Set a Virtual Machine Using VM Virtual Box

The BTI bioinformatics Course uses Virtual Box to virtualize a Linux operating system (OS) inside any computer. The virtual machine (VM) is a Linux OS, Debian distribution for 64 bits computers.

Steps:

1. Download and install VirtualBox following the package instructions. For more info consult the user manual. Please download and install the latest VirtualBox version for your operative system.

2. Check the if you have a 64 bits or 32 bits system (Windows or MacOS) and download the *.ova file from SGN ftp siteSome Windows 64 bits systems doesn’t have activate the acceleration VT-x/AMD-V, causing the inability to use  64 bits virtual machines. You will need to enable the VT-x/AMD-V in the Bios of your computer

If you are running a 32-bit computer you can come to our office to find an alternative 64-bit laptop that you may use for the course.

3. Create a VM Folder in your system and copy/move the .ova file

4. Open the VirtualBox program.

6. Select the option File > Import Appliance

Screen Shot 2013-03-21 at 6.18.32 PM Screen Shot 2013-03-21 at 6.18.44 PM

7. Click “Open Appliance”. Select the .ova file and click “Continue”.

Screen Shot 2013-03-21 at 6.21.40 PM

8. Enable “Reinitialize the MAC address of all the network cards” and click “Import”.

Screen Shot 2013-03-21 at 6.21.56 PM

Troubleshooting

  • I have a Mac computer, I am using Safari and I can not download the whole file.

Safari has some problems to deal with big files and the ftp site, but you can resolve it just using Firefox

  • I have downloaded the file and when I tried to use the file it says “File Corrupted” or something similar.

Probably the download was interrupted at some point. We recommend to use a wire connection to download the file because it  is a big file and the chances that something fail during the download are high. Once you have download the file you can do a md5sum to verify that the file is complete. You can find the md5sum codes at: md5sum. In Mac computer you only need to open the terminal, type “cd ~/Downloads” (Or the dir where you downloaded the file) and then “md5 BioDebian64_BTIBIC_2017.ova”. In a Windows computer, you can use WinMD5.

  • I have downloaded and unzipped the file but it does not work.

Make sure you have a 64-bit machine. Come to our office for further troubleshooting if you cannot find the problem.

VM Data:

  • Name: BTI_debian_jessie_2017.ova Base Memory: 1024 Mb
  • Storage: 25.51 Gb
  • Operating System: Debian release 8.3 (Jessie)
  • Username: bioinfo Password: bioinfo

Installed Software:

  • Emacs 23.2.1 – GNU Text editor.
  • Htop 0.8.3 – interactive processes viewer.
  • Screen 4.00.03 – Terminal Multiplexor with VT100/ANSI terminal emulator
  • Perl-doc 5.10.1 – documentation for Perl
  • Git 1.7.2.5 – Version control system software
  • zlib1g-dev – Compression library (development, used to compile Bwa)
  • libncurses5-dev – Terminal library (development, used to compile samtools)
  • libgsl0-dev 1.14 – GNU Scientific binaries (used to compile ea-utils)
  • libboost1.42-all-dev – Boost++ library (used for accesory script)
  • gsl-bin 1.14 – GNU Scientific binaries (used to compile ea-utils)
  • g++ 4.4.5 – GNU compiler
  • cmake 2.8.2 – Open software build system tool (used to install bamtools)
  • Blast 2.2.21 – NCBI Basic Local Alignment Search Tool
  • Blast+ 2.2.27 – NCBI Basic Local Alignment Search Tool (new version)
  • Bioperl 1.6.1-2 – Perl Tools for computational molecular biology
  • GenoToolBox – Collection of Perl Scripts to manipulate sequences
  • Bwa 0.7.2 – Burrows-Wheeler aligner
  • Bowtie 0.12.9 – An ultrafast, memory efficient short read aligner
  • Bowtie2 2.2.1 – An ultrafast, memory efficient short read aligner (version 2)
  • Tophat 1.3.2 –  Fast splice junction mapper for RNA-seq reads (legacy version)
  • Tophat2 2.0.8 – Fast splice junction mapper for RNA-seq reads
  • Cufflinks 2.0.2 (1.3.0 for 32bits)- Assembly transcripts, estimates their abundances and test differential expression
  • Samtools 0.1.19 – Utilities to manipulate SAM/BAM files (read alignment files)
  • Bedtools 2.17.0 – Utilities to intersect SAM/BAM/BED/GFF files
  • FastQC 0.10.1 – Tool for quality control of NGS data
  • Ea-utils 1.1.2-537 – Collection of programs to process fastq reads
  • Bamtools 2.2.3 – Utilities and libraries to work with BAM files
  • Prinseq 0.20.3 – Program to process fastq files, including read duplication filtering
  • FastX-Toolkit 0.0.3 – Collection of programs to process fastq files
  • Picard Tools 1.87 – Collection of Java Scripts to manipulate SAM/BAM files
  • R-base 2.15.3 – Software environment for statistical computing and graphics
  • R-studio 0.97 – IDE for R
  • SOAPdenovo 1.05 (NA for 32 bits) – Genome assembler
  • SOAPdenovo-Trans 1.01 (NA for 32 bits) – RNAseq assembler
  • Trinity 2013-02-25 (NA for 32 bits) – A RNAseq assembler
  • SnpEff 3.2 – A tool to identify SNP types
  • Freebayes 0.9.9 – A program to call SNPs
  • GATK 2.4.7 – Collection of programs to manipulate genomic data including SNP calling
  • JBrowse 1.11-5
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