mirdeep2 Installer

1. Whats included in this installer ?

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

  1. mirdeep2 - Discovering known and novel miRNAs from small RNA sequencing data

2. Download and check integrity

Download the script from this link https://molbiocloud.com/help/tiki-download_file.php?fileId=57

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)

1. change to the directory where you downloaded the script using the below command;

cd Downloads

1. make sure the downloaded file (mirdeepinstaller) is in there, using the “ls” command;


2. make sure the file is not tampered by executing the following command in your terminal;

sha256sum mirdeepinstaller

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;

df8313d767407e8f7d82d7d1aeed72f38af58fc945b96191f52eb09c3b8b7767  mirdeepinstaller

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.


chmod 755 mirdeepinstaller
sudo ./mirdeepinstaller > mirdeep2log


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

Test if mirdeep2 works, by executing the command ‘miRDeep2.pl’ in the terminal.

The example tutorial files are in the “/usr/local/molbiocloud/mirdeep2/tutorial_dir/” folder.

You can run the example tutorial using the below commands;

cp -r /usr/local/molbiocloud/mirdeep2/tutorial_dir .
cd tutorial_dir
bash run_tut.sh

4. Issues ?

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