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genotoul-bioinfo
jflow
Commits
adc05238
Commit
adc05238
authored
Mar 19, 2015
by
Jerome Mariette
Browse files
add resources section help
parent
c265656a
Changes
3
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Inline
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docs/jflow-advanced-configuration.html
View file @
adc05238
...
...
@@ -67,9 +67,9 @@
<!--Nav Bar -->
<nav
class=
"col-xs-3 bs-docs-sidebar"
>
<ul
id=
"sidebar"
class=
"nav nav-stacked fixed"
>
<li><a
href=
"#email"
class=
"active"
>
Email
</a></li>
<li><a
href=
"#ressources"
>
Ressources
</a></li>
<li><a
href=
"#components"
>
Components
</a></li>
<li><a
href=
"#email"
class=
"active"
>
Email
section
</a></li>
<li><a
href=
"#ressources"
>
Ressources
section
</a></li>
<li><a
href=
"#components"
>
Components
section
</a></li>
<li><a
href=
"#more"
>
More configuration
</a></li>
</ul>
</nav>
...
...
@@ -104,14 +104,14 @@ from_password =
<section
id=
"ressources"
>
<h1
class=
"page-header"
>
Ressources
<small>
section
</small></h1>
<p>
It can be usefull to You must edit the
<code>
application.properties
</code>
file to configure the application.
Here under the required parameters, for advanced configuration please see
<a
href=
"./jflow-advanced-configuration.html"
>
this page
</a>
...
</p>
<p>
In a production environment, it can be useful to set an ensemble of variables, such as path to databanks, for
multiple workflows. Thus, jflow gives access to ressources settled within the
<code>
application.properties
</code>
file.
All the values settled within this section are then accessible from any
<code>
Component
</code>
or
<code>
Workflow
</code>
through the
<code>
get_resource()
</code>
class method.
</p>
<pre
class=
"pre-hl "
><code
class=
"ini"
>
[resources]
typo3_src = http://prdownloads.sourceforge.net/typo3/typo3_src+dummy-4.7.12.zip
#phix_bwa = /bank/bwadb/phi.fa
#ecoli_bwa = /bank/bwadb/ecoli536
#yeast_bwa = /bank/bwadb/yeast.nt
</code></pre>
ecoli_db = /path/to/ecoli536
phix_db = /path/to/phi.fa
...
</code></pre>
</section>
<section
id=
"components"
>
...
...
docs/jflow-core-component.html
View file @
adc05238
...
...
@@ -87,6 +87,7 @@
<ul
class=
"nav nav-stacked"
>
<li><a
href=
"#pre_process"
>
Pre process
</a></li>
<li><a
href=
"#post_process"
>
Post process
</a></li>
<li><a
href=
"#get_resource"
>
Get Resource
</a></li>
</ul>
</li>
<li><a
href=
"#external_components"
>
External components
</a></li>
...
...
@@ -1233,6 +1234,35 @@ fastq2fasta.py --input splC.fastq --fasta splC.fasta --qual splC.qual</code></pr
<p><code>
post_process()
</code>
is executed right after the
<code>
process
</code>
method and cannot be used to call a
<code>
ShellFunction
</code>
or a
<code>
PythonFunction
</code>
. This method can be useful to perform some database transactions and to synchronize data.
</p>
</div>
<div
id=
"get_resource"
class=
"subgroup"
>
<h2>
Get shared resources
</h2>
<p>
The method
<code>
get_resource()
</code>
, giving a specific resource, returns the defined value within the
<code>
resource
</code>
section of the jflow configuration file.
</p>
<h3>
Options
</h3>
<p>
There is one required argument : resource.
</p>
<div
class=
"table-responsive"
>
<table
class=
"table table-bordered table-striped"
>
<thead>
<tr>
<th>
Name
</th>
<th>
Type
</th>
<th>
Required
</th>
<th>
Default value
</th>
<th>
Description
</th>
</tr>
</thead>
<tbody>
<tr>
<td>
resource
</td>
<td>
string
</td>
<td>
true
</td>
<td>
None
</td>
<td>
The resource name for which is requested the configured value.
</td>
</tr>
</tbody>
</table>
</div>
</div>
</section>
<section
id=
"external_components"
class=
"group"
>
...
...
docs/jflow-core-workflow.html
View file @
adc05238
...
...
@@ -86,6 +86,7 @@
<li><a
href=
"#set_to_address"
>
Set to address
</a></li>
<li><a
href=
"#set_subject"
>
Set subject
</a></li>
<li><a
href=
"#set_message"
>
Set message
</a></li>
<li><a
href=
"#get_resource"
>
Get resource
</a></li>
</ul>
</li>
</ul>
...
...
@@ -762,6 +763,35 @@ bwamem = self.add_component("BWAmem", [bwaindex.databank, self.reads])</code></p
</table>
</div>
</div>
<div
id=
"get_resource"
class=
"subgroup"
>
<h2>
Get shared resources
</h2>
<p>
The method
<code>
get_resource()
</code>
, giving a specific resource, returns the defined value within the
<code>
resource
</code>
section of the jflow configuration file.
</p>
<h3>
Options
</h3>
<p>
There is one required argument : resource.
</p>
<div
class=
"table-responsive"
>
<table
class=
"table table-bordered table-striped"
>
<thead>
<tr>
<th>
Name
</th>
<th>
Type
</th>
<th>
Required
</th>
<th>
Default value
</th>
<th>
Description
</th>
</tr>
</thead>
<tbody>
<tr>
<td>
resource
</td>
<td>
string
</td>
<td>
true
</td>
<td>
None
</td>
<td>
The resource name for which is requested the configured value.
</td>
</tr>
</tbody>
</table>
</div>
</div>
</section>
</div>
</div>
...
...
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