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genotoul-bioinfo
jflow
Commits
f9895fb8
Commit
f9895fb8
authored
Nov 17, 2015
by
Ibouniyamine Nabihoudine
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parent
cb9ea8c3
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4
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docs/jflow_advanced_configuration.html
View file @
f9895fb8
...
...
@@ -71,6 +71,7 @@
<li><a
href=
"#storage"
>
Storage
</a></li>
<li><a
href=
"#softwares"
>
Softwares
</a></li>
<li><a
href=
"#components"
>
Components
</a></li>
<li><a
href=
"#workflows"
>
Workflows
</a></li>
<li><a
href=
"#resources"
>
Resources
</a></li>
</ul>
</nav>
...
...
@@ -269,6 +270,16 @@ BWAIndex.batch_options = -l mem=1G -l h_vmem=1G -q myflowq
BWAmem.batch_options = -l mem=10G -l h_vmem=10G -q myflow2q
</code></pre>
</section>
<section
id=
"workflows"
>
<h1
class=
"page-header"
>
Workflows
<small>
section
</small></h1>
<p>
Each workflow has a default group. In this section you can set a group name for each one of your workflow,
thus while using the
<code>
availablewf()
</code>
plugin, you will be able to specify which group of workflow you want to get.
You can set the group of a workflow by adding a line of the following schema : [workflow_classname].group = [group_name].
</p>
<pre
class=
"pre-hl "
><code
class=
"ini"
>
[workflows]
QuickStart.group = tutorial
</code></pre>
</section>
<section
id=
"ressources"
>
<h1
class=
"page-header"
>
Ressources
<small>
section
</small></h1>
<p>
In a production environment, it can be useful to set an ensemble of variables, such as path to databanks, for
...
...
docs/jflow_plugin.html
View file @
f9895fb8
...
...
@@ -186,6 +186,20 @@
<td>
[]
</td>
<td>
Defines the workflow classes that should not be displayed.
</td>
</tr>
<tr>
<td>
filter_groups
</td>
<td>
list
</td>
<td>
false
</td>
<td>
[]
</td>
<td>
Defines the workflow groups that should be filtered.
</td>
</tr>
<tr>
<td>
select
</td>
<td>
boolean
</td>
<td>
false
</td>
<td>
false
</td>
<td>
If true the workflows filtered using the filter_groups option will be displayed, if false they will not.
</td>
</tr>
</tbody>
</table>
</div>
...
...
src/jflow/config_reader.py
View file @
f9895fb8
...
...
@@ -23,7 +23,7 @@ import logging
from
configparser
import
RawConfigParser
,
NoOptionError
from
jflow.utils
import
which
,
display_error_message
from
jflow.workflow
import
Workflow
class
JFlowConfigReader
(
object
):
"""
...
...
@@ -124,6 +124,6 @@ class JFlowConfigReader(object):
try
:
return
self
.
reader
.
get
(
"workflows"
,
workflow_class
+
".group"
)
except
:
return
""
return
Workflow
.
DEFAULT_GROUP
\ No newline at end of file
src/jflow/workflow.py
View file @
f9895fb8
...
...
@@ -145,7 +145,7 @@ class Workflow(threading.Thread):
self
.
id
=
id
self
.
name
=
self
.
get_name
()
self
.
description
=
self
.
get_description
()
self
.
__group
=
self
.
jflow_config_reader
.
get_workflow_group
(
self
.
__class__
.
__name__
)
or
self
.
DEFAULT_GROUP
self
.
__group
=
self
.
jflow_config_reader
.
get_workflow_group
(
self
.
__class__
.
__name__
)
# define the parameters
self
.
params_order
=
[]
...
...
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