Commit a6756ef5 authored by Jerome Mariette's avatar Jerome Mariette
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......@@ -65,10 +65,7 @@ definition or check file formats.
To our knowledge, Jflow, presented in this article, is the only WMS designed to
be embedded in any web application, thanks to its organization as five Jquery
(http://jquery.com/) plugins. The remaining of the paper is organized as follows:
in Section~\ref{Methods}, Jflow web plugins and its python API are described.
Section~\ref{Example}, presents a concrete integration. Conclusions and further
work are discussed in the last section.
(http://jquery.com/) plugins.
\section{Methods}
......@@ -115,7 +112,10 @@ data type compliance for each parameter. Job submission, status
checking and error handling, rely on Makeflow (Albrecht et al., 2012) and
weaver (Bui et al., 2012). Therefore Jflow manages error recovery and supports
most distributed resource management systems (Condor, SGE, Work Queue or a
single multicore machine, \ldots).
single multicore machine, \ldots). Changing Makeflow by an other jobs submiter
can be done by implementing a new \textit{Engine} subclass. This one is in
charge to create, in the right format, and execute the workflow directed acyclic
graph (DAG).
\section{Example}
......@@ -136,12 +136,16 @@ form using the \textit{wfform} plugin. Considering the parameter type, Jflow
adapts its display. For example, a date is displayed as a calendar and a boolean
as a checkbox.
Being dedicated to biological data, NG6 inputs are often experimental
samples, composed of read files and metadata such as sample name, tissue,
developpement stage. To help biologists to enter such information, Jflow uses
structured data inputs. Such parameter sets are displayed within the
\textit{wfform} plugin as a spreadsheet, allowing to copy and paste multiple
lines.
One of a common analysis performed by NG6 is to check the contamination of
experimental samples. This can be done by aligning the samples sequences against
a reference genome. Biological samples are often composed of read files and
metadata such as sample name, tissue, developpement stage. To help biologists to enter
such information, Jflow uses structured data inputs. Such parameter sets are
displayed within the \textit{wfform} plugin as a spreadsheet, allowing to copy
and paste multiple lines. The reference genome is a single file represented in
the form by a standard text input with a button allowing to browse and upload
local files. At execution, Jflow will iterate on the table content to align
each samples against the reference genome.
\begin{figure}[ht]
\centering
......@@ -163,7 +167,7 @@ To monitor running workflows, NG6 provides a table in a specific page. The
table is filled by the \textit{activewf} plugin. In the same way as
described above, the \textit{wfstatus} is built on a modal box when a
\textit{select.activewf} event is thrown by the \textit{activewf} plugin, as
presented on Figure~\ref{fig::jflow_example}. This view shows the workflow's
presented in Figure~\ref{fig::jflow_example}. This view shows the workflow's
execution graph where nodes represent components and edges links between inputs
and outputs.
......
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