[ARVADOS] updated: 1.3.0-3126-gdc5eea343

Thu Sep 10 15:09:53 UTC 2020

Summary of changes:
 doc/_config.yml                                    |   1 -
 .../about-guide.html.textile.liquid                |  33 ------
 doc/user/index.html.textile.liquid                 | 127 +++------------------
 3 files changed, 17 insertions(+), 144 deletions(-)
 delete mode 100644 doc/user/getting_started/about-guide.html.textile.liquid

       via  dc5eea3434fe1a818958827ec798fcd840c4b262 (commit)
      from  f5dabd0c83ee5412157ca4965f66d1f3bd78a604 (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 dc5eea3434fe1a818958827ec798fcd840c4b262
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Thu Sep 10 11:09:05 2020 -0400

    16601: Drop use cases/features, put welcome back back the way it was
    
    Some version of use cases/features will be incorporated into
    arvados.org instead.
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/doc/_config.yml b/doc/_config.yml
index 5a25aa383..44f8112c1 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -23,7 +23,6 @@ navbar:
   userguide:
     - Welcome:
       - user/index.html.textile.liquid
-      - user/getting_started/about-guide.html.textile.liquid
       - user/getting_started/community.html.textile.liquid
     - Walkthough:
       - user/tutorials/wgs-tutorial.html.textile.liquid
diff --git a/doc/user/getting_started/about-guide.html.textile.liquid b/doc/user/getting_started/about-guide.html.textile.liquid
deleted file mode 100644
index c6a96fa03..000000000
--- a/doc/user/getting_started/about-guide.html.textile.liquid
+++ /dev/null
@@ -1,33 +0,0 @@
----
-layout: default
-navsection: userguide
-title: About this guide
-...
-{% comment %}
-Copyright (C) The Arvados Authors. All rights reserved.
-
-SPDX-License-Identifier: CC-BY-SA-3.0
-{% endcomment %}
-
-This guide provides a reference for using Arvados to solve scientific big data problems.
-
-The examples in this guide use the Arvados instance located at <a href="{{site.arvados_workbench_host}}/" target="_blank">{{site.arvados_workbench_host}}</a>.  If you are using a different Arvados instance replace @{{ site.arvados_workbench_host }}@ with your private instance in all of the examples in this guide.
-
-h2. Typographic conventions
-
-This manual uses the following typographic conventions:
-
-<notextile>
-<ul>
-<li>Code blocks which are set aside from the text indicate user input to the system.  Commands that should be entered into a Unix shell are indicated by the directory where you should  enter the command ('~' indicates your home directory) followed by '$', followed by the highlighted <span class="userinput">command to enter</span> (do not enter the '$'), and possibly followed by example command output in black.  For example, the following block indicates that you should type <code>ls foo.*</code> while in your home directory and the expected output will be "foo.input" and "foo.output".
-<pre><code>~$ <span class="userinput">ls foo.*</span>
-foo.input foo.output
-</code></pre>
-</li>
-
-<li>Code blocks inline with text emphasize specific <code>programs</code>, <code>files</code>, or <code>options</code> that are being discussed.</li>
-<li>Bold text emphasizes <b>specific items</b> to review on Arvados Workbench pages.</li>
-<li>A sequence of steps separated by right arrows (<span class="rarr">→</span>) indicate a path the user should follow through the Arvados Workbench.  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.
-</li>
-</ul>
-</notextile>
diff --git a/doc/user/index.html.textile.liquid b/doc/user/index.html.textile.liquid
index 414c9681c..e24afc9a4 100644
--- a/doc/user/index.html.textile.liquid
+++ b/doc/user/index.html.textile.liquid
@@ -11,118 +11,25 @@ SPDX-License-Identifier: CC-BY-SA-3.0
 
 Arvados is an "open source":copying/copying.html platform for managing, processing, and sharing genomic and other large scientific and biomedical data.  With Arvados, bioinformaticians run and scale compute-intensive workflows, developers create biomedical applications, and IT administrators manage large compute and storage resources.
 
-<div class="container">
-<div class="row">
-<div class="col-sm-5">
-h3. Flexibility
+This guide provides a reference for using Arvados to solve scientific big data problems.
 
-Run anywhere — in the cloud on AWS, Azure and GCP, as well as on premise and hybrid clusters. Scale compute resources dynamically, as needed.
-</div>
+The examples in this guide use the Arvados instance located at <a href="{{site.arvados_workbench_host}}/" target="_blank">{{site.arvados_workbench_host}}</a>.  If you are using a different Arvados instance replace @{{ site.arvados_workbench_host }}@ with your private instance in all of the examples in this guide.
 
-<div class="col-sm-5">
-h3. Scale
+h2. Typographic conventions
 
-Manage petabytes of data and run workflows that use thousands of cores of compute simultaneously.
-</div>
-</div>
+This manual uses the following typographic conventions:
 
-<div class="row">
-<div class="col-sm-5">
-h3. Freedom
+<notextile>
+<ul>
+<li>Code blocks which are set aside from the text indicate user input to the system.  Commands that should be entered into a Unix shell are indicated by the directory where you should  enter the command ('~' indicates your home directory) followed by '$', followed by the highlighted <span class="userinput">command to enter</span> (do not enter the '$'), and possibly followed by example command output in black.  For example, the following block indicates that you should type <code>ls foo.*</code> while in your home directory and the expected output will be "foo.input" and "foo.output".
+<pre><code>~$ <span class="userinput">ls foo.*</span>
+foo.input foo.output
+</code></pre>
+</li>
 
-Use 100% free and open software that you can control. Software that is developed in public, backed by both strong commercial support and an active community.
-</div>
-
-<div class="col-sm-5">
-h3. Confidence
-
-Be confident in your results. Easily identify the origin and verify the content of every dataset. Track every CWL workflow you run, reliably reproducing any output.
-</div>
-</div>
-
-<div class="row">
-<div class="col-sm-5">
-h3. Decentralization
-
-Run on distributed data using federated multi-cluster workflows. Federation brings compute to the data, allowing you to work on sequestered data and avoid expensive data transfers.
-</div>
-
-<div class="col-sm-5">
-h3. Security
-
-Collaborate on projects by selectively and securely sharing your data and workflows. Share with the world by publishing your results.
-</div>
-</div>
-</div>
-
-h2. Some uses of Arvados
-
-A lab performing human whole genome DNA sequencing uses Arvados to analyze data directly from the sequencer.  The data is uploaded to the cloud as it is generated, so that when the sequencer is finished, the analysis workflow begins immediately to perform alignment, variant calling and report generation.
-
-A multi-national biotech company uses Arvados to store and analyze research data, with clusters on different continents.  Arvados permissions enable them to control which research groups can access which data, while federation features enable them to search and link their data across all their clusters.
-
-A research consortium uses Arvados for storage, data cleaning, and training machine learning models to identify candidate genes that are risk factors for a major illness.
-
-A resource for publishing and analyzing sequences of a deadly virus uses Arvados to catalog sequence data and run analysis to construct a pangenome graph of viral variants.
-
-A hospital uses Arvados in precision oncology, to run workflows that analyze cancer tumors in order to select personalized courses of treatment.
-
-A long-running university study uses Arvados to archive data and make it available for public download.
-
-A research group stores digital pathology image files in Arvados.  The researchers use third party software to view the image files, with integration based on Arvados support for the S3 API.
-
-A bioinformatics graduate student uses Arvados to access compute resources in the cloud without needing to become an AWS or Azure expert, and avoids a huge cloud bill by efficiently using storage and compute resources.
-
-A company seeking regulatory approval for a treatment uses Arvados to analyze data showing efficacy.  The company submits well-documented results to the regulator including the input data, the workflow that produced the results, and a provenance trace from Arvados showing how the results were obtained.
-
-A company requiring GxP compliance for data storage and analysis platform chooses Arvados.  The compliance process goes smoothly because Arvados follows security best practices and can flexibly implement different access control policies.
-
-h2. Features and capabilities of Arvados
-
-h3. File management (Keep)
-
-* Provides robust storage of very large files, with end-to-end integrity checking.
-* Files are organized into collections and projects, and shared with users and groups.
-* Files stored in Arvados can be accessed through the Arvados API, mounted as a "file system":tutorials/tutorial-keep-mount-gnu-linux.html , over HTTP with the WebDAV protocol, and S3-API compatible endpoint.
-* Supports storage backends including POSIX file system, AWS S3 (and S3-API compatible endpoints) and Azure blob store.
-* Data access is independent of storage backend, and data can be transparently migrated between different backend storage systems.
-* Can add and query metadata properties on collections.
-* Collections can be referenced with a immutable hash-based identifier called a "portable data hash", similar to a git commit.
-* Collections can record a version history of changes.
-* Optimizes storage costs by de-duplicating data.  Files can be referenced in multiple collections without being stored multiple times.
-
-h3. Compute management (Crunch)
-
-* Runs "Common Workflow Language":https://commonwl.org workflows.
-* Workflow steps run in parallel, with work dispatched to cloud (AWS or Azure) or a SLURM cluster.
-* Manages the full elastic compute lifecycle on cloud, with instances created, scheduled and shut down based on demand.
-* Supports AWS preemptable instances.
-* Optimizes costs by running on the cheapest instance that meets workflow requirements.
-* Workflow steps runs in a container.
-* Records input files, output files, logs, and container image with immutable hash-based identifiers.
-* Optimizes compute costs by re-using past results where workflow steps are identical, while avoiding mistakes by detecting when inputs have changed.
-* Displays streaming logs to monitor progress of workflow steps in real time.
-* Collects resource usage (CPU/RAM/disk/network) statistics for each workflow step.
-
-h3. User interface and integration
-
-* Web interface enables users to upload, download, and manage files, and to run workflows.
-* Has command line tools that are useful power users, batch operations, and automation.
-* Provides a variety of APIs and SDKs for integration or developing applications on top of Arvados.
-* Software development kits are available for Python, R, Go, Java, Ruby.
-* Manage access to git repositories using Arvados permissions.
-* Manage access to shell accounts using Arvados permissions.
-
-h3. Federated computing
-
-* Users can have a consistent identity across a network of Arvados clusters.
-* Users can search across federated Arvados clusters.
-* Clients can access data hosted on other federated clusters with their "home cluster" identity and credentials.
-* Workflow steps can be dispatched to run on other clusters in the federation to optimize for data locality or regulatory compliance.
-
-h3. Installation and management
-
-* Has regular releases, packaged for popular Linux distributions including Debian, Ubuntu, and Centos.
-* Has extensive documentation for installation, configuration, and administration.
-* Has formulas to manage a cluster using SaltStack
-* Managed installations, commercial support, and software development for Arvados available through Curii Corporation.  Contact "info at curii.com":mailto:info at curii.com .
+<li>Code blocks inline with text emphasize specific <code>programs</code>, <code>files</code>, or <code>options</code> that are being discussed.</li>
+<li>Bold text emphasizes <b>specific items</b> to review on Arvados Workbench pages.</li>
+<li>A sequence of steps separated by right arrows (<span class="rarr">→</span>) indicate a path the user should follow through the Arvados Workbench.  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.
+</li>
+</ul>
+</notextile>

-----------------------------------------------------------------------


hooks/post-receive
-- 


