GPRO SERVER SIDE


1.1 - ABOUT THE GPRO SERVER SIDE

GPRO Suite is a Client Side + Server Side solution where applications like RNASeq, VariantSeq, DeNovoSeq and STATools (i.e. the Client Side apps) provide Graphical User Interfaces (GUI) to execute a series of workflows and pipelines installed in a bioinformatic server infrastructure we call GPRO Server Side.

The GPRO Server Side has the following requirements and dependencies:

Note that pipeline dependencies are CLI third party software, those usually considered as the State-Of-The-Art (or the most popular) in the field. In Table 1 below we summarize and cite all CLI third party software used by the Server Side as dependencies of the Client Side pipelines.

The table is structured according to the steps that are part of the different pipelines. If a CLI software is included in an application, it will show a ✓ in its corresponding column or a X if it is not included.
Table 1.- CLI third party software used as dependencies by the server side
Pipeline Step Tools RNASeq DeNovoSeq VariantSeq

Quality analysis and Preprocessing

FastQC (Andrews 2016)

FastqMidCleaner (biotechvana script)

Cutadapt (Martin 2011)

Prinseq (Schmieder and Edwards 2011)

Trimmomatic (Bolger, et al. 2014)

FastxToolkit (Hannon Lab 2016)

CANU (Koren, et al. 2017)

No No

FastqCollapser (biotechvana script)

FastqIntersect (biotechvana script)

Mapping on reference genome or transcriptome

TopHat (Kim et al. 2013)

No

Hisat2 (Kim et al. 2015)

No

Bowtie2 (Langmead and Salzberg 2012)

No

BWA (Li and Durbin 2009)

No

STAR (Dobin et al. 2013)

No No

Quantification

Corset (Davidson and Oshlack 2017)

No No

Htseq (Anders 2015)

No No

Post Processing

GATK (MacKena et al. 2010;DePristo et al. 2011)

No No

Picard (Wysoker et al. 2011)

No No

SAMtools (Li et al. 2009)

No No

Bed Tools (Quinlan and Hall 2010)

No No

Transcriptome assembly

Cufflinks (Trapnell et al. 2012)

No No

Oases (Schulz et al. 2012)

No No

SOAPdenovo-trans (Xie et al. 2014)

No No

Genome assembly

Velvet (Zerbino and Birney 2008)

No No

SOAPdenovo2 (Luo et al. 2012)

No No

CANU (Koren et al. 2017)

No No

SPAdes (Bankevich et al. 2012)

No No

Gap filling and scaffolding

Gap closer (Luo et al. 2012)

No No

BESST (Sahlin et al. 2014)

No No

OPERA (Gao et al. 2011)

No No

Differential expression

DESeq (Love et al. 2014)

No No

EdgeR (Robinson et al. 2010)

No No

Cuffdiff (Trapnell et al. 2012)

No No

CummeRbund (Goff et al. 2013)

No No

Enrichment Analysis

GOseq (Young et al. 2010)

No No

Gene Prediction

Augustus (Stanke et al. 2008)

No No

Gene Annotation

BLAST (Altschul et al. 1990)

No No

HMMER (Mistry et al. 2013)

No No

Training Sets

GATK (MacKena et al. 2010;DePristo et al. 2011)

No No

Variant Calling

GATK (MacKena et al. 2010;DePristo et al. 2011)

No No

VarScan2 (Koboldt et al. 2012)

No No

Variant filtering

GATK (MacKena et al. 2010;DePristo et al. 2011)

No No

Annotation of Variant Effects

Variant Effect Predictor (McLaren et al. 2016)

No No

1.2 - SERVER SIDE DOCKER

The GPRO Server Side can be installed in remote servers for Cloud Computing or in the user PC if it has disk space and RAM enough (at least 16Gb of RAM). Installation of the Server side requires complex steps to setup Linux, Apache, MySQL, and PHP (LAMP stack) as well as manual installation of all third-party CLI software used as dependencies of the pipelines and the databases and scripts needed to handle incoming requests to run and manage third party tools and pipelines.

Taking all this into primary consideration, what we have done is to deploy the Server Side into a docker container (Merkel 2014) in order to facilitate its installation. To this end, we distribute an image of the GPRO Server Side docker that can be downloaded at: https://hub.docker.com/r/biotechvana/gpro. This image of the GPRO Server Side is currently limited to one or two users, but we are committed and working to release a forthcoming version of the GPRO server side docker with new implementations to manage multiple users.

The installation of the GPRO Server Side docker is very easy

First of all, download the Docker Desktop software from https://www.docker.com/products/docker-desktop and install it.

Then run following command on the terminal of the Docker Desktop:

local_path="/path/to/local_home"

> docker run -d -p 80:80 -p 20-22:20-22 -p 65500-65515:65500-65515 -v /path/to/local_home:/home/gpro_user biotechvana/gpro

If you run the aforeshown command the Server Side will consider the word g_user as your default user name and password. In other words, your user name will be g_user and your password will also be g_user. Otherwise, if you are interested in running the docker with your own user name and your own password you can also run the docker run command as follows:

local_path="/path/to/local_home"

GPRO_USER="myUserName"

GPRO_USER_PASS="myUserNamePass"

> docker run -d -p 80:80 -p 20-22:20-22 -p 65500-65515:65500-65515 -v /path/to/local_home:/home/gpro_user biotechvana/gpro

For example, if you chose DirkGently as user name and HolisticDetective as password then you will name to run the command as follows:

local_path="/path/to/local_home"

GPRO_USER="DirkGently"

GPRO_USER_PASS="HolisticDetective"

> docker run -d -p 80:80 -p 20-22:20-22 -p 65500-65515:65500-65515 -v /path/to/local_home:/home/gpro_user biotechvana/gpro

1.3 - LINKING THE CLIENT SIDE WITH THE SERVER SIDE

After installed and running the server side image in the Docker Desktop you must link your GPRO application of interest to the Server Side in order to run the server side analyses, pipelines or workflows. As previously said, the Client Side applications of the Suite that are dependent of the Server Side are RNAseq , VariantSeq , DeNovoSeq (manual in preparation) and STATools (manual in preparation). Please visit their respective manuals for detailed instructions about how to link each application with the Server Side and automatically run the docker desktop each time you open the application linked to the Server Side

1.4 - ACKNOWLEDGEMENTS

This work was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 642095 for the OPATHY consortium, by the pre-doctoral research fellowship from Industrial Doctorates of MINECO (Grant 659 DI-17-09134); by the State Plan for Scientific and Technical Research and Innovation 2017-2020 under the Grant TSI-100903-2019-11 from the Secretary of State for Digital Advancement from Ministry of Economic Affairs and Digital Transformation, Spain; and by Expedient IDI-2021-158274-a from Ministry of Science and Innovation, Spain

1.5 - LITERATURE CITED








GPRO licensing and Usage           Former versions

Biotechvana


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