From: Peter Amstutz Date: Mon, 16 Dec 2013 17:16:22 +0000 (-0500) Subject: * Fixed links X-Git-Tag: 1.1.0~2825^2~6 X-Git-Url: https://git.arvados.org/arvados.git/commitdiff_plain/5e9fbf33f20ecbc8584ca16f9e736763bc70e2e2?hp=2183113c4c357e07719251854e3d249cdcd394dd * Fixed links * Added bootstrap and jquery snapshots --- diff --git a/doc/_includes/parallel_hash_script.py b/doc/_includes/parallel_hash_script.py index 46730cfb95..4601b6b1f8 100644 --- a/doc/_includes/parallel_hash_script.py +++ b/doc/_includes/parallel_hash_script.py @@ -49,9 +49,7 @@ if this_task['sequence'] == 0: # Now tell the Arvados API server that this task executed successfully, # even though it doesn't have any output. - arvados.api().job_tasks().update(uuid=arvados.current_task()['uuid'], - body={'success':True} - ).execute() + this_task.set_output(None) else: # The task sequence was not 0, so it must be a parallel worker task # created by the first task diff --git a/doc/_layouts/default.html b/doc/_layouts/default.html index b2a524e4a5..d190aef4ce 100644 --- a/doc/_layouts/default.html +++ b/doc/_layouts/default.html @@ -8,7 +8,7 @@ - + - + h3. Prerequisites -* Log in to a VM "using SSH":ssh-access.html -* Put an "API token":api-tokens.html in your @ARVADOS_API_TOKEN@ environment variable +* Log in to a VM "using SSH":{{site.basedoc}}/user/getting_started/ssh-access.html +* Put an "API token":{{site.basedoc}}/user/reference/api-tokens.html in your @ARVADOS_API_TOKEN@ environment variable * Put the API host name in your @ARVADOS_API_HOST@ environment variable If everything is set up correctly, the command @arv -h user current@ will display your account information. diff --git a/doc/user/getting_started/check-environment.textile b/doc/user/getting_started/check-environment.textile index c28863e1c7..192338f61e 100644 --- a/doc/user/getting_started/check-environment.textile +++ b/doc/user/getting_started/check-environment.textile @@ -11,7 +11,7 @@ Check that you are able to access the Arvados API server using the following com notextile. 
$ arv user current
-If you receive the message "ARVADOS_API_HOST and ARVADOS_API_TOKEN need to be defined as environment variables", follow the instructions for "getting an API token,":api-tokens.html then return to this document. +If you receive the message "ARVADOS_API_HOST and ARVADOS_API_TOKEN need to be defined as environment variables", follow the instructions for "getting an API token,":{{site.basedoc}}/user/reference/api-tokens.html then return to this document. When @arv user current@ is able to access the API server, it will print out the unique identifier associated with your account. Here is an example (you will receive a different identifier): @@ -44,4 +44,4 @@ This unique identifier represents your identity in the Arvados system and is sim -You are now ready proceed to the first tutorial: "Fetching data from Arvados using Keep.":intro-keep.html +You are now ready proceed to the first tutorial: "Fetching data from Arvados using Keep.":{{site.basedoc}}/user/tutorials/intro-keep.html diff --git a/doc/user/index.textile b/doc/user/index.textile index 0fe81c23af..7dbe511d6c 100644 --- a/doc/user/index.textile +++ b/doc/user/index.textile @@ -34,9 +34,9 @@ foo
  • Code blocks inline with text emphasize specific programs, files, or options that are being discussed.
  • Bold text emphasizes specific items to look when discussing Arvados Workbench pages.
    • -
  • A sequence of steps separated by right arrows (%(rarr)→%) indicate a path the user should follow through the Arvados Workbench to access some piece of information under discussion. The steps indicate a menu, hyperlink, column name, field name, or other label on the page that guide the user where to look or click. +
  • A sequence of steps separated by right arrows (→) indicate a path the user should follow through the Arvados Workbench to access some piece of information under discussion. The steps indicate a menu, hyperlink, column name, field name, or other label on the page that guide the user where to look or click.
    • -Now begin by "accessing the Arvados workbench.":workbench.html +Now begin by "accessing the Arvados workbench.":getting_started/workbench.html diff --git a/doc/user/reference/api-tokens.textile b/doc/user/reference/api-tokens.textile index 1532e9a3df..49fd9a402e 100644 --- a/doc/user/reference/api-tokens.textile +++ b/doc/user/reference/api-tokens.textile @@ -18,7 +18,7 @@ Access the Arvados workbench using this link: Use the menu to navigate to _Access %(rarr)→% API Tokens._ There should be one or more rows. The column *api_token* contains the actual token string that you will use. Copy the value of *api_token* for the first row onto the clipboard. -Next, open a shell on the system on which you intend to use the Arvados client (refer to "Accessing Arvados over ssh":ssh-access.html ) and enter the following (replace the value of @ARVADOS_API_TOKEN@ with the value you copied from the Workbench): +Next, open a shell on the system on which you intend to use the Arvados client (refer to "Accessing Arvados over ssh":{{site.basedoc}}/user/getting_started/ssh-access.html ) and enter the following (replace the value of @ARVADOS_API_TOKEN@ with the value you copied from the Workbench): bc. $ export ARVADOS_API_HOST={{ site.arvados_api_host }} $ export ARVADOS_API_TOKEN=2jv9kd1o39t0pcfu7aueem7a1zjxhak73w90tzq3gx0es7j1ld diff --git a/doc/user/reference/intro-jobs.textile b/doc/user/reference/intro-jobs.textile index 7f9f9687d0..dd51cbc76c 100644 --- a/doc/user/reference/intro-jobs.textile +++ b/doc/user/reference/intro-jobs.textile @@ -2,7 +2,7 @@ layout: default navsection: userguide title: "Reference: Jobs" -navorder: 323 +navorder: 923 --- h1. Reference: Jobs diff --git a/doc/user/tutorials/intro-keep.textile b/doc/user/tutorials/intro-keep.textile index d4b34f29f7..920ad0d610 100644 --- a/doc/user/tutorials/intro-keep.textile +++ b/doc/user/tutorials/intro-keep.textile @@ -9,7 +9,7 @@ h1. Fetching data from Arvados using Keep This tutorial introduces you to the Arvados file storage system. -*This tutorial assumes that you are "logged into an Arvados VM instance":ssh-access.html#login, and have a "working environment.":check-environment.html* +*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.basedoc}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.basedoc}}/user/getting_started/check-environment.html* 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-firstscript.textile b/doc/user/tutorials/tutorial-firstscript.textile index 554185c010..4caec36254 100644 --- a/doc/user/tutorials/tutorial-firstscript.textile +++ b/doc/user/tutorials/tutorial-firstscript.textile @@ -9,7 +9,7 @@ h1. Tutorial: Writing a Crunch script 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":ssh-access.html#login, and have a "working environment.":check-environment.html* +*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.basedoc}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.basedoc}}/user/getting_started/check-environment.html* 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-gatk-variantfiltration.textile b/doc/user/tutorials/tutorial-gatk-variantfiltration.textile index 5083d7470b..06ca3fb18b 100644 --- a/doc/user/tutorials/tutorial-gatk-variantfiltration.textile +++ b/doc/user/tutorials/tutorial-gatk-variantfiltration.textile @@ -9,18 +9,12 @@ h1. Tutorial: GATK VariantFiltration Here you will use the GATK VariantFiltration program to assign pass/fail scores to variants in a VCF file. +*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.basedoc}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.basedoc}}/user/getting_started/check-environment.html* + -h3. Prerequisites - -* Log in to a VM "using SSH":ssh-access.html -* Put an "API token":api-tokens.html in your @ARVADOS_API_TOKEN@ environment variable -* Put the API host name in your @ARVADOS_API_HOST@ environment variable - -If everything is set up correctly, the command @arv -h user current@ will display your account information. - h3. Get the GATK binary distribution. - -h3. Prerequisites - -* Log in to a VM "using SSH":ssh-access.html -* Put an "API token":api-tokens.html in your @ARVADOS_API_TOKEN@ environment variable -* Put the API host name in your @ARVADOS_API_HOST@ environment variable -* Run the @python@ interactive shell. +*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.basedoc}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.basedoc}}/user/getting_started/check-environment.html* If everything is set up correctly, you will be able to import the arvados SDK: