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 License

Quality analysis and Preprocessing

FastQC [v0.11.5] (Andrews 2016)

GPLv3

FastqMidCleaner [1.0.0]

GPLv3

Cutadapt [1.18] (Martin 2011)

MIT

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

GPLv3

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

GPLv3

FastxToolkit [0.0.13] (Hannon Lab 2016)

AGPLv3

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)

No No MIT

Quantification

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)

No No MIT

SAMtools [1.8] (Li et al. 2009)

No No MIT

Transcriptome assembly

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

No No MIT

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)

No No MIT

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)

No No EASEL

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

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

Notes

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 https://github.com/dkoboldt/varscan/releases ). 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   0.0.0.0:20-22->20-22/tcp, :::20-22->20-22/tcp, 0.0.0.0:80->80/tcp, :::80->80/tcp,  
0.0.0.0:65500-65515->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.

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           TSI-100903-2019-11

Biotechvana


Valencia Lab
Parc Cientific Universitat de Valencia
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
Contact us
Phone: +34 960 06 74 93
Email: biotechvana@biotechvana.com

Supported by


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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