started/ssh-access-unix.html#login or "Windows":{{site.baseurl}}/user/getting_started/ssh-access-windows.html#login).
 
-Click on the link with your _email address_ in the upper right corner to access your account menu, then click on the menu item *Manage account* to go to the account management page. On the *Manage account* page, you will see the *Current Token* panel, which lists your current token and instructions to set up your environment.
+Click on the dropdown menu icon <span class="fa fa-lg fa-user"></span> <span class="caret"></span> in the upper right corner of the top navigation menu to access your account menu, then click on the menu item *Manage account* to go to the account management page. On the *Manage account* page, you will see the *Current Token* panel, which lists your current token and instructions to set up your environment.
 
 h2. Setting environment variables
 

diff --git a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
index 6fe88fe156c5a78577b9a271730e7da938d721a6..e3703e8264aa0b3755eef586de4181307aaf1487 100644 (file)
--- a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
@@ -82,19 +82,19 @@ You can now run your script on your local workstation or VM using @arv-crunch-jo
 2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473  release job allocation
 2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473  Freeze not implemented
 2014-08-06_15:16:35 qr1hi-8i9sb-qyrat80ef927lam 14473  collate
-2014-08-06_15:16:36 qr1hi-8i9sb-qyrat80ef927lam 14473  output uuid qr1hi-4zz18-n91qrqfp3zivexo
+2014-08-06_15:16:36 qr1hi-8i9sb-qyrat80ef927lam 14473  collated output manifest text to send to API server is 105 bytes with access tokens
 2014-08-06_15:16:36 qr1hi-8i9sb-qyrat80ef927lam 14473  output hash c1b44b6dc41ef334cf1136033ca950e6+54
 2014-08-06_15:16:37 qr1hi-8i9sb-qyrat80ef927lam 14473  finish
 2014-08-06_15:16:38 qr1hi-8i9sb-qyrat80ef927lam 14473  log manifest is 7fe8cf1d45d438a3ca3ac4a184b7aff4+83
 </code></pre>
 </notextile>
 
-Although the job runs locally, the output of the job has been saved to Keep, the Arvados file store.  The "output uuid" line (fourth from the bottom) provides the UUID of the Arvados collection where the script's output has been saved.  Copy the output identifier and use @arv-ls@ to list the contents of your output collection, and @arv-get@ to download it to the current directory:
+Although the job runs locally, the output of the job has been saved to Keep, the Arvados file store.  The "output hash" line (third from the bottom) provides the portable data hash of the Arvados collection where the script's output has been saved.  Copy the output hash and use @arv-ls@ to list the contents of your output collection, and @arv-get@ to download it to the current directory:
 
 <notextile>
-<pre><code>~/tutorial/crunch_scripts$ <span class="userinput">arv-ls qr1hi-4zz18-n91qrqfp3zivexo</span>
+<pre><code>~/tutorial/crunch_scripts$ <span class="userinput">arv-ls c1b44b6dc41ef334cf1136033ca950e6+54</span>
 ./md5sum.txt
-~/tutorial/crunch_scripts$ <span class="userinput">arv-get qr1hi-4zz18-n91qrqfp3zivexo/ .</span>
+~/tutorial/crunch_scripts$ <span class="userinput">arv-get c1b44b6dc41ef334cf1136033ca950e6+54/ .</span>
 0 MiB / 0 MiB 100.0%
 ~/tutorial/crunch_scripts$ <span class="userinput">cat md5sum.txt</span>
 44b8ae3fde7a8a88d2f7ebd237625b4f c1bad4b39ca5a924e481008009d94e32+210/var-GS000016015-ASM.tsv.bz2

diff --git a/doc/user/tutorials/tutorial-keep-get.html.textile.liquid b/doc/user/tutorials/tutorial-keep-get.html.textile.liquid
index 1f980edcd0c55c56a16b4ec8bc44a90363a392a1..1e894e7c25141ba00aa722ad2adef22fd508e37f 100644 (file)
--- a/doc/user/tutorials/tutorial-keep-get.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-keep-get.html.textile.liquid
@@ -74,6 +74,6 @@ This will create a sharing link for the collection as shown below. You can copy
 
 !{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/shared-collection.png!
 
-A user with this url can download this collection by simply accessing this url. It will present a downloadable version of the collection as shown below.
+A user with this url can download this collection by simply accessing this url using browser. It will present a downloadable version of the collection as shown below.
 
 !{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/download-shared-collection.png!

diff --git a/doc/user/tutorials/tutorial-keep.html.textile.liquid b/doc/user/tutorials/tutorial-keep.html.textile.liquid
index 0d8dfb344d5b939d12317c3be2b2c3d922a213a5..07b2e8cacfcade73bdc3890cf95e289e17cb8589 100644 (file)
--- a/doc/user/tutorials/tutorial-keep.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-keep.html.textile.liquid
@@ -48,9 +48,9 @@ In both examples, the @arv keep put@ command created a collection. The first col
 
 h3. Locate your collection in Workbench
 
-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 keep put@ will appear under the *name* column.
+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 name printed by @arv keep 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...*<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.
+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...* 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.
 
 !{display: block;margin-left: 25px;margin-right: auto;}{{ site.baseurl }}/images/workbench-move-selected.png!
 
@@ -76,4 +76,4 @@ Click on the *Browse...* button and select the files you would like to upload. S
 
 *Note:* If you leave the collection page during the upload, the upload process will be aborted and you will need to upload the files again.
 
-*Note:* You can also use the Upload tab to add files to an existing collection.
+*Note:* You can also use the Upload tab to add additional files to an existing collection.

diff --git a/doc/user/tutorials/tutorial-submit-job.html.textile.liquid b/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
index 7cc4b885490b0fe54db4ee59d73cf1cc043ba45b..f4ddb6fcfde601c70439287072338e4b5027725e 100644 (file)
--- a/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-submit-job.html.textile.liquid
@@ -20,7 +20,9 @@ All Crunch scripts are managed through the Git revision control system.  Before
 ~$ <span class="userinput">git config --global user.email $USER@example.com</span></code></pre>
 </notextile>
 
-On the Arvados Workbench, navigate to "Code repositories":https://{{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@git.{{ site.arvados_api_host }}:$USER/$USER.git</code></notextile>.
+On the Arvados Workbench, click on the dropdown menu icon <span class="fa fa-lg fa-user"></span> <span class="caret"></span> in the upper right corner of the top navigation menu 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, you will see *Repositories* panel. In this panel, you should see a repository with your user name listed in the *name* column.  Next to *name* is the column *URL*. Copy the *URL* value associated with your repository.  This should look like <notextile><code>git@git.{{ site.arvados_api_host }}:$USER/$USER.git</code></notextile>.
 
 Next, on the Arvados virtual machine, clone your Git repository:
 
@@ -100,7 +102,7 @@ In the editor, enter the following template:
 
 <notextile> {% code 'tutorial_submit_job' as javascript %} </notextile>
 
-* @"repository"@ is the name of a git repository to search for the script version.  You can access a list of available git repositories on the Arvados Workbench under "Code repositories":https://{{site.arvados_workbench_host}}/repositories.
+* @"repository"@ is the name of a git repository to search for the script version.  You can access a list of available git repositories on the Arvados Workbench in the *Manage account* page using the <span class="fa fa-lg fa-user"></span> <span class="caret"></span> top navigation menu icon.
 * @"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, a tag, or a branch (in which case it will use 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.
 * @"script"@ specifies the filename of the script to run.  Crunch expects to find this in the @crunch_scripts/@ subdirectory of the Git repository.
 * @"runtime_constraints"@ describes the runtime environment required to run the job.  These are described in the "job record schema":{{site.baseurl}}/api/schema/Job.html