Commit b958cd53 authored by Jerome Mariette's avatar Jerome Mariette
Browse files

correction CK article

parent 480aa4c4
......@@ -49,7 +49,7 @@ Building rich web environments aimed at helping scientists analyze their data is
a common trend in bioinformatics. Specialized web portals such as MG-RAST (Meyer
et al., 2008), MetaVir (Roux et al., 2011) or NG6 (Mariette et al., 2012) provide
multiple services and analysis tools in an integrated manner for specific
experiments or data types. These applications requires WMS features to manage
experiments or data types. These applications require WMS features to manage
and execute their computational pipelines.
Generic WMS, such as Galaxy (Goecks et al., 2010), provide a user friendly
......@@ -97,15 +97,15 @@ step. Adding a component to the system requires to write a Python
component creation. To wrap a single command line, the developer can give a
position or a flag for each parameter. Jflow also embeds an XML parser which
allows to run genuine Mobyle (Neron et al., 2009) components. Finally, to
allow developers to integrate components from other WMS, Jflow provides a class
skeleton. This class only requires to implement the parsing step. A workflow
chains several components. A Jflow workflow is built as a \textit{Workflow}
subclass. Components are added to the workflow as variables and chained linking
outputs and inputs.
allow developers to integrate components from other WMS, Jflow provides a
skeleton class. This class only requires to implement the parsing step. A
workflow chains several components. A Jflow workflow is built as a
\textit{Workflow} subclass. Components are added to the workflow as variables
and chained linking outputs and inputs.
To define the parameters presented to the final user, Jflow gives access to
different class methods. Each parameter has at least a name, a user help text
and a data type. For files or directories parameters, it is possible to set
and a data type. For file or directory parameters, it is possible to set
required file format, size limitation and location. Jflow handles server side
files with regular expressions, but also URLs and client side files, in which
case, it automatically uploads them. Before running the workflow, Jflow checks
......@@ -115,7 +115,7 @@ weaver (Bui et al., 2012). Therefore Jflow manages error recovery and supports
most distributed resource management systems (Condor, SGE, Work Queue or a
single multi core machine, \ldots). Replacing Makeflow by an other job submitter
requires to implement a new \textit{Engine} subclass. This class creates and
execute the workflow directed acyclic graph (DAG).
executes the workflow directed acyclic graph (DAG).
\section{Example}
......@@ -129,23 +129,21 @@ the data and checking its quality. Different workflows are available considering
data type and sequencing technology.
Workflows are listed by the \textit{availablewf} plug-in built within a
NG6 modal box. It requests the server to get the workflows implemented by the
developer. A \textit{select.availablewf} event thrown by the
NG6 modal box. A \textit{select.availablewf} event thrown by the
\textit{availablewf} plug-in is listened and caught to generate the parameter
form using the \textit{wfform} plug-in. Considering the parameter type, Jflow
adapts its display. For example, a date is displayed as a calendar and a boolean
adapts its display. For example, a date is shown as a calendar and a boolean
as a check box.
Biologists use NG6 to check sequencing reads quality, including experimental
samples contamination measure (quantification/search). The first input of this
analysis is the contaminant reference genome fasta file, displayed as a file
selector. The second input is a parameter set describing the biological samples.
It includes the read files and meta data such as sample name, tissue and
development stage. To help biologists populate it, Jflow uses a structured
data input rendered by the \textit{wfform} plug-in as a spreadsheet. It allows
to
copy and paste multiple lines. Jflow iterates then on the table content to
launch each sample processing.
samples contamination measure. The first input of this analysis is the
contaminant reference genome fasta file, displayed as a file selector. The
second input is a parameter set describing the biological samples. It includes
the read files and meta data such as sample name, tissue and development stage.
To help biologists populate it, Jflow uses a structured data input rendered by
the \textit{wfform} plug-in as a spreadsheet. It allows to copy and paste
multiple lines. Jflow iterates then on the table content to launch each sample
processing.
\begin{figure}[ht]
\centering
......@@ -182,9 +180,9 @@ same application, which makes it really user friendly.
\section{Conclusion}
Jflow is a simple and efficient solution to embed WMS features within a web
application. It is, to our knowledge, the only WMS designed with that purpose.
application. It is, to our knowledge, the only WMS designed with this purpose.
It is already embedded in RNAbrowse (Mariette et al., 2014) and NG6 (Mariette et
al., 2012), where Jflow has been used to process more than 2 000 sequencing runs
al., 2012), where it has been used to process more than 2 000 sequencing runs
on a 5 000 cores HPC.
\paragraph{Conflict of Interest\textcolon} none declared.
......
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