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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 ==

 * [http://www.molgenis.org/raw-attachment/wiki/ComputeVM/install_tools.sh 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                   R/3.1.2-goolf-1.7.20
   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
   Perl/5.20.2-goolf-1.7.20-bare
}}}


 * [http://www.molgenis.org/raw-attachment/wiki/ComputeVM/create_resources.sh 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.

 * [http://www.molgenis.org/raw-attachment/wiki/ComputeVM/BWA-0.7.12-goolf-1.7.20.eb BWA-0.7.12]
 * [http://www.molgenis.org/raw-attachment/wiki/ComputeVM/BEDTools-2.23.0-goolf-1.7.20.eb BEDTools-2.23.0]
 * [http://www.molgenis.org/raw-attachment/wiki/ComputeVM/tabix-0.2.6-goolf-1.7.20.eb tabix-0.2.6] Note: tabix module should be installed before installing BCFtools
 * [http://www.molgenis.org/raw-attachment/wiki/ComputeVM/BCFtools-1.2-goolf-1.7.20.eb BCFtools-1.2]
 * [http://www.molgenis.org/raw-attachment/wiki/ComputeVM/FastQC-0.11.3-Java-1.7.0_76.eb FastQC-0.11.3]
 * [http://www.molgenis.org/raw-attachment/wiki/ComputeVM/GATK-3.3-0-Java-1.7.0_21.eb GATK-3.3-0]
 * [http://www.molgenis.org/raw-attachment/wiki/ComputeVM/Java-1.7.0_76.eb Java-1.7.0_76]
 * [http://www.molgenis.org/raw-attachment/wiki/ComputeVM/Molgenis-Compute-v15.04.1-Java-1.7.0_76.eb Molgenis-Compute-v15.04.1]
 * [http://www.molgenis.org/raw-attachment/wiki/ComputeVM/Perl-5.20.2-goolf-1.7.20-bare.eb Perl-5.20.2]
 * [http://www.molgenis.org/raw-attachment/wiki/ComputeVM/picard-1.130-Java-1.7.0_76.eb picard-1.130]
 * [http://www.molgenis.org/raw-attachment/wiki/ComputeVM/picard.py Picard after installation update script]
 * [http://www.molgenis.org/raw-attachment/wiki/ComputeVM/snpEff-v4.1d-Java-1.7.0_76.eb snpEff-v4.1d]
 * [http://www.molgenis.org/raw-attachment/wiki/ComputeVM/VCFtools-0.1.12b-goolf-1.7.20-Perl-5.20.2-bare.eb VCFtools-0.1.12b]

== Easy build files for R ==

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

* [http://www.molgenis.org/raw-attachment/wiki/ComputeVM/zlib-1.2.8-goolf-1.7.20.eb zlib-1.2.8-goolf-1.7.20.eb] Note: zlib should be installed before installing libpng
* [http://www.molgenis.org/raw-attachment/wiki/ComputeVM/libpng-1.6.16-goolf-1.7.20.eb libpng-1.6.16-goolf-1.7.20.eb]
* [http://www.molgenis.org/raw-attachment/wiki/ComputeVM/NASM-2.11.06-goolf-1.7.20.eb NASM-2.11.06-goolf-1.7.20.eb] Note: NASM should be installed before installing libjpgturbo
* [http://www.molgenis.org/raw-attachment/wiki/ComputeVM/libjpeg-turbo-1.4.0-goolf-1.7.20.eb libjpeg-turbo-1.4.0-goolf-1.7.20.eb]
* [http://www.molgenis.org/raw-attachment/wiki/ComputeVM/libreadline-6.3-goolf-1.7.20.eb libreadline-6.3-goolf-1.7.20.eb]
* [http://www.molgenis.org/raw-attachment/wiki/ComputeVM/ncurses-5.9-goolf-1.7.20.eb ncurses-5.9-goolf-1.7.20.eb]
* [http://www.molgenis.org/raw-attachment/wiki/ComputeVM/R-3.1.2-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.
* [https://molgenis26.target.rug.nl/downloads/ComputeVM/molgenisimage0707.gz molgenisimage0707.gz]