# Install perl packages
sudo cpanm Bio::Perl Text::CSV::Hashify Readonly File::Copy Getopt::Declare File::Spec

# Install kallisto
See https://pachterlab.github.io/kallisto/download

# Install hmmsearch
See https://hmmer.org

# Install hmmcompete
See https://www.mdpi.com/2072-6651/9/8/245/s1
or https://github.com/koualab/hmmcompete

# Download itap
git clone https://github.com/koualab/itap.git $HOME/itap

# Copy itap to bin folder and hmm db to db folder
sudo cp itap /usr/local/bin
sudo mkdir /usr/share/itap/db
sudo cp itap/db/* /usr/share/itap/db

# Add path to $PATH
echo "$PATH:/usr/share/itap/db/" >> ~/.bashrc

itap -t transcripts.fa.gz -f reads_R1.fq.gz -r reads_R2.fq.gz

General:
	--transcripts, -t    Specify transcriptome file [required]
	--forward_reads, -f  Specify forward reads file [required]
	--reverse_reads, -r  Specify reverse reads file [required]

Outputs:
	--outdir, -o  Specify output folder name
	--dbdir       Specify path to databases folder
	--force       Force reuse of output folder

Setup:
	--hmm         Specify the path to personal hmm lib
	--quiet       Decrease verbosity

Computation:
	--cpus        Specify number of threads

Standard meta-options:
	--version, -v   Print program version and exit
	--usage, -u     Print program usage and exit
	--man           Print man page
	--help, -h      Print help and exit