News

Enlighten Your Research Global Award: Virtual Machine Images for Life Science Research

Denver (USA) 18 November 2013 – One of the four prestigious "Enlighten Your Research Global" has been awarded to an idea developed by an ELIXIR working group for the sharing of virtual machines over research and education networks.

• Posted: 10 years ago (Updated: 10 years ago)
• Author: george
• Categories: MCF
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MOLGENIS/compute at IWSG-2013

​MOLGENIS/compute was presented at 5th International Workshop on Science Gateways, IWSG 2013, Zurich, Switzerland

• Posted: 11 years ago
• Author: george
• Categories: MCF
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Visual Analytics for Bio-Workflows at NBIC-2013

​Towards visual analytics of bio-workflows presentation was given at the NBIC-2013 conference, Lunteren, Netherlands

• Posted: 11 years ago (Updated: 11 years ago)
• Author: george
• Categories: MCF
• Comments (0)

Visual Analytics for Bio-Workflows at BIOINFORMATICS-2013

"Visualization of bioinformatics workflows for ease of understanding and design activities" paper will be presented at the BIOSTEC-BIOINFORMATICS-2013 conference, on February 11th, 2013, Bercelona, Spain. [​http://www.molgenis.org/raw-attachment/blog ...

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• Posted: 12 years ago (Updated: 12 years ago)
• Author: george
• Categories: MCF
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MOLGENIS/compute workshop at BioAssist meeting

MOLGENIS/compute workshop took place at the NBIC Bio Assist meeting, in Utrect, Oct.12, 2012

• Posted: 12 years ago (Updated: 12 years ago)
• Author: george
• Categories: MCF
• Comments (0)

MOLGENIS/compute at IWSG-Life 2012

MOLGENIS/compute demo was given at the 4th International Workshop on Science Gateways for Life Sciences, May 23-25 2012, Amsterdam, Netherlands

• Posted: 12 years ago
• Author: george
• Categories: MCF
• Comments (0)

MOLGENIS/compute at NBIC-2012

MOLGENIS/compute demo was given at the NBIC-2012 conference in Lunteren, Netherlands, Apr.23, 2012

• Posted: 12 years ago
• Author: george
• Categories: MCF
• Comments (0)

MOLGENIS/compute at BIOINFORMATICS-2012

MOLGENIS/compute was accepted as a full paper and presented at the International Conference on Bioinformatics Models, Methods and Algorithms, Algarve, Portugal, Feb.3 2012. (BIOINFORMATICS 2012 received 109 submissions, of which 14% were accepted as ...

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• Posted: 12 years ago (Updated: 12 years ago)
• Author: george
• Categories: MCF
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MOLGENIS/compute at NPC-2011

Poster: "Monitoring and error-handling of bioinformatics workflow execution in a distributed environment" will be presented at the Netherlands Proteomics Conference, NPC-2011, Utrecht, Netherlands, January 13, 2011

• Posted: 14 years ago (Updated: 12 years ago)
• Author: george
• Categories: MCF
• Comments (0)

MOLGENIS/compute at PDP-2011

MOLGENIS/compute will be presented at the 19th Euromicro International Conference on Parallel, Distributed and Network-Based Computing, PDP 2011, Ayia Napa, Cyprus, February 9-11, 2011. [​http://www.molgenis.org/raw-attachment/blog/mcf-cyprus/pdp-201 ...

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• Posted: 14 years ago (Updated: 12 years ago)
• Author: george
• Categories: MCF
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About Compute5 VM

We created the Open Stack image and shell scripts, which can be used to download and install all necessary tools and resources to run Next Generation Sequencing analysis workflow.

Notice: This is work in progress page

Installation Scripts

• ​Tools installation script for NGS analysis workflow After running the tool installation script, your environment should look as follows:

-------------------------------------- /srv/molgenis/.local/easybuild/modules/all ---------------------------------------
   Autoconf/2.69-GCC-4.8.4                   Perl/5.20.2-goolf-1.7.20-bare
   Automake/1.15-GCC-4.8.4                   ScaLAPACK/2.0.2-gompi-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0
   BCFtools/1.2-goolf-1.7.20                 gompi/1.7.20
   BEDTools/2.23.0-goolf-1.7.20              goolf/1.7.20
   BWA/0.7.12-goolf-1.7.20                   hwloc/1.10.1-GCC-4.8.4
   EasyBuild/2.0.0                           libjpeg-turbo/1.4.0-goolf-1.7.20
   FFTW/3.3.4-gompi-1.7.20                   libpng/1.6.16-goolf-1.7.20
   FastQC/0.11.3-Java-1.7.0_51               libreadline/6.3-goolf-1.7.20
   GATK/3.4-0-Java-1.7.0_51                  libtool/2.4.5-GCC-4.8.4
   GCC/4.8.4                                 ncurses/5.9-goolf-1.7.20
   Java/1.7.0_51                             numactl/2.0.10-GCC-4.8.4
   M4/1.4.17-GCC-4.8.4                       picard/1.130-Java-1.7.0_51
   NASM/2.11.06-goolf-1.7.20                 snpEff/4.1d-Java-1.7.0_51
   OpenBLAS/0.2.13-GCC-4.8.4-LAPACK-3.5.0    tabix/0.2.6-goolf-1.7.20
   OpenMPI/1.8.4-GCC-4.8.4                   zlib/1.2.8-goolf-1.7.20

• ​Resources download and set-up script for NGS analysis workflow

Easy build files for bioinformatics tools

These files are already present in our prepared VM, but they also can be used separately, if users want to install NGS workflow resources in their environment.

• ​BWA-0.7.12
• ​BEDTools-2.23.0
• ​tabix-0.2.6 Note: tabix module should be installed before installing BCFtools
• ​BCFtools-1.2
• ​FastQC-0.11.3
• ​GATK-3.3-0
• ​Java-1.7.0_76
• ​Molgenis-Compute-v15.04.1
• ​Perl-5.20.2
• ​picard-1.130
• ​Picard after installation update script
• ​snpEff-v4.1d
• ​VCFtools-0.1.12b

Easy build files for R

R installation requires a number of additional modules to be installed first:

• ​zlib-1.2.8-goolf-1.7.20.eb Note: zlib should be installed before installing libpng
• ​libpng-1.6.16-goolf-1.7.20.eb
• ​NASM-2.11.06-goolf-1.7.20.eb Note: NASM should be installed before installing libjpgturbo
• ​libjpeg-turbo-1.4.0-goolf-1.7.20.eb
• ​libreadline-6.3-goolf-1.7.20.eb
• ​ncurses-5.9-goolf-1.7.20.eb
• ​R-3.1.2-goolf-1.7.20.eb

Adding own software to the VM

To add software to the VM ...

Open Stack Image of the NGS VM

Please notice that the size of the image is 5GB.