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MolBioCloud Tools Update Feb 2018

1. Whats included in this update ?

This update script includes the addition/update of the following tools;

  1. subread; 1.6.0
  2. fastqc; v0.11.7
  3. bwa; Version: 0.7.15-r1140
  4. picard; 2.17.6
  5. gatk; 4.0.1.0
  6. bedtools; 2.27.1
  7. telseq; 0.0.1
  8. delly; 0.7.8
  9. telomerehunter; 1.0.4
  10. msisensor; 0.02
  11. htseq; 0.9.1
  12. bcftools; 1.6
  13. gatk; 3
  14. samtools tview issues term fix
  15. meme; 4.12.0
  16. vcftools; 0.1.15
  17. BEAST; v1.8.4
  18. Tracer; v1.6
  19. FigTree; v1.4.3
  20. Prosite database
  21. Rebase database

2. Download and check integrity

Download the script from this link https://molbiocloud.com/help/tiki-download_file.php?fileId=20 

Check for the integrity of the downloaded file using the following commands (changing to your downloads directory and then checking for the generated sha256sum match)

#change to the directory where you downloaded the script
cd Downloads
# make sure the downloaded file is in there 'mbcupdatefeb2018'
ls
sha256sum mbcupdatefeb2018

Make sure the output of the “sha256sum” matches exactly as the signature given below; If there are mismatches, try downloading the file again or contact us for help;

02fe1d5c45481b93d82b9a1aed3a8b790a65c3e6d5a9a61bd4897f413b778c02  mbcupdatefeb2018

3. How to run the update script ?

The setup assumes that you have not made any system level changes. If the install does not behave as expected, probably the system configuration has been changed. If you face any issues after this update, please let us know ASAP, so that we can help you troubleshoot the issue.

Once the downloaded files integrity is confirmed, run the script using the command as shown below (the run might take about 5 to 10 minutes).

chmod 755 mbcupdatefeb2018
sudo ./mbcupdatefeb2018 > mbcupdatefeb2018log

After installation is complete, either log out of your machine and then log back in to start using the new updates OR run the following command in your terminal;

source /etc/profile.d/markcbm.sh

4. Issues ?

If you have any issues with running the update script or need any other information regarding this, please do not hesitate to contact us at contact at molbiocloud.com

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