conf_script_dy111 reflects change to uhdas and moving templates to

mexec_processing_scripts and exec to mexec-exec git (so nothing
should need to be copied from older cruises)

cruisedir_setup_scripts/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
+
+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
+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 $shipudr available"
+mkdir -p techsas/netcdf_files_links
+mkdir -p techsas/netcdf_files_copy
+cd techsas
+ln -s /local/users/pstar/mounts/techsas netcdf_files_rawdir_ship
+ln -s netcdf_files_rawdir_ship netcdf_files_rawdir
+ln -s netcdf_files_copy/$CRUISE/NetCDF netcdf_files_rawdir_local
+mkdir techsas_link_logs
+cd ..
+#other directories (for processed underway data) are generated by running m_setup