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compute_environment.cfg
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compute_environment.cfg
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#!/bin/bash
#If you are running in a torque cluster environment, these variables tell the fmriprep pipeline to load specific modules
#before executing the pipeline. This sets up relevant fmriprep software dependencies in the execution environment.
#On the other hand, if all of these programs are already in the system path (e.g., installed locally), the modules are
#irrelevant and can be commented out for your environment.
export G=/gpfs/group/mnh5174/default #filesystem root for shared storage (and programs)
torque_modules_root=$G/sw/modules #where user-owned module files live on the cluster
#afni_module=afni/19.0.26
afni_module=afni/20.1.05
fsl_module=fsl/6.0.1
ants_module=ants/2.2.0
freesurfer_module=freesurfer/stable-pub-v6.0.0
r_module=r/3.6.0
pandoc_module=pandoc/2.9.2.1
c3d_module=c3d/1.1.0
node_module=node/12.16.3
fmriprep_virtualenv="$G/lab_resources/fmriprep_python" #virtual environment containing fmriprep
#ensure that locations of dcm2niix and heudiconv are in the PATH and preferred over alternatives
dcm2niix_location="$G/lab_resources/bin/dcm2niix"
heudiconv_location="$G/lab_resources/lab_python3/bin/heudiconv" #heudiconv 0.8 in python3 (preferred)
#heudiconv_location="$G/lab_resources/lab_python/bin/heudiconv" #heudiconv 0.5.1 in python2 (deprecated)
mriqc_location="$G/lab_resources/lab_python3/bin/mriqc" #is the binary sufficient to run, or do we need to load the virtualenv?
local_binaries_location="$G/bin"
#general qsub arrangements
#qsub_allocation=mnh5174_c_g_sc_default
#qsub_allocation=m5m_a_g_sc_default
qsub_allocation=open
#parameters for fmriprep qsub
fmriprep_walltime=36:00:00 #36 hours
fmriprep_nthreads=4 #number of threads in compute job
#parameters for heudiconv
heudiconv_walltime=2:00:00
#parameters for mriqc
mriqc_walltime=32:00:00
mriqc_nthreads=3
#Setup for dcm2niix and heudiconv -- do not modify
#If you don't need to add these programs to your path, just set the dcm2niix_location and heudiconv_location variables to empty
if [ -n "$dcm2niix_location" ]; then
[ ! -r "$dcm2niix_location" ] && echo "Cannot access dcm2niix at $dcm2niix_location" && exit 1
curloc=$(which dcm2niix) || true
if [ "$curloc" != "$dcm2niix_location" ]; then
export PATH="$(dirname $dcm2niix_location):$PATH" #add to front of path
fi
fi
if [ -n "$heudiconv_location" ]; then
[ ! -r "$heudiconv_location" ] && echo "Cannot access heudiconv at $heudiconv_location" && exit 1
curloc=$(which heudiconv) || true
if [ "$curloc" != "$heudiconv_location" ]; then
export PATH="$(dirname $heudiconv_location):$PATH" #add to front of path
fi
fi