giving executable permsission to the function for getting the GFF3 files
giving executable permsission to the function for getting the GFF3 files
#!/bin/bash
#
# This script is part of
# RACS v1.0 (2018/2019) -- Open source tools for Analizing ChIP-Seq data
#
# Shell script provided to obtain dataset for:
#
# Tetrahymena Thermophila
# GFF3: http://www.ciliate.org/system/downloads/T_thermophila_June2014.gff3
# FASTA: http://www.ciliate.org/system/downloads/T_thermophila_June2014_assembly.fasta
# and
#
# Oxytricha Trifallax"
# GFF3: http://oxy.ciliate.org/system/downloads/Oxytricha_trifallax_022112.gff3
# FASTA: http://oxy.ciliate.org/system/downloads/Oxytricha_trifallax_022112_assembly.fasta
###
# Tetrahymena Thermophila
TT_gff3_URL="http://www.ciliate.org/system/downloads/T_thermophila_June2014.gff3"
TT_fasta_URL="http://www.ciliate.org/system/downloads/T_thermophila_June2014_assembly.fasta"
#
# Oxytricha Trifallax
OXY_gff3_URL="http://oxy.ciliate.org/system/downloads/Oxytricha_trifallax_022112.gff3"
OXY_fasta_URL="http://oxy.ciliate.org/system/downloads/Oxytricha_trifallax_022112_assembly.fasta"
###
# select tool for downloading data...
CMD=`which curl`
if [ -z "$CMD" ]
then
CMD=`which wget`
else
CMD=$CMD" -L -O"
fi
echo "using $CMD..."
# Specify datasets for Tetrahymena Thermophila and Oxytrichia ....
datasets=" ${TT_gff3_URL} ${TT_fasta_URL} ${OXY_gff3_URL} ${OXY_fasta_URL} "
# download data...
for i in $datasets; do
echo $i;
$CMD $i;
done