[ARVADOS] updated: d92c79edf54df96d259d3c99eb2a5461b4111340
git at public.curoverse.com
git at public.curoverse.com
Tue Jul 8 11:41:41 EDT 2014
Summary of changes:
doc/_includes/_tutorial_expectations.liquid | 1 +
doc/user/getting_started/check-environment.html.textile.liquid | 2 +-
doc/user/reference/api-tokens.html.textile.liquid | 2 +-
doc/user/reference/sdk-cli.html.textile.liquid | 2 +-
doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid | 2 +-
doc/user/topics/tutorial-job-debug.html.textile.liquid | 2 +-
doc/user/topics/tutorial-job1.html.textile.liquid | 2 +-
doc/user/topics/tutorial-trait-search.html.textile.liquid | 2 +-
doc/user/tutorials/running-external-program.html.textile.liquid | 2 +-
doc/user/tutorials/tutorial-firstscript.html.textile.liquid | 2 +-
doc/user/tutorials/tutorial-keep.html.textile.liquid | 3 +--
doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid | 2 +-
12 files changed, 12 insertions(+), 12 deletions(-)
create mode 100644 doc/_includes/_tutorial_expectations.liquid
via d92c79edf54df96d259d3c99eb2a5461b4111340 (commit)
via 0f8504de1ab3a0ff2e33d23cc421a150cacf5d86 (commit)
from d27def0b6177ee6f628e6f11fffd0280c8d72558 (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 d92c79edf54df96d259d3c99eb2a5461b4111340
Author: radhika <radhika at curoverse.com>
Date: Tue Jul 8 11:24:12 2014 -0400
2380: ssh doc references are updated to point to the right env.
diff --git a/doc/_includes/_tutorial_expectations.liquid b/doc/_includes/_tutorial_expectations.liquid
new file mode 100644
index 0000000..86ac64c
--- /dev/null
+++ b/doc/_includes/_tutorial_expectations.liquid
@@ -0,0 +1 @@
+*This tutorial assumes that you are logged into an Arvados VM instance ("Unix":{{site.baseurl}}/user/getting_started/ssh-access-unix.html#login or "Windows":{{site.baseurl}}/user/getting_started/ssh-access-windows.html#login), and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
diff --git a/doc/user/getting_started/check-environment.html.textile.liquid b/doc/user/getting_started/check-environment.html.textile.liquid
index 2908e6e..c9d4778 100644
--- a/doc/user/getting_started/check-environment.html.textile.liquid
+++ b/doc/user/getting_started/check-environment.html.textile.liquid
@@ -4,7 +4,7 @@ navsection: userguide
title: "Checking your environment"
...
-First you should "log into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login if you have not already done so.
+First you should log into an Arvados VM instance ("Unix":{{site.baseurl}}/user/getting_started/ssh-access-unix.html#login or "Windows":{{site.baseurl}}/user/getting_started/ssh-access-windows.html#login) if you have not already done so.
If @arv user current@ is able to access the API server, it will print out information about your account. Check that you are able to access the Arvados API server using the following command:
diff --git a/doc/user/reference/api-tokens.html.textile.liquid b/doc/user/reference/api-tokens.html.textile.liquid
index 317e7a0..8a333ff 100644
--- a/doc/user/reference/api-tokens.html.textile.liquid
+++ b/doc/user/reference/api-tokens.html.textile.liquid
@@ -8,7 +8,7 @@ The Arvados API token is a secret key that enables the @arv@ command line client
Access the Arvados Workbench using this link: "https://{{ site.arvados_workbench_host }}/":https://{{ site.arvados_workbench_host }}/ (Replace @{{ site.arvados_api_host }}@ with the hostname of your local Arvados instance if necessary.)
-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":{{site.baseurl}}/user/getting_started/ssh-access.html.
+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 ("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 user icon <span class="glyphicon glyphicon-user"></span> in the upper right corner to access the user settings menu. Click on the menu item *Manage API tokens* to go to the "Api client authorizations" page.
diff --git a/doc/user/reference/sdk-cli.html.textile.liquid b/doc/user/reference/sdk-cli.html.textile.liquid
index f44fef2..3f62254 100644
--- a/doc/user/reference/sdk-cli.html.textile.liquid
+++ b/doc/user/reference/sdk-cli.html.textile.liquid
@@ -4,7 +4,7 @@ navsection: userguide
title: "Command line interface"
...
-*First, you should be "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
+*First, you should be logged into an Arvados VM instance ("Unix":{{site.baseurl}}/user/getting_started/ssh-access-unix.html#login or "Windows":{{site.baseurl}}/user/getting_started/ssh-access-windows.html#login), and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
h3. Usage
diff --git a/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid b/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
index ea608b4..fa33f67 100644
--- a/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
+++ b/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
@@ -6,7 +6,7 @@ title: "Using GATK with Arvados"
This tutorial demonstrates how to use the Genome Analysis Toolkit (GATK) with Arvados. In this example we will install GATK and then create a VariantFiltration job to assign pass/fail scores to variants in a VCF file.
-*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
+{% include 'tutorial_expectations' %}
h2. Installing GATK
diff --git a/doc/user/topics/tutorial-job-debug.html.textile.liquid b/doc/user/topics/tutorial-job-debug.html.textile.liquid
index bc1932e..8b0df36 100644
--- a/doc/user/topics/tutorial-job-debug.html.textile.liquid
+++ b/doc/user/topics/tutorial-job-debug.html.textile.liquid
@@ -6,7 +6,7 @@ title: "Debugging a Crunch script"
To test changes to a script by running a job, the change must be pushed to your hosted repository, and the job might have to wait in the queue before it runs. This cycle can be an inefficient way to develop and debug scripts. This tutorial demonstrates an alternative: using @arv-crunch-job@ to run your job in your local VM. This avoids the job queue and allows you to execute the script directly from your git working tree without committing or pushing.
-*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
+{% include 'tutorial_expectations' %}
This tutorial uses *@you@* to denote your username. Replace *@you@* with your user name in all the following examples.
diff --git a/doc/user/topics/tutorial-job1.html.textile.liquid b/doc/user/topics/tutorial-job1.html.textile.liquid
index cf09804..b687d71 100644
--- a/doc/user/topics/tutorial-job1.html.textile.liquid
+++ b/doc/user/topics/tutorial-job1.html.textile.liquid
@@ -6,7 +6,7 @@ title: "Running a Crunch job on the command line"
This tutorial introduces how to run individual Crunch jobs using the @arv@ command line tool.
-*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
+{% include 'tutorial_expectations' %}
You will create a job to run the "hash" Crunch script. The "hash" script computes the MD5 hash of each file in a collection.
diff --git a/doc/user/topics/tutorial-trait-search.html.textile.liquid b/doc/user/topics/tutorial-trait-search.html.textile.liquid
index 976f16e..a95e30d 100644
--- a/doc/user/topics/tutorial-trait-search.html.textile.liquid
+++ b/doc/user/topics/tutorial-trait-search.html.textile.liquid
@@ -6,7 +6,7 @@ title: "Querying the Metadata Database"
This tutorial introduces the Arvados Metadata Database. The Metadata Database stores information about files in Keep. This example will use the Python SDK to find public WGS (Whole Genome Sequencing) data for people who have reported a certain medical condition.
-*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
+{% include 'tutorial_expectations' %}
In the tutorial examples, three angle brackets (>>>) will be used to denote code to enter at the interactive Python prompt.
diff --git a/doc/user/tutorials/running-external-program.html.textile.liquid b/doc/user/tutorials/running-external-program.html.textile.liquid
index da6df59..ab31015 100644
--- a/doc/user/tutorials/running-external-program.html.textile.liquid
+++ b/doc/user/tutorials/running-external-program.html.textile.liquid
@@ -6,7 +6,7 @@ title: "Using Crunch to run external programs"
This tutorial demonstrates how to use Crunch to run an external program by writting a wrapper using the Python SDK.
-*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
+{% include 'tutorial_expectations' %}
In this tutorial, you will use the external program @md5sum@ to compute hashes instead of the built-in Python library used in earlier tutorials.
diff --git a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
index 5365b5a..570f74c 100644
--- a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid
@@ -7,7 +7,7 @@ title: "Writing a pipeline"
In this tutorial, we will write the "hash" script demonstrated in the first tutorial.
-*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
+{% include 'tutorial_expectations' %}
This tutorial uses *@you@* to denote your username. Replace *@you@* with your user name in all the following examples.
diff --git a/doc/user/tutorials/tutorial-keep.html.textile.liquid b/doc/user/tutorials/tutorial-keep.html.textile.liquid
index fac3530..3546c5c 100644
--- a/doc/user/tutorials/tutorial-keep.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-keep.html.textile.liquid
@@ -6,8 +6,7 @@ title: "Storing and Retrieving data using Keep"
This tutorial introduces you to the Arvados file storage system.
-
-*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
+{% include 'tutorial_expectations' %}
The Arvados distributed file system is called *Keep*. Keep is a content-addressable file system. This means that files are managed using special unique identifiers derived from the _contents_ of the file, rather than human-assigned file names (specifically, the MD5 hash). This has a number of advantages:
* Files can be stored and replicated across a cluster of servers without requiring a central name server.
diff --git a/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid b/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
index 045b8ec..efcc875 100644
--- a/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
@@ -6,7 +6,7 @@ title: "Writing a multi-step pipeline"
A pipeline in Arvados is a collection of crunch scripts, in which the output from one script may be used as the input to another script.
-*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
+{% include 'tutorial_expectations' %}
This tutorial uses *@you@* to denote your username. Replace *@you@* with your user name in all the following examples.
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