Installation

install python modules pip install -r requirements.txt

mkdir files/ mkdir files/data/ mkdir files/libs/ mkdir files/output/

-> shortstack git clone https://github.com/MikeAxtell/ShortStack.git files/libs/

• samtools 1.2
  wget "https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2" && tar xfj samtools-1.2.tar.bz2 && (cd samtools-1.2 && make) export PATH=/home/trigo/runs3/miRNA-MITE/samtools-1.2:${PATH}
• ViennaRNA wget https://www.tbi.univie.ac.at/RNA/download/ubuntu/ubuntu_17_04/viennarna_2.4.3-1_i386.deb sudo dpkg -i viennarna_2.4.3-1_i386.deb OR wget https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.2.tar.gz tar -zxvf ViennaRNA-2.4.3.tar.gz cd ViennaRNA-2.4.3 ./configure make sudo make install

nohup ./files/libs/ShortStack/ShortStack --readfile files/data/T --outdir files/output/sstack_genesseqs_mirna21 --genomefile files/output/genes_sequences.fasta --bowtie_cores 3 &