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check_deps.sh
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check_deps.sh
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#!/bin/bash
orthofinder_test=$(which orthofinder.py 2> /dev/null)
if [ $? -gt 0 ] || [ -z "${orthofinder_test}" ]
then
orthofinder_test=$(which orthofinder 2> /dev/null)
if [ $? -gt 0 ] || [ -z "${orthofinder_test}" ]
then
orthofinder_msg="OrthoFinder not installed"
orthofinder_test="0"
orthofinder_cmd="orthofinder"
else
orthofinder_msg="OrthoFinder OK"
orthofinder_test="1"
orthofinder_cmd="orthofinder"
fi
else
orthofinder_msg="OrthoFinder OK"
orthofinder_test="1"
orthofinder_cmd="orthofinder.py"
fi
diamond_test=$(which diamond 2> /dev/null)
if [ $? -gt 0 ] || [ -z "${diamond_test}" ]
then
diamond_msg="Diamond not installed"
diamond_test="0"
else
diamond_msg="Diamond OK"
diamond_test="1"
fi
parallel_test=$(which parallel 2> /dev/null)
if [ $? -gt 0 ] || [ -z "${parallel_test}" ]
then
parallel_msg="GNU Parallel not installed"
parallel_test="0"
else
parallel_msg="GNU Parallel OK"
parallel_test="1"
fi
flps_test=$(which fLPS2 2> /dev/null)
if [ $? -gt 0 ] || [ -z "${flps_test}" ]
then
flps_msg="fLPS2 not installed"
flps_test="0"
else
flps_msg="fLPS2 OK"
flps_test="1"
fi
seg_test=$(which seg 2> /dev/null)
if [ $? -gt 0 ] || [ -z "${seg_test}" ]
then
seg_msg="seg not installed"
seg_test="0"
else
seg_msg="seg OK"
seg_test="1"
fi
bed_test=$(which bedtools 2> /dev/null)
if [ $? -gt 0 ] || [ -z "${bed_test}" ]
then
bed_msg="bedTools not installed"
bed_test="0"
else
bed_msg="bedTools OK"
bed_test="1"
fi
echo -e "${orthofinder_test}\t${orthofinder_msg}\t${orthofinder_cmd}\n${diamond_test}\t${diamond_msg}\n${parallel_test}\t${parallel_msg}\n${flps_test}\t${flps_msg}\n${seg_test}\t${seg_msg}\n${bed_test}\t${bed_msg}"