[arvados] created: 2.6.0-363-g0e21f0f4f
git repository hosting
git at public.arvados.org
Fri Jul 7 21:20:24 UTC 2023
at 0e21f0f4f9a5f828a339894bc8eb1882a42946ab (commit)
commit 0e21f0f4f9a5f828a339894bc8eb1882a42946ab
Author: Brett Smith <brett.smith at curii.com>
Date: Fri Jul 7 17:19:13 2023 -0400
20684: Note tutorial expectations for all Crunch CLI tools
Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith at curii.com>
diff --git a/doc/user/cwl/costanalyzer.html.textile.liquid b/doc/user/cwl/costanalyzer.html.textile.liquid
index c435916e3..1d20c85f5 100644
--- a/doc/user/cwl/costanalyzer.html.textile.liquid
+++ b/doc/user/cwl/costanalyzer.html.textile.liquid
@@ -9,6 +9,8 @@ Copyright (C) The Arvados Authors. All rights reserved.
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
+{% include 'tutorial_expectations' %}
+
{% include 'notebox_begin' %}
This is only applicable when Arvados runs in a cloud environment and @arvados-dispatch-cloud@ is used to dispatch @crunch@ jobs. The per node-hour price for each defined InstanceType most be supplied in "config.yml":{{site.baseurl}}/admin/config.html.
diff --git a/doc/user/cwl/crunchstat-summary.html.textile.liquid b/doc/user/cwl/crunchstat-summary.html.textile.liquid
index 6d03bfa7b..55bc702b6 100644
--- a/doc/user/cwl/crunchstat-summary.html.textile.liquid
+++ b/doc/user/cwl/crunchstat-summary.html.textile.liquid
@@ -9,6 +9,8 @@ Copyright (C) The Arvados Authors. All rights reserved.
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
+{% include 'tutorial_expectations' %}
+
The @crunchstat-summary@ tool can be used to analyze workflow and container performance. It can be installed from packages (@apt install python3-crunchstat-summary@ or @yum install rh-python36-python-crunchstat-summary@), or in a Python virtualenv (@pip install crunchstat_summary@). @crunchstat-summary@ analyzes the crunchstat lines from the logs of a container or workflow and generates a report in text or html format.
h2(#syntax). Syntax
diff --git a/doc/user/debugging/container-shell-access.html.textile.liquid b/doc/user/debugging/container-shell-access.html.textile.liquid
index 91347e66f..9c2498004 100644
--- a/doc/user/debugging/container-shell-access.html.textile.liquid
+++ b/doc/user/debugging/container-shell-access.html.textile.liquid
@@ -9,6 +9,8 @@ Copyright (C) The Arvados Authors. All rights reserved.
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
+{% include 'tutorial_expectations' %}
+
{% include 'notebox_begin' %}
To use this feature, your Arvados installation must be configured to allow container shell access. See "the install guide":{{site.baseurl}}/install/container-shell-access.html for more information.
commit d457f4781318aa4428830742c9956c427b2ca4ff
Author: Brett Smith <brett.smith at curii.com>
Date: Fri Jul 7 17:18:15 2023 -0400
20684: Note crunchstat-summary can be installed in a virtualenv
Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith at curii.com>
diff --git a/doc/user/cwl/crunchstat-summary.html.textile.liquid b/doc/user/cwl/crunchstat-summary.html.textile.liquid
index adeb9e7fe..6d03bfa7b 100644
--- a/doc/user/cwl/crunchstat-summary.html.textile.liquid
+++ b/doc/user/cwl/crunchstat-summary.html.textile.liquid
@@ -9,7 +9,7 @@ Copyright (C) The Arvados Authors. All rights reserved.
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
-The @crunchstat-summary@ tool can be used to analyze workflow and container performance. It can be installed from packages (@apt install python3-crunchstat-summary@ or @yum install rh-python36-python-crunchstat-summary@). @crunchstat-summary@ analyzes the crunchstat lines from the logs of a container or workflow and generates a report in text or html format.
+The @crunchstat-summary@ tool can be used to analyze workflow and container performance. It can be installed from packages (@apt install python3-crunchstat-summary@ or @yum install rh-python36-python-crunchstat-summary@), or in a Python virtualenv (@pip install crunchstat_summary@). @crunchstat-summary@ analyzes the crunchstat lines from the logs of a container or workflow and generates a report in text or html format.
h2(#syntax). Syntax
commit 69994ab5950595ba50abdb616004dcb3b99566c0
Author: Brett Smith <brett.smith at curii.com>
Date: Fri Jul 7 17:03:46 2023 -0400
20684: Copyedit tutorial expectations include
* Fix run-on sentence
* Clean up punctuation spacing
Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith at curii.com>
diff --git a/doc/_includes/_tutorial_expectations.liquid b/doc/_includes/_tutorial_expectations.liquid
index d4d05078f..3499b5930 100644
--- a/doc/_includes/_tutorial_expectations.liquid
+++ b/doc/_includes/_tutorial_expectations.liquid
@@ -5,5 +5,5 @@ SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
{% include 'notebox_begin' %}
-This tutorial assumes that you have access to the "Arvados command line tools":{{ site.baseurl }}/user/getting_started/setup-cli.html and have set the "API token":{{site.baseurl}}/user/reference/api-tokens.html and confirmed a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html .
+This tutorial assumes that you have access to "Arvados command line tools":{{ site.baseurl }}/user/getting_started/setup-cli.html, configured your "API token":{{site.baseurl}}/user/reference/api-tokens.html, and confirmed a "working environment":{{site.baseurl}}/user/getting_started/check-environment.html.
{% include 'notebox_end' %}
commit 531475b372ee4052f24d4931095ef4f0dd632507
Author: Brett Smith <brett.smith at curii.com>
Date: Fri Jul 7 16:57:38 2023 -0400
20684: Expand "Getting started at the command line" documentation
* Add more structure to the page
* Be explicit that we usually recommend using a VM
* Highlight that using our package repository is the simplest way to
install tools
* List all the tools you can install, with more details
Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith at curii.com>
diff --git a/doc/user/getting_started/setup-cli.html.textile.liquid b/doc/user/getting_started/setup-cli.html.textile.liquid
index 46ea770ef..999f848c1 100644
--- a/doc/user/getting_started/setup-cli.html.textile.liquid
+++ b/doc/user/getting_started/setup-cli.html.textile.liquid
@@ -11,10 +11,35 @@ SPDX-License-Identifier: CC-BY-SA-3.0
Many operations in Arvados can be performed using either the web Workbench or through command line tools. Some operations can only be done using the command line.
-To use the command line tools, you can either log into an Arvados-managed VM instance where those tools are pre-installed, or install the Arvados tools on your own system.
+To use the command line tools, you can either log into an Arvados virtual machine where those tools are pre-installed, or install the Arvados tools on your own system.
-To log into an Arvados-managed VM, see instructions for "Webshell":{{site.baseurl}}/user/getting_started/vm-login-with-webshell.html or "Unix":{{site.baseurl}}/user/getting_started/ssh-access-unix.html or "Windows":{{site.baseurl}}/user/getting_started/ssh-access-windows.html .
+h2. Option 1: Using an Arvados virtual machine
-To install the Arvados tools on your own system, you should install the "Command line SDK":{{site.baseurl}}/sdk/cli/install.html (requires Ruby) and "Python SDK":{{site.baseurl}}/sdk/python/sdk-python.html (requires Python). You may also want to install "arvados-cwl-runner":{{site.baseurl}}/sdk/python/arvados-cwl-runner.html to submit workflows and "arvados-fuse":{{site.baseurl}}/sdk/python/arvados-fuse.html to mount keep as a filesystem.
+This is the command line interface we recommend for most day-to-day work, because the tools are all preinstalled and preconfigured for you. You can log in to any virtual machine where you have permission by using:
-Once you are logged in or have command line tools installed, see "getting an API token":{{site.baseurl}}/user/reference/api-tokens.html and "check your environment":{{site.baseurl}}/user/getting_started/check-environment.html .
+* "the Webshell client":{{site.baseurl}}/user/getting_started/vm-login-with-webshell.html accessible through Arvados Workbench
+* "Unix SSH clients":{{site.baseurl}}/user/getting_started/ssh-access-unix.html
+* "Windows SSH clients":{{site.baseurl}}/user/getting_started/ssh-access-windows.html
+
+h2. Option 2: Installing Arvados tools on your own system
+
+This option gives you more flexibility in your work, but takes more time to set up.
+
+h3. Configure Arvados package repositories for your system
+
+Doing this isn't strictly required for most tools, but will streamline the installation process. Follow the "Arvados package repository instructions":{{site.baseurl}}/install/packages.html.
+
+h3. Install individual tool packages
+
+Here are the client packages you can install on your system. You can skip any you don't want or need except for the Python SDK (most other tools require it).
+
+* "Python SDK":{{site.baseurl}}/sdk/python/sdk-python.html: This provides an Arvados API client in Python, as well as low-level command line tools.
+* "Command-line SDK":{{site.baseurl}}/sdk/cli/install.html: This provides the high-level @arv@ command and user interface to the Arvados API.
+* "FUSE Driver":{{site.baseurl}}/sdk/python/arvados-fuse.html: This provides the @arv-mount@ command and FUSE driver that lets you access Keep using standard Linux filesystem tools.
+* "CWL Runner":{{site.baseurl}}/sdk/python/arvados-cwl-runner.html: This provides the @arvados-cwl-runner@ command to register and run workflows in Crunch.
+* "crunchstat-summary":{{site.baseurl}}/user/cwl/crunchstat-summary.html: This tool provides performance reports for Crunch containers.
+* "arvados-client":{{site.baseurl}}/user/debugging/container-shell-access.html: This tool provides subcommands for inspecting Crunch containers, both interactively while they're running and after they've finished.
+
+h2. After Installation: Check your environment
+
+Once you are logged in or have command line tools installed, move on to "getting an API token":{{site.baseurl}}/user/reference/api-tokens.html and "checking your environment":{{site.baseurl}}/user/getting_started/check-environment.html.
commit e450259e10ade43c5f24772896bb0f1fdc892cc8
Author: Brett Smith <brett.smith at curii.com>
Date: Fri Jul 7 16:27:19 2023 -0400
20684: Clean up FUSE references in a-c-r install instructions
It looks like this page started as a copy of the corresponding FUSE
page, and we didn't update all the references.
Arvados-DCO-1.1-Signed-off-by: Brett Smith <brett.smith at curii.com>
diff --git a/doc/sdk/python/arvados-cwl-runner.html.textile.liquid b/doc/sdk/python/arvados-cwl-runner.html.textile.liquid
index 1cfbd6054..b721b4f1e 100644
--- a/doc/sdk/python/arvados-cwl-runner.html.textile.liquid
+++ b/doc/sdk/python/arvados-cwl-runner.html.textile.liquid
@@ -10,17 +10,17 @@ Copyright (C) The Arvados Authors. All rights reserved.
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
-The Arvados FUSE driver is a Python utility that allows you to see the Keep service as a normal filesystem, so that data can be accessed using standard tools. This driver requires the Python SDK installed in order to access Arvados services.
+The Arvados CWL Runner is a Python tool that allows you to register and submit workflows to Arvados. You can oversee a running workflow on your local system, or let that run inside an Arvados container. This tool requires the Python SDK installed in order to access Arvados services.
h2. Installation
-If you are logged in to a managed Arvados VM, the @arv-mount@ utility should already be installed.
+If you are logged in to a managed Arvados VM, the @arvados-cwl-runner@ utility should already be installed.
-To use the FUSE driver elsewhere, you can install from a distribution package, or PyPI.
+To use the CWL Runner elsewhere, you can install it from a distribution package or PyPI.
h2. Option 1: Install from distribution packages
-First, "add the appropriate package repository for your distribution":{{ site.baseurl }}/install/packages.html
+First, "add the appropriate package repository for your distribution":{{ site.baseurl }}/install/packages.html.
{% assign arvados_component = 'python3-arvados-cwl-runner' %}
@@ -32,13 +32,14 @@ Run @pip install arvados-cwl-runner@ in an appropriate installation environment,
Note:
-The SDK uses @pycurl@ which depends on the @libcurl@ C library. To build the module you may have to first install additional packages. On Debian 10 this is:
+The Python SDK uses @pycurl@ which depends on the @libcurl@ C library. To build the module you may have to first install additional packages. On Debian 10 this is:
-<pre>
-$ apt-get install git build-essential python3-dev libcurl4-openssl-dev libssl1.0-dev python3-llfuse
-</pre>
+<notextile>
+<pre><code># <span class="userinput">apt-get install git build-essential python3-dev libcurl4-openssl-dev libssl1.0-dev</span>
+</code></pre>
+</notextile>
-h3. Check Docker access
+h2. Check Docker access
In order to pull and upload Docker images, @arvados-cwl-runner@ requires access to Docker. You do not need Docker if the Docker images you intend to use are already available in Arvados.
@@ -66,6 +67,6 @@ Server:
If this returns an error, contact the sysadmin of your cluster for assistance.
-h3. Usage
+h2. Usage
-Please refer to the "Accessing Keep from GNU/Linux":{{site.baseurl}}/user/tutorials/tutorial-keep-mount-gnu-linux.html tutorial for more information.
+Please refer to the "Starting a Workflow at the Command Line":{{site.baseurl}}/user/cwl/cwl-runner.html tutorial for more information.
-----------------------------------------------------------------------
hooks/post-receive
--
More information about the arvados-commits
mailing list