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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.
MOLGENIS/compute at IWSG-2013
MOLGENIS/compute was presented at 5th International Workshop on Science Gateways, IWSG 2013, Zurich, Switzerland
Visual Analytics for Bio-Workflows at NBIC-2013
Towards visual analytics of bio-workflows presentation was given at the NBIC-2013 conference, Lunteren, Netherlands
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 ...
MOLGENIS/compute workshop at BioAssist meeting
MOLGENIS/compute workshop took place at the NBIC Bio Assist meeting, in Utrect, Oct.12, 2012
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
MOLGENIS/compute at NBIC-2012
MOLGENIS/compute demo was given at the NBIC-2012 conference in Lunteren, Netherlands, Apr.23, 2012
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 ...
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
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 ...
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
- 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
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.
Attachments (24)
- BWA-0.7.12-goolf-1.7.20.eb (936 bytes) - added by 10 years ago.
- BCFtools-1.2-goolf-1.7.20.eb (798 bytes) - added by 10 years ago.
- BEDTools-2.23.0-goolf-1.7.20.eb (881 bytes) - added by 10 years ago.
- FastQC-0.11.3-Java-1.7.0_76.eb (930 bytes) - added by 10 years ago.
- GATK-3.3-0-Java-1.7.0_21.eb (1.0 KB) - added by 10 years ago.
- Java-1.7.0_76.eb (496 bytes) - added by 10 years ago.
- Molgenis-Compute-v15.04.1-Java-1.7.0_76.eb (1.1 KB) - added by 10 years ago.
- Perl-5.20.2-goolf-1.7.20-bare.eb (383 bytes) - added by 10 years ago.
- Perl-5.20.2-goolf-1.7.20-bare.2.eb (383 bytes) - added by 10 years ago.
- picard-1.130-Java-1.7.0_76.eb (522 bytes) - added by 10 years ago.
- picard-1.130-Java-1.7.0_76.2.eb (522 bytes) - added by 10 years ago.
- snpEff-v4.1d-Java-1.7.0_76.eb (952 bytes) - added by 10 years ago.
- tabix-0.2.6-goolf-1.7.20.eb (929 bytes) - added by 10 years ago.
- VCFtools-0.1.12b-goolf-1.7.20-Perl-5.20.2-bare.eb (1.7 KB) - added by 10 years ago.
- picard.py (3.6 KB) - added by 10 years ago.
- zlib-1.2.8-goolf-1.7.20.eb (697 bytes) - added by 9 years ago.
- libjpeg-turbo-1.4.0-goolf-1.7.20.eb (616 bytes) - added by 9 years ago.
- libpng-1.6.16-goolf-1.7.20.eb (414 bytes) - added by 9 years ago.
- libreadline-6.3-goolf-1.7.20.eb (1.1 KB) - added by 9 years ago.
- ncurses-5.9-goolf-1.7.20.eb (571 bytes) - added by 9 years ago.
- NASM-2.11.06-goolf-1.7.20.eb (769 bytes) - added by 9 years ago.
- R-3.1.2-goolf-1.7.20.eb (2.3 KB) - added by 9 years ago.
-
install_tools.sh (1.6 KB) - added by 9 years ago.
NGS Tools Installation script
- create_resources.sh (5.1 KB) - added by 9 years ago.
Download all attachments as: .zip
