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

The GPRO Server Side has the following requirements and dependencies:

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.- Pipeline dependencies hosted at the GPRO Server Side
Pipeline Step Tools RNASeq DeNovoSeq VariantSeq License

Quality analysis and Preprocessing

FastQC [v0.11.5] (Andrews 2016)


FastqMidCleaner [1.0.0]


Cutadapt [1.18] (Martin 2011)


Prinseq [PRINSEQ-lite 0.20.4] (Schmieder and Edwards 2011)


Trimmomatic [0.36] (Bolger, et al. 2014)


FastxToolkit [0.0.13] (Hannon Lab 2016)


CANU (Koren, et al. 2017)

No No GPLv3

FastqCollapser [1.0.0]

No GPLv3

FastqIntersect [1.0.0]

No GPLv3

Mapping on reference genome or transcriptome

TopHat [v2.1.1] (Kim et al. 2013)

No Boost Software 1.0

Hisat2 [2.2.1] (Kim et al. 2015)

No GPLv3

Bowtie2 [2.2.9] (Langmead and Salzberg 2012)

No GPLv3

BWA [0.7.15-r1140] (Li and Durbin 2009)

No GPLv3

STAR [2.7.0f] (Dobin et al. 2013)



Corset [1.06] (Davidson and Oshlack 2017)

No No BSD 2-Clause

Htseq [0.12.4] (Anders 2015)

No No GPLv3

Post Processing

Bed Tools [v2.29.2] (Quinlan and Hall 2010)

No No GPLv2

GATK [v4.1.2.0] (MacKena et al. 2010;Cibulskis et al. 2013;DePristo et al. 2011)

No No Apache-2.0

Picard [2.19.0] (Wysoker et al. 2011)


SAMtools [1.8] (Li et al. 2009)


Transcriptome assembly

Cufflinks [v2.2.1](Trapnell et al. 2012)


Oases (Schulz et al. 2012)

No No GPLv3

SOAPdenovo-trans (Xie et al. 2014)

No No GPLv3

Genome assembly

Velvet (Zerbino and Birney 2008)

No No GPLv3

SOAPdenovo2 (Luo et al. 2012)

No No GPLv3

CANU (Koren et al. 2017)

No No GPLv2

SPAdes (Bankevich et al. 2012)

No No GPLv3

Gap filling and scaffolding

Gap closer (Luo et al. 2012)

No No GPLv3

BESST (Sahlin et al. 2014)

No No GPLv3

OPERA (Gao et al. 2011)


Differential expression

DESeq [2.1.28] (Love et al. 2014)

No No GPLv3

EdgeR [3.30.3] (Robinson et al. 2010)

No No GPLv2

Cuffdiff [v2.2.1] (Trapnell et al. 2012)

No No Boost Software 1.0

CummeRbund [2.30.0] (Goff et al. 2013)

No No Artistic-2.0

Enrichment Analysis

GOseq [1.40.0] (Young et al. 2010)

No No LGPLv3

Gene Prediction

Augustus (Stanke et al. 2008)

No No Artistic-1.0

Gene Annotation

BLAST (Altschul et al. 1990)

No No Public Domain

HMMER (Mistry et al. 2013)


Variant Effect Predictor [105.0] (McLaren et al. 2016)

No No Apache-2.0

Training Sets

GATK [v4.1.2.0] (MacKena et al. 2010;Cibulskis et al. 2013;DePristo et al. 2011)

No No Apache-2.0

Variant Calling

GATK [v4.1.2.0] (MacKena et al. 2010;Cibulskis et al. 2013;DePristo et al. 2011)

No No Apache-2.0

VarScan2 [v2.4.3] (Koboldt et al. 2012)

No No VarScan

Variant filtering

GATK [v4.1.2.0] (MacKena et al. 2010;Cibulskis et al. 2013;DePristo et al. 2011)

No No Apache-2.0


The GPRO Server Side can be installed in remote servers or in the user PC provided that if it has enough disk space and RAM (at least 500 Gb of hard disk and 16Gb of RAM). Installation of the GPRO Server Side involves complex steps to setup Linux, Apache, MySQL, and PHP (LAMP stack) as well as manual installation of the distinct third-party CLI software shown in Table 1 as well as GPRO databases, and multiple distinct scripts needed to handle requests of client applications to the Server Side. However we have deployed it into a docker container(Merkel 2014) to facilitate its installation. An image of this docker can be downloaded from: The current version of this docker is limited to one or two users, but we are committed to release a forthcoming version for multiple users.

To install the GPRO Server Side docker, please proceed as follows

First, download the Docker Desktop software from and install it.

If you want to install the Server Side docker with default user name and password, please run the following command on the terminal of the Docker Desktop:


> 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

In doing so, 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 be g_user, too.

Otherwise, if you are interested in running the docker with your own user name and password, please run the following command on the Docker Desktop terminal:




> 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:




> 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


All third-party command line interface software are integrated in the server-side docker image excepting Varscan2. This is because the license for VarScan2 usage distinguishes between academic users and commercial users. Academic users can use VarScan2 without restrictions for academic purposes, while commercial users need to contact the VarScan2 authors to get the corresponding commercial license (for more details see ). Taking this into consideration, the server-side image does not include VarScan2 and this tool must be integrated by the own user into the running container. The rest of CLI software dependencies used by “RNAseq” and “VariantSeq” are already installed in the docker image and have licenses of use allowing unrestricted use for every kind of author (if they are appropriately cited and accredited). To integrate VarScan2 in the docker please proceed as follows.

To manage the image you need to get image name first if you did not set it in the run command, you can get the image name by running docker ps

$ docker ps
################## Sample output
# CONTAINER ID   IMAGE          COMMAND        CREATED       STATUS       PORTS                                                                                                                                                     NAMES
# 5121b762b39f   d82c97fcc2c7   "/gpro_init"   2 hours ago   Up 2 hours>20-22/tcp, :::20-22->20-22/tcp,>80/tcp, :::80->80/tcp,>65500-65515/tcp, :::65500-65515->65500-65515/tcp   hungry_boyd

Here the name is hungry_boyd

Adding VarScan to the gpro server : run the following command:

$ docker exec hungry_boyd gpro install varscan

Commercial users should proceed in the same way but must contact first the VarScan2 authors to get the license if they want to comply with the VarScan2 terms of use.


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


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


GPRO licensing and Usage           Former versions           TSI-100903-2019-11


Valencia Lab
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Carrer del Catedràtic Agustín Escardino, 9. 46980 Paterna (Valencia) Spain
Madrid Lab
Parque Científico de Madrid
Campus de Cantoblanco
Calle Faraday 7, 28049 Madrid Spain
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Hipra Scientific S.L.U, Polypeptide Therapeutic Solutions S.L., Biotechvana S.L. and Nostrum Biodiscovery constitute the consortium of enterprises participating in the project "Research of a new vaccine for a human respiratory disease", granted by the CDTI (Center for Industrial Technological Development), and supported by the Ministry of Science and Innovation and financed by the European Union – NextGenerationEU. The main objective of this project is to design a safe immunogenic and effective vaccine against the respiratory syncytial virus.

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