conf_script_dy111

#!/bin/csh -f

####### names and directories #######

set mexecloc = '/local/users/pstar/programs' #this is the directory containing general_sw plus mexec and mexec_processing_scripts repositories
set cruiseloc = '/local/users/pstar' #this is the directory where your cruise processing directores live
set mexecver = 'v3'

set cruise = 'dy111'
set CRUISE = 'DY111'

#underway system and ship data remote mount points
#on jcr
###set usys = 'scs'
###set shipudr = '/mnt/data/cruise/jcr/current/scs/Compress'
###set shipcdr = '/mnt/data/cruise/jcr/current/ctd/$CRUISE'
###set shipvdr = '/mnt/data/cruise/jcr/current/adcp'
###set shipldr = '/mnt/data/cruise/jcr/current/ladcp'
###set isladcp = 1
#on cook/disco
set usys = 'techsas'
set shipudr = '/mnt/techsas/$CRUISE/NetCDF'
set shipcdr = '/mnt/CTD'

####### now actually set things up #######
#shouldn't need to change anything below this

if (! -e $cruiseloc/$cruise/mcruise/data) then
  mkdir -p $cruiseloc/$cruise/mcruise/data
endif
mkdir -p $cruiseloc/$cruise/mcruise/sw/general_sw

#link to generic cruise directory
#this is just so that you can have $cruiseloc/cruise/data/mexec_processing_scripts on your matlab path in ~/matlab/startup.m and be ready to run m_setup.m for the current cruise
if (-e $cruiseloc/cruise) then
  /bin/rm $cruiseloc/cruise
endif
cd $cruiseloc
ln -s $cruise/mcruise cruise

#make links to software and scripts
cd $cruise/mcruise/data
ln -s $mexecloc/mexec_processing_scripts_$mexecver mexec_processing_scripts
cd ../sw
ln -s $mexecloc/mexec_$mexecver mexec
cd general_sw
foreach d1 (`ls $mexecloc/general_sw`)
  ln -s $mexecloc/general_sw/$d1 $d1
end
cd ../..

echo "edit linkscripts and possibly other files in mexec-exec"
echo "edit m_setup.m to change data time origin, cruise name"
echo "and possibly some paths e.g. versions of external software packages"

#set up rest of data directory structure
cd data
mkdir -p mexec_housekeeping/version
mkdir mexec_housekeeping/history
mkdir -p collected_files/figures
mkdir -p ctd/RAW_CTD_FILES
mkdir ctd/ASCII_FILES
mkdir ctd/BOTTLE_CFC
mkdir ctd/BOTTLE_CO2
mkdir ctd/BOTTLE_NUT
mkdir ctd/BOTTLE_OXY
mkdir ctd/BOTTLE_SAL
mkdir ctd/BOTTLE_SHORE
mkdir ctd/WINCH
mkdir -p ladcp/ctd
mkdir -p ladcp/ix/checkpoints
mkdir ladcp/ix/raw
mkdir ladcp/ix/DL_GPS
mkdir ladcp/ix/DL_GPS_BT
mkdir ladcp/ix/DL_GPS_BT_SADCP
mkdir ladcp/rawdata
#mkdir -p ladcp/uh/pro
#mkdir ladcp/uh/raw
#cp $oldcruise/data/ladcp/uh/LADall ladcp/uh
mkdir plots
mkdir station_depths
mkdir -p vmadcp/mproc
mkdir -p vmadcp/postprocessing
mkdir -p vmadcp/atsea
mkdir -p vmadcp/spprocessing
#ln -s $shipudr scs_raw #flag for scs or techsas?
#mkdir scs_sed
#mkdir scs_mat
#echo "run sedexec_startall once $shipudr available"
mkdir -p techsas/netcdf_files_links
cd techsas
ln -s /local/users/pstar/mounts/techsas netcdf_files_rawdir_ship
ln -s netcdf_files_rawdir_ship netcdf_files_rawdir
ln -s netcdf_files_copy/$CRUISE/NetCDF netcdf_files_rawdir_local
mkdir techsas_link_logs
cd ..
#other directories (for processed underway data) are generated by running m_setup