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Fix some issues after the removal of agave
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Joe Stubbs committed Aug 22, 2019
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4 changes: 2 additions & 2 deletions docs/agave/archive/tutorials/_app-management-tutorial.md.erb
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An app, in the context of Tapis, is an executable code available for invocation through Tapis's Jobs service on a specific execution system. Put another way, an app is a piece of code that you can run on a specific system. If a single code needs to be run on multiple systems, each combination of app and system needs to be defined as an app.

Apps are language agnostic and may or may not carry with them their own dependencies. (More on bundling your app in a moment.) Any code that can be forked at the command line or submitted to a batch scheduler can be registered as an Tapis app and run through the Jobs service.
Apps are language agnostic and may or may not carry with them their own dependencies. (More on bundling your app in a moment.) Any code that can be forked at the command line or submitted to a batch scheduler can be registered as a Tapis app and run through the Jobs service.

The Apps service is the central registry for all Tapis apps. The Apps service provides permissions, validation, archiving, and revision information about each app in addition to the usual discovery capability. The rest of this tutorial explains in detail how to register an app to the Apps service, how to manage and share apps, and what the different application scopes mean.

Expand Down Expand Up @@ -244,7 +244,7 @@ Now that you have your app bundled up and ready to go, it is time to register it

<p class="table-caption">Table 1. Attributes of a JSON app description.</p>

Table 1 lists the top level attributes of an Tapis app descxription. App descriptions are conceptually broken into three section: details, arguments, and outputs. App details include generic information common to all apps such as the name, description, label, etc. Note that the name and version are combined and used to uniquely identify your app globally. One implication of this is that there is no concept of enforced application taxonomy in the API. Historically users have used a naming convention to imply a logical grouping and the version field with a <a href="http://semver.org/" title="Semantic Versioning" target="_blank">Semantic Versioning</a> value of x.y.z to denote changes over time.
Table 1 lists the top level attributes of a Tapis app descxription. App descriptions are conceptually broken into three section: details, arguments, and outputs. App details include generic information common to all apps such as the name, description, label, etc. Note that the name and version are combined and used to uniquely identify your app globally. One implication of this is that there is no concept of enforced application taxonomy in the API. Historically users have used a naming convention to imply a logical grouping and the version field with a <a href="http://semver.org/" title="Semantic Versioning" target="_blank">Semantic Versioning</a> value of x.y.z to denote changes over time.

<aside class="notice">Note that the name and version are combined and used to uniquely identify your app globally. </aside>

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10 changes: 5 additions & 5 deletions docs/agave/archive/tutorials/app-management-tutorial/_app-development-tutorial.rst
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:format: html


We will now go through the process of building and deploying an Tapis application to provide 'samtools sort' functionality on TACC's Stampede system. The following tutorial assumes you have properly installed and configured the iPlant SDK on Stampede. They assume you have defined an environment variable IPLANTUSERNAME as your iPlant username (e.g. IPLANTUSERNAME=youriplantusername).
We will now go through the process of building and deploying a Tapis application to provide 'samtools sort' functionality on TACC's Stampede system. The following tutorial assumes you have properly installed and configured the iPlant SDK on Stampede. They assume you have defined an environment variable IPLANTUSERNAME as your iPlant username (e.g. IPLANTUSERNAME=youriplantusername).

Tapis application packaging
---------------------------
Expand Down Expand Up @@ -30,7 +30,7 @@ package-name-version.dot.dot
<ol>
<li>Build the application locally on the executionSystem</li>
<li>Ensure that you are able to run it directly on the executionSystem</li>
<li>Describe the application using an Tapis app description</li>
<li>Describe the application using a Tapis app description</li>
<li>Create a shell template for running the app</li>
<li>Upload the application directory to a storageSystem</li>
<li>Post the app description to the Tapis apps service</li>
Expand Down Expand Up @@ -190,9 +190,9 @@ You can monitor your jobs in the queue using
showq -u your_tacc_username
Assuming all goes according to plan, you'll end up with a sorted BAM called :raw-html-m2r:`<em>sorted.bam</em>`\ , and your bin directory (but not the bin.tgz file) should be erased. Congratulations, you're in the home stretch: it's time to turn the test script into an Tapis app.
Assuming all goes according to plan, you'll end up with a sorted BAM called :raw-html-m2r:`<em>sorted.bam</em>`\ , and your bin directory (but not the bin.tgz file) should be erased. Congratulations, you're in the home stretch: it's time to turn the test script into a Tapis app.

Craft an Tapis app description
Craft a Tapis app description
------------------------------

In order for Tapis to know how to run an instance of the application, we need to provide quite a bit of metadata about the application. This includes a unique name and version, the location of the application bundle, the identities of the execution system and destination system for results, whether its an HPC or other kind of job, the default number of processors and memory it needs to run, and of course, all the inputs and parameters for the actual program. It seems a bit over-complicated, but only because you're comfortable with the command line already. Your goal here is to allow your applications to be portable across systems and present a web-enabled, rationalized interface for your code to consumers.
Expand Down Expand Up @@ -261,7 +261,7 @@ Each time you (or another user) requests an instance of samtools sort, Tapis cop

.. raw:: html

<aside class="notice">If you've never deployed an Tapis-based app, you may not have an applications directory in your home folder. Since this is where we recommend you store the apps, create one.</aside>
<aside class="notice">If you've never deployed a Tapis-based app, you may not have an applications directory in your home folder. Since this is where we recommend you store the apps, create one.</aside>


.. code-block:: shell
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10 changes: 5 additions & 5 deletions docs/agave/archive/tutorials/app-management-tutorial/_app-wrapper-tutorial.rst
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Expand Up @@ -89,7 +89,7 @@ package-name-version.dot.dot
1. Build the application locally on the executionSystem
2. Ensure that you are able to run it directly on the executionSystem
3. Describe the application using an Tapis app description
3. Describe the application using a Tapis app description
4. Create a shell template for running the app
5. Upload the application directory to a storageSystem
6. Post the app description to the Tapis apps service
Expand Down Expand Up @@ -241,9 +241,9 @@ You can monitor your jobs in the queue using
showq -u your_tacc_username
Assuming all goes according to plan, you'll end up with a sorted BAM called :raw-html-m2r:`<em>sorted.bam</em>`\ , and your bin directory (but not the bin.tgz file) should be erased. Congratulations, you're in the home stretch: it's time to turn the test script into an Tapis app.
Assuming all goes according to plan, you'll end up with a sorted BAM called :raw-html-m2r:`<em>sorted.bam</em>`\ , and your bin directory (but not the bin.tgz file) should be erased. Congratulations, you're in the home stretch: it's time to turn the test script into a Tapis app.
Craft an Tapis app description
Craft a Tapis app description
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
In order for Tapis to know how to run an instance of the application, we need to provide quite a bit of metadata about the application. This includes a unique name and version, the location of the application bundle, the identities of the execution system and destination system for results, whether its an HPC or other kind of job, the default number of processors and memory it needs to run, and of course, all the inputs and parameters for the actual program. It seems a bit over-complicated, but only because you're comfortable with the command line already. Your goal here is to allow your applications to be portable across systems and present a web-enabled, rationalized interface for your code to consumers.
Expand All @@ -260,7 +260,7 @@ Open up samtools-sort.json in a text editor or :raw-html-m2r:`<a href="../exampl
Overview
^^^^^^^^
Your file :raw-html-m2r:`<em>samtools-sort.json</em>` is written in :raw-html-m2r:`<a href="http://www.json.org/">JSON</a>`\ , and conforms to an Tapis-specific data model. You can find fully fleshed out details about all fields under :raw-html-m2r:`<em>Parameters -> Data Type -> Model</em>` at the :raw-html-m2r:`<a href="http://agaveapi.co/live-docs/#!/apps/add_post_1">Tapis API live docs on the /apps service</a>`. We will dive into key elements here:
Your file :raw-html-m2r:`<em>samtools-sort.json</em>` is written in :raw-html-m2r:`<a href="http://www.json.org/">JSON</a>`\ , and conforms to a Tapis-specific data model. You can find fully fleshed out details about all fields under :raw-html-m2r:`<em>Parameters -> Data Type -> Model</em>` at the :raw-html-m2r:`<a href="http://agaveapi.co/live-docs/#!/apps/add_post_1">Tapis API live docs on the /apps service</a>`. We will dive into key elements here:
To make this file work for you, you will be, at a minimum, editting:
Expand Down Expand Up @@ -351,7 +351,7 @@ Application metadata
<td>executionSystem</td>
<td>X</td>
<td>string</td>
<td>An Tapis-registered EXECUTION system upon which you have execute and app registration permissions where jobs will run</td>
<td>a Tapis-registered EXECUTION system upon which you have execute and app registration permissions where jobs will run</td>
</tr>
<tr>
<td>helpURI</td>
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4 changes: 2 additions & 2 deletions docs/agave/documentation/user-guide/_app-management-tutorial.md.erb
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

An app, in the context of Tapis, is an executable code available for invocation through Tapis's Jobs service on a specific execution system. Put another way, an app is a piece of code that you can run on a specific system. If a single code needs to be run on multiple systems, each combination of app and system needs to be defined as an app.

Apps are language agnostic and may or may not carry with them their own dependencies. (More on bundling your app in a moment.) Any code that can be forked at the command line or submitted to a batch scheduler can be registered as an Tapis app and run through the Jobs service.
Apps are language agnostic and may or may not carry with them their own dependencies. (More on bundling your app in a moment.) Any code that can be forked at the command line or submitted to a batch scheduler can be registered as a Tapis app and run through the Jobs service.

The Apps service is the central registry for all Tapis apps. The Apps service provides permissions, validation, archiving, and revision information about each app in addition to the usual discovery capability. The rest of this tutorial explains in detail how to register an app to the Apps service, how to manage and share apps, and what the different application scopes mean.

Expand Down Expand Up @@ -244,7 +244,7 @@ Now that you have your app bundled up and ready to go, it is time to register it

<p class="table-caption">Table 1. Attributes of a JSON app description.</p>

Table 1 lists the top level attributes of an Tapis app descxription. App descriptions are conceptually broken into three section: details, arguments, and outputs. App details include generic information common to all apps such as the name, description, label, etc. Note that the name and version are combined and used to uniquely identify your app globally. One implication of this is that there is no concept of enforced application taxonomy in the API. Historically users have used a naming convention to imply a logical grouping and the version field with a <a href="http://semver.org/" title="Semantic Versioning" target="_blank">Semantic Versioning</a> value of x.y.z to denote changes over time.
Table 1 lists the top level attributes of a Tapis app descxription. App descriptions are conceptually broken into three section: details, arguments, and outputs. App details include generic information common to all apps such as the name, description, label, etc. Note that the name and version are combined and used to uniquely identify your app globally. One implication of this is that there is no concept of enforced application taxonomy in the API. Historically users have used a naming convention to imply a logical grouping and the version field with a <a href="http://semver.org/" title="Semantic Versioning" target="_blank">Semantic Versioning</a> value of x.y.z to denote changes over time.

<aside class="notice">Note that the name and version are combined and used to uniquely identify your app globally. </aside>

Expand Down
10 changes: 5 additions & 5 deletions .../documentation/user-guide/app-management-tutorial/_app-development-tutorial.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
:format: html


We will now go through the process of building and deploying an Tapis application to provide 'samtools sort' functionality on TACC's Stampede system. The following tutorial assumes you have properly installed and configured the iPlant SDK on Stampede. They assume you have defined an environment variable IPLANTUSERNAME as your iPlant username (e.g. IPLANTUSERNAME=youriplantusername).
We will now go through the process of building and deploying a Tapis application to provide 'samtools sort' functionality on TACC's Stampede system. The following tutorial assumes you have properly installed and configured the iPlant SDK on Stampede. They assume you have defined an environment variable IPLANTUSERNAME as your iPlant username (e.g. IPLANTUSERNAME=youriplantusername).

Tapis application packaging
---------------------------
Expand Down Expand Up @@ -30,7 +30,7 @@ package-name-version.dot.dot
<ol>
<li>Build the application locally on the executionSystem</li>
<li>Ensure that you are able to run it directly on the executionSystem</li>
<li>Describe the application using an Tapis app description</li>
<li>Describe the application using a Tapis app description</li>
<li>Create a shell template for running the app</li>
<li>Upload the application directory to a storageSystem</li>
<li>Post the app description to the Tapis apps service</li>
Expand Down Expand Up @@ -190,9 +190,9 @@ You can monitor your jobs in the queue using
showq -u your_tacc_username
Assuming all goes according to plan, you'll end up with a sorted BAM called :raw-html-m2r:`<em>sorted.bam</em>`\ , and your bin directory (but not the bin.tgz file) should be erased. Congratulations, you're in the home stretch: it's time to turn the test script into an Tapis app.
Assuming all goes according to plan, you'll end up with a sorted BAM called :raw-html-m2r:`<em>sorted.bam</em>`\ , and your bin directory (but not the bin.tgz file) should be erased. Congratulations, you're in the home stretch: it's time to turn the test script into a Tapis app.

Craft an Tapis app description
Craft a Tapis app description
------------------------------

In order for Tapis to know how to run an instance of the application, we need to provide quite a bit of metadata about the application. This includes a unique name and version, the location of the application bundle, the identities of the execution system and destination system for results, whether its an HPC or other kind of job, the default number of processors and memory it needs to run, and of course, all the inputs and parameters for the actual program. It seems a bit over-complicated, but only because you're comfortable with the command line already. Your goal here is to allow your applications to be portable across systems and present a web-enabled, rationalized interface for your code to consumers.
Expand Down Expand Up @@ -261,7 +261,7 @@ Each time you (or another user) requests an instance of samtools sort, Tapis cop

.. raw:: html

<aside class="notice">If you've never deployed an Tapis-based app, you may not have an applications directory in your home folder. Since this is where we recommend you store the apps, create one.</aside>
<aside class="notice">If you've never deployed a Tapis-based app, you may not have an applications directory in your home folder. Since this is where we recommend you store the apps, create one.</aside>


.. code-block:: shell
Expand Down
10 changes: 5 additions & 5 deletions ...gave/documentation/user-guide/app-management-tutorial/_app-wrapper-tutorial.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -89,7 +89,7 @@ package-name-version.dot.dot
1. Build the application locally on the executionSystem
2. Ensure that you are able to run it directly on the executionSystem
3. Describe the application using an Tapis app description
3. Describe the application using a Tapis app description
4. Create a shell template for running the app
5. Upload the application directory to a storageSystem
6. Post the app description to the Tapis apps service
Expand Down Expand Up @@ -241,9 +241,9 @@ You can monitor your jobs in the queue using
showq -u your_tacc_username
Assuming all goes according to plan, you'll end up with a sorted BAM called :raw-html-m2r:`<em>sorted.bam</em>`\ , and your bin directory (but not the bin.tgz file) should be erased. Congratulations, you're in the home stretch: it's time to turn the test script into an Tapis app.
Assuming all goes according to plan, you'll end up with a sorted BAM called :raw-html-m2r:`<em>sorted.bam</em>`\ , and your bin directory (but not the bin.tgz file) should be erased. Congratulations, you're in the home stretch: it's time to turn the test script into a Tapis app.
Craft an Tapis app description
Craft a Tapis app description
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
In order for Tapis to know how to run an instance of the application, we need to provide quite a bit of metadata about the application. This includes a unique name and version, the location of the application bundle, the identities of the execution system and destination system for results, whether its an HPC or other kind of job, the default number of processors and memory it needs to run, and of course, all the inputs and parameters for the actual program. It seems a bit over-complicated, but only because you're comfortable with the command line already. Your goal here is to allow your applications to be portable across systems and present a web-enabled, rationalized interface for your code to consumers.
Expand All @@ -260,7 +260,7 @@ Open up samtools-sort.json in a text editor or :raw-html-m2r:`<a href="../exampl
Overview
^^^^^^^^
Your file :raw-html-m2r:`<em>samtools-sort.json</em>` is written in :raw-html-m2r:`<a href="http://www.json.org/">JSON</a>`\ , and conforms to an Tapis-specific data model. You can find fully fleshed out details about all fields under :raw-html-m2r:`<em>Parameters -> Data Type -> Model</em>` at the :raw-html-m2r:`<a href="http://agaveapi.co/live-docs/#!/apps/add_post_1">Tapis API live docs on the /apps service</a>`. We will dive into key elements here:
Your file :raw-html-m2r:`<em>samtools-sort.json</em>` is written in :raw-html-m2r:`<a href="http://www.json.org/">JSON</a>`\ , and conforms to a Tapis-specific data model. You can find fully fleshed out details about all fields under :raw-html-m2r:`<em>Parameters -> Data Type -> Model</em>` at the :raw-html-m2r:`<a href="http://agaveapi.co/live-docs/#!/apps/add_post_1">Tapis API live docs on the /apps service</a>`. We will dive into key elements here:
To make this file work for you, you will be, at a minimum, editting:
Expand Down Expand Up @@ -351,7 +351,7 @@ Application metadata
<td>executionSystem</td>
<td>X</td>
<td>string</td>
<td>An Tapis-registered EXECUTION system upon which you have execute and app registration permissions where jobs will run</td>
<td>a Tapis-registered EXECUTION system upon which you have execute and app registration permissions where jobs will run</td>
</tr>
<tr>
<td>helpURI</td>
Expand Down

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