Doing a miRNA seq analysis. I don't know anything about command line scripts. I am trying to get started on the analysis by installing miRDeep2. Can't seem to get the install right because I am extremely confused with all the commands. From my understanding, with the miRDeep2 package, there is a file called install.pl that seems to have a script that will automatically install all the necessary files needed for the package. Can anyone give me some tutorial on how to start running this program and how I can at least install it?
install mirdeep2 by visiting this website: https://github.com/rajewsky-lab/mirdeep2 download the zipped folder with everything and extract it to your desktop move into the folder from the command line and then type: turn on bash sudo perl install.pl source ~/.bash_profile perl install.pl
When this gives you an error for Font::TTF, run the following items: sudo apt-get install libfont-ttf-perl sudo apt-get install libpdf-api2-perl visit http://eddylab.org/software/squid/squid.tar.gz move into that folder using cd ./configure sudo make sudo make install
isit http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/downloads/randfold-2.0.1.tar.gz cd into your randfold folder sudo make sudo mv randfold_folder_name_here /usr/local/bin/ alias randfold="/usr/local/bin/randfold/randfold"
cd back into your mirdeep2 folder Now run sudo perl install.pl again and see if that fixes your problems