
#**************************************************
#source this script to your .cshrc file will setup
#some defaults for EM software
#
#usage: put this line in your .cshrc file: "source /dors/cryoem/scripts/eladEMdefaults.csh" 
#
#Elad Binshtein 051818
#update 04092019
#**************************************************

	## cuda ##
sbset cuda80
sbset cuda90
sbset cuda91

	##focus cofig##
#ln -sfn /home/binshtem/.2dx ~
if (! -e ~/.2dx/) then
	mkdir ~/.2dx/
        ln -sf /dors/cryoem/home/binshtem/.2dx/2dx.cfg ~/.2dx/
endif

	## for relion2.0/3.0##
setenv RELION_PDFVIEWER_EXECUTABLE evince
setenv RELION_MOTIONCORR_EXECUTABLE /programs/x86_64-linux/motioncor2/1.0.5/MotionCor2_Cuda8.0_v1.0.5 ##for relion2
setenv RELION_MOTIONCOR2_EXECUTABLE /programs/x86_64-linux/motioncor2/1.2.1/motioncor2 ##for relion2.1/3
setenv RELION_CTFFIND_EXECUTABLE /home/sbgrid/programs/x86_64-linux/ctffind4/4.1.8/bin/ctffind
setenv RELION_GCTF_EXECUTABLE /programs/x86_64-linux/gctf/1.06/bin/Gctf-v1.06_sm_30_cu8.0_x86_64
setenv RELION_RESMAP_EXECUTABLE /programs/x86_64-linux/resmap/1.1.4/ResMap-1.1.4-linux64
setenv RELION_SUMMOVIE_EXECUTABLE /programs/x86_64-linux/summovie/1.0.2/bin/summovie
setenv RELION_UNBLUR_EXECUTABLE /programs/x86_64-linux/unblur/1.0.2/bin/unblur
setenv RELION_WARNING_LOCAL_MPI 8
setenv RELION_QSUB_TEMPLATE /dors/cryoem/scripts/accre_script/slurm_relion2_sbgrid_cpu.sh ## template for accre, for GPU change to slurm_relion2_gpu.sh
setenv RELION_QUEUE_NAME "pascal"
setenv RELION_QSUB_COMMAND "sbatch"
setenv RELION_QSUB_EXTRA1 "Walltime:"
setenv RELION_QSUB_EXTRA1_DEFAULT "0-05:00:00"
setenv RELION_QSUB_EXTRA2 "Memory Per CPU:"
setenv RELION_QSUB_EXTRA2_DEFAULT "5G"
setenv RELION_QSUB_EXTRA3 "GPU:"
setenv RELION_QSUB_EXTRA3_DEFAULT "4"
setenv RELION_QSUB_EXTRA4 "Account:"
setenv RELION_QSUB_EXTRA4_DEFAULT "csb_gpu_acc"
setenv RELION_QSUB_EXTRA5 "Local Scratch Disk Space:"
setenv RELION_QSUB_EXTRA5_DEFAULT 

	##******* for relion3.0 ********##
setenv RELION_QSUB_EXTRA_COUNT 5


