File | Date | Author | Commit |
---|---|---|---|
Example | 2020-06-15 |
![]() |
[f28897] Delete aa |
Script | 2020-06-15 |
![]() |
[c9c197] Delete 2_get_stemloop.pl |
data | 2019-04-02 |
![]() |
[ffef59] minor tweak |
.deepsource.toml | 2022-02-16 |
![]() |
[59a4b6] Add .deepsource.toml |
LICENSE | 2022-07-08 |
![]() |
[c8e651] Update LICENSE |
README.md | 2022-07-07 |
![]() |
[2dd3c0] Update README.md |
install.sh | 2022-07-07 |
![]() |
[9f43b5] Update install.sh |
miRPV.sh | 2022-07-07 |
![]() |
[09af5e] Update miRPV.sh |
miRPV is an Automated tool that allows users to predict and validate microRNA from genome/gene sequence.
The installation has been tested on Ubuntu 18.04. If it has to be installed on another platform, please use the virtual machine image preinstalled with miRPV.
1) Clone this repository
git clone https://github.com/pradyumnasagar/miRPV.git
cd miRPV
2) Install dependencies
sudo apt install -y cowsay enscript dialog build-essential manpages-dev curl gfortran
3) create a conda environment
conda create -n miRPV python=2
conda activate miRPV
4) Run the installation script
The installer will ask root permission to install the following packages please provide it when asked.
HairpIndex, cowsay, enscript, dailog, build-essential, manpages-dev
bash install.sh -p <path of miRPV folder>
5) Follow the on-screen guide
MATLAB Compiler Runtime (MCR) is used to Extract miRNA features, as it is Matlab code. Suppose it does not install via install.sh script install it separately from the Software directory.
Once all the tools and dependence are installed correctly, Activate Conda environment and run from the miRPV folder.
conda activate miRPV
bash miRPV.sh
Provide the project name.
* Give the input query fasta input (keep the fine in the miRPV directory).
* When asked to select the target prediction, select "Yes" or "NO."
* miRPV will ask to provide a reference sequence if the target prediction is selected. Keep the reference sequence in the miRPV folder and enter the name of the reference sequence in the terminal.
* After successful analysis, the results are saved in the output directory with the project name.
If there is any issue in installation, please check the failed package log, install the dependencies, and run again.
conda install Perl-cpan-shell
Getopt::Long
conda install Perl-getopt-long
threads
conda install Perl-threaded
threads::shared
conda install Perl-mce-shared
CWD (CPAN)
conda install Perl-pathtools
or
perl -MCPAN -e 'install CWD'
File::chdir
conda install Perl-file-chdir
UNAFold
conda install -c bioconda oligoarrayaux
gfortran
conda install -c anaconda gfortran_linux-64
libsvm
conda install libsvm
ct2out
gfortran ct2out.f -o ct2out
or
g77 -o ct2out ct2out.f
cp ct2out /bin/
mlsc@manipal.edu