[ARVADOS] updated: 7a47332fa99627c3ed0e22a02c54afcb6d128ef5
git at public.curoverse.com
git at public.curoverse.com
Tue May 26 15:52:23 EDT 2015
Summary of changes:
doc/_includes/_tutorial_expectations_workstation.liquid | 3 +++
doc/user/reference/api-tokens.html.textile.liquid | 2 +-
doc/user/topics/arv-docker.html.textile.liquid | 4 ++--
doc/user/topics/arv-web.html.textile.liquid | 3 +++
doc/user/topics/run-command.html.textile.liquid | 2 ++
doc/user/topics/tutorial-parallel.html.textile.liquid | 2 +-
doc/user/tutorials/tutorial-firstscript.html.textile.liquid | 8 ++++----
doc/user/tutorials/tutorial-keep-get.html.textile.liquid | 2 +-
doc/user/tutorials/tutorial-keep.html.textile.liquid | 6 +++---
doc/user/tutorials/tutorial-submit-job.html.textile.liquid | 6 ++++--
10 files changed, 24 insertions(+), 14 deletions(-)
create mode 100644 doc/_includes/_tutorial_expectations_workstation.liquid
via 7a47332fa99627c3ed0e22a02c54afcb6d128ef5 (commit)
via 6bc89efda1447c479642c7459d14a7afa440019d (commit)
from 8a2a84af560d9de68cf0d0c9e34e0d1f19b65e43 (commit)
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commit 7a47332fa99627c3ed0e22a02c54afcb6d128ef5
Author: radhika <radhika at curoverse.com>
Date: Tue May 26 15:51:44 2015 -0400
6093: a few more updates
diff --git a/doc/_includes/_tutorial_expectations_workstation.liquid b/doc/_includes/_tutorial_expectations_workstation.liquid
new file mode 100644
index 0000000..75fb256
--- /dev/null
+++ b/doc/_includes/_tutorial_expectations_workstation.liquid
@@ -0,0 +1,3 @@
+{% include 'notebox_begin' %}
+This tutorial assumes that you have installed the Arvados "Command line SDK":{{site.baseurl}}/sdk/cli/install.html and "Python SDK":{{site.baseurl}}/sdk/python/sdk-python.html on your workstation and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html
+{% include 'notebox_end' %}
diff --git a/doc/user/topics/arv-docker.html.textile.liquid b/doc/user/topics/arv-docker.html.textile.liquid
index 0a0693f..821b105 100644
--- a/doc/user/topics/arv-docker.html.textile.liquid
+++ b/doc/user/topics/arv-docker.html.textile.liquid
@@ -14,7 +14,7 @@ This page will demonstrate how to:
# Upload that image to Arvados for use by Crunch jobs
# Share your image with others
-{% include 'tutorial_expectations' %}
+{% include 'tutorial_expectations_workstation' %}
You also need ensure that "Docker is installed,":https://docs.docker.com/installation/ the Docker daemon is running, and you have permission to access Docker. You can test this by running @docker version at . If you receive a permission denied error, your user account may need to be added to the @docker@ group. If you have root access, you can add yourself to the @docker@ group using @$ sudo addgroup $USER docker@ then log out and log back in again; otherwise consult your local sysadmin.
@@ -197,6 +197,6 @@ h2. Share Docker images
Docker images are subject to normal Arvados permissions. If wish to share your Docker image with others (or wish to share a pipeline template that uses your Docker image) you will need to use @arv keep docker@ with the @--project-uuid@ option to upload the image to a shared project.
<notextile>
-<pre><code>$ <span class="userinput">arv keep docker --project-uuid zzzzz-j7d0g-u7zg1qdaowykd8d arvados/jobs-with-r</span>
+<pre><code>$ <span class="userinput">arv keep docker --project-uuid qr1hi-j7d0g-xxxxxxxxxxxxxxx arvados/jobs-with-r</span>
</code></pre>
</notextile>
diff --git a/doc/user/topics/arv-web.html.textile.liquid b/doc/user/topics/arv-web.html.textile.liquid
index cf3a3cc..44e5fd8 100644
--- a/doc/user/topics/arv-web.html.textile.liquid
+++ b/doc/user/topics/arv-web.html.textile.liquid
@@ -6,11 +6,14 @@ title: "Using arv-web"
@arv-web@ enables you to run a custom web service from the contents of an Arvados collection.
+{% include 'tutorial_expectations_workstation' %}
+
h2. Usage
@arv-web@ enables you to set up a web service based on the most recent collection in a project. An arv-web application is a reproducible, immutable application bundle where the web app is packaged with both the code to run and the data to serve. Because Arvados Collections can be updated with minimum duplication, it is efficient to produce a new application bundle when the code or data needs to be updated; retaining old application bundles makes it easy to go back and run older versions of your web app.
<pre>
+$ cd $HOME/arvados/services/arv-web
usage: arv-web.py [-h] --project-uuid PROJECT_UUID [--port PORT]
[--image IMAGE]
diff --git a/doc/user/topics/run-command.html.textile.liquid b/doc/user/topics/run-command.html.textile.liquid
index 5ffeb18..f02a6e6 100644
--- a/doc/user/topics/run-command.html.textile.liquid
+++ b/doc/user/topics/run-command.html.textile.liquid
@@ -6,6 +6,8 @@ title: "run-command reference"
The @run-command@ crunch script enables you run command line programs.
+{% include 'tutorial_expectations_workstation' %}
+
h1. Using run-command
The basic @run-command@ process evaluates its inputs and builds a command line, executes the command, and saves the contents of the output directory back to Keep. For large datasets, @run-command@ can schedule concurrent tasks to execute the wrapped program over a range of inputs (see @task.foreach@ below.)
diff --git a/doc/user/topics/tutorial-parallel.html.textile.liquid b/doc/user/topics/tutorial-parallel.html.textile.liquid
index 7a430a9..6d0058b 100644
--- a/doc/user/topics/tutorial-parallel.html.textile.liquid
+++ b/doc/user/topics/tutorial-parallel.html.textile.liquid
@@ -4,7 +4,7 @@ navsection: userguide
title: "Concurrent Crunch tasks"
...
-In the previous tutorials, we used @arvados.job_setup.one_task_per_input_file()@ to automatically create concurrent jobs by creating a separate task per file. For some types of jobs, you may need to split the work up differently, for example creating tasks to process different segments of a single large file. In this this tutorial will demonstrate how to create Crunch tasks directly.
+In the previous tutorials, we used @arvados.job_setup.one_task_per_input_file()@ to automatically create concurrent jobs by creating a separate task per file. For some types of jobs, you may need to split the work up differently, for example creating tasks to process different segments of a single large file. This tutorial will demonstrate how to create Crunch tasks directly.
Start by entering the @crunch_scripts@ directory of your Git repository:
commit 6bc89efda1447c479642c7459d14a7afa440019d
Author: radhika <radhika at curoverse.com>
Date: Tue May 26 11:56:29 2015 -0400
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 768c7d1..a30209a 100644
--- 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 6fe88fe..e3703e8 100644
--- 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 1f980ed..1e894e7 100644
--- 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 0d8dfb3..07b2e8c 100644
--- 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 7cc4b88..f4ddb6f 100644
--- 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 $USER at example.com</span></code></pre>
</notextile>
-On the Arvados Workbench, navigate to "Code repositories":https://{{site.arvados_workbench_host}}/repositories. You should see a repository with your user name listed in the *name* column. Next to *name* is the column *push_url*. Copy the *push_url* value associated with your repository. This should look like <notextile><code>git at git.{{ site.arvados_api_host }}:$USER/$USER.git</code></notextile>.
+On the Arvados Workbench, click on the dropdown menu icon <span class="fa fa-lg fa-user"></span> <span class="caret"></span> in the upper right corner of the top navigation menu to access the user settings menu, and click on the menu item *Manage account* to go to the account management page.
+
+On the *Manage account* page, you will see *Repositories* panel. In this panel, you should see a repository with your user name listed in the *name* column. Next to *name* is the column *URL*. Copy the *URL* value associated with your repository. This should look like <notextile><code>git at git.{{ site.arvados_api_host }}:$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
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