put conf scripts here, removed old vmadcp (vmdas) scripts, some other reorganisation

conf_script_TPL

-# copy TPLs and edit oceanlogger
-
-set in = scs_raw
-set ot = scs_sed
-
-cd ~
-cd cruise
-cd data
-
-/bin/cp -p $in/*TPL $ot
-
-cd $ot
-
-cat << ! >! wk
-126,oceanlogger-sampletimeyyyy,YYYY
-126,oceanlogger-sampletimeddd,DDD
-126,oceanlogger-sampletimehhmmss,HH:MM:SS
-!
-
-cat oceanlogger.TPL | sed -n '2,$p' >> wk
-
-mv oceanlogger.TPL oceanlogger.TPL_original
-mv wk oceanlogger.TPL

cruisedir_setup_scripts/conf_script_dy105

+#!/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 = 'dy105'
+set CRUISE = 'DY105'
+set oldcruise = 'jc159' #this is the cruise to copy templates and exec from
+set OLDCRUISE = 'JC159'
+
+#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'
+set shipvdr1 = '/mnt/adcp75'
+set shipvdr2 = '/mnt/adcp150'
+
+####### 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
+#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
+
+#copy data/exec and data/templates
+cd $cruiseloc/$cruise/mcruise/data
+#cp -Rp $cruiseloc/$oldcruise/mcruise/data/templates .
+#cp -Rp $cruiseloc/$oldcruise/mcruise/data/exec . 
+cp -Rp $cruiseloc/$oldcruise/data/templates .
+cp -Rp $cruiseloc/$oldcruise/data/exec . 
+echo "edit linkscripts and possibly other files in exec"
+
+#modify m_setup
+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 are generated by running m_setup

cruisedir_setup_scripts/conf_script_jr17001

+#!/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 = 'jr18002'
+set CRUISE = 'JR18002'
+set oldcruise = 'jr17001' #this is the cruise to copy templates and exec from
+set OLDCRUISE = 'JR17001'
+
+#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'
+#set shipvdr1 = '/mnt/adcp75'
+#set shipvdr2 = '/mnt/adcp150'
+
+####### now actually set things up #######
+#shouldn't need to change anything below this
+
+if (! -e $cruiseloc/$cruise/data) then
+  mkdir -p $cruiseloc/$cruise/data
+endif
+mkdir -p $cruiseloc/$cruise/sw
+
+#link to generic cruise
+#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 cruise
+
+#make links to software and scripts
+cd $cruise/data
+ln -s $mexecloc/mexec_processing_scripts_$mexecver mexec_processing_scripts
+cd ../sw
+ln -s $mexecloc/mexec_$mexecver mexec
+foreach d1 (`ls $mexecloc/general_sw`)
+  ln -s $mexecloc/general_sw/$d1 $d1
+end
+
+#copy and modify data/exec and data/templates
+cd $mexecloc/$cruise/data
+cp -Rp $mexecloc/$oldcruise/data/templates .
+cp -Rp $mexecloc/$oldcruise/data/exec . 
+cd exec
+foreach f1 (`find ./ -maxdepth 1 -type f -name '*script*'`)
+  set "s:$oldcruise:$cruise:" $f1 | sed "s:$OLDCRUISE:CRUISE:" | set "s:mexecloc:$mexecloc:" | sed "s:shipudr:$shipudr:" | sed "s:shipcdr:$shipcdr:" | sed "s:shipldr:$shipldr:" > tmp
+  mv tmp $f1
+end
+#however you may still need to edit files in exec, specifically the linkscripts, to reflect naming conventions of data files on remote machines
+
+#modify m_setup
+
+#set up data directory structure
+

cruisedir_setup_scripts/conf_script_jr18002

+#!/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 = 'jr18002'
+set CRUISE = 'JR18002'
+set oldcruise = 'jr17001' #this is the cruise to copy templates and exec from
+set OLDCRUISE = 'JR17001'
+
+#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'
+#set shipvdr1 = '/mnt/adcp75'
+#set shipvdr2 = '/mnt/adcp150'
+
+####### 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
+
+#link to generic cruise
+#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
+foreach d1 (`ls $mexecloc/general_sw`)
+  ln -s $mexecloc/general_sw/$d1 $d1
+end
+
+#copy data/exec and data/templates
+cd $cruiseloc/$cruise/mcruise/data
+cp -Rp $cruiseloc/$oldcruise/mcruise/data/templates .
+cp -Rp $cruiseloc/$oldcruise/mcruise/data/exec . 
+echo "edit linkscripts and possibly other files in exec"
+
+#modify m_setup
+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/rawdata
+mkdir -p ladcp/uh/pro
+mkdir ladcp/uh/raw
+#cp $oldcruise/data/ladcp/uh/LADall ladcp/uh
+mkdir plots
+mkdir station_depths
+mkdir -p vmadcp/{$cruise}_os75
+#mkdir -p vmadcp/$cruise_os150
+ln -s $shipudr scs_raw #flag for scs or techsas?
+mkdir scs_sed
+mkdir scs_mat
+echo "run sedexec_startall once $shipudr available"
+#other directories are generated by running m_setup

cruisedir_setup_scripts/conf_script_jr18003

+#!/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 directories live
+set mexecver = 'v3'
+
+set cruise = 'jr18003'
+set CRUISE = 'JR18003'
+set oldcruise = 'jr18002' #this is the cruise to copy templates and exec from
+set OLDCRUISE = 'JR18002'
+
+#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'
+#set shipvdr1 = '/mnt/adcp75'
+#set shipvdr2 = '/mnt/adcp150'
+
+####### 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
+
+#link to generic cruise
+#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
+foreach d1 (`ls $mexecloc/general_sw`)
+  ln -s $mexecloc/general_sw/$d1 $d1
+end
+
+#copy data/exec and data/templates
+cd $cruiseloc/$cruise/mcruise/data
+cp -Rp $cruiseloc/$oldcruise/mcruise/data/templates .
+cp -Rp $cruiseloc/$oldcruise/mcruise/data/exec . 
+echo "edit linkscripts and possibly other files in exec"
+
+#modify m_setup
+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 collected_files/ctdlists
+mkdir -p collected_files/samlists
+mkdir -p ctd/RAW_CTD_FILES
+mkdir ctd/ASCII_FILES
+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/rawdata
+mkdir plots
+mkdir station_depths
+mkdir -p vmadcp/{$cruise}_os75
+ln -s $shipudr scs_raw #flag for scs or techsas?
+mkdir scs_sed
+mkdir scs_mat
+echo "run sedexec_startall once $shipudr available"
+#other directories are generated by running m_setup

ctd_linkscript~

-#!/bin/csh -f
-#
-#copy the raw and SBE-processed CTD files from the ship machine
-#then make links to the files to be ingested by mexec using the expected name format
-
-cd /local/users/pstar/cruise/data
-
-set cpre = JC159
-set cruise = jc159
-set ctdloc = /local/users/pstar/mounts/mnt_cruise_data/Specific_Equipment/CTD/
-
-rsync -av ${ctdloc}/Processed\ Data/*.cnv ctd/ASCII_FILES/
-rsync -av ${ctdloc}/Raw\ Data/*.bl ctd/ASCII_FILES/
-rsync -av ${ctdloc}/Processed\ Data/*.ros ctd/ASCII_FILES/
-rsync -av ${ctdloc}/Raw\ Data/*.hex ctd/RAW_CTD_FILES/
-rsync -av ${ctdloc}/Raw\ Data/*.XMLCON ctd/RAW_CTD_FILES/
-rsync -av ${ctdloc}/Raw\ Data/*.hdr ctd/RAW_CTD_FILES/
-rsync -av ${ctdloc}/Processed\ Data/*.btl ctd/ASCII_FILES/
-
-cd ctd/ASCII_FILES
-
-foreach i (`ls ${cpre}_???_Align_CTM.cnv`)
-   set num = `awk -v nm="$i" 'BEGIN {print substr(nm,index(nm,"_Align")-3,3)}'`
-   set linkfile = ctd_${cruise}_${num}_ctm.cnv 
-   echo $linkfile
-   if (! -e $linkfile) then
-      echo Making link $linkfile for raw file $i
-     ln -s $i $linkfile
-   endif
-end
-
-foreach i (`ls ${cpre}_???.bl`)
-   set num = `awk -v nm="$i" 'BEGIN {print substr(nm,index(nm,".bl")-3,3)}'`
-   set linkfile = ctd_${cruise}_${num}.bl
-   if (! -e $linkfile) then
-      echo Making link $linkfile for raw file $i
-      ln -s $i $linkfile
-   endif
-end
-
-cd ../..

oxy_linkscript_jr302

-#!/bin/csh -f
-#
-#Script by BAK on cruise jc032 to create symbolic links.
-#Modified by BGW for cruise di346
-#Modified by CPA to import oxygen files from /Drobo 
-#The assumption is that the raw files are named
-#in a way that identifies the instrument, eg
-# ctd_jc032_001_ctm.cnv
-#
-#
-# The initial foreach command will need to be modified for each cruise.
-#cd data
-#cd ctd
-# modded bak di368
-# modded bak jr302 8 jun 2014 to use rsync
-cd
-cd cruise/data
-cd ctd
-cd BOTTLE_OXY 
-
-rsync -av jcrfs_oxy/* .
-
-
-
-foreach i (`ls JR302OXY???.csv`)
-#echo $i
-set num = `echo $i | awk '{print substr($1,9,3)}'`
-set cruise = 'jr302'
-#echo $num
-
-set linkfile = oxy_${cruise}_${num}.csv
-#echo $linkfile
-
-if (! -e $linkfile) then
-  echo Making link $linkfile for raw file $i
-  ln -s $i $linkfile
-endif
-end

oxy_linkscript_jr302_unc

-#!/bin/csh -f
-#
-#Script by BAK on cruise jc032 to create symbolic links.
-#Modified by BGW for cruise di346
-#Modified by CPA to import oxygen files from /Drobo 
-#The assumption is that the raw files are named
-#in a way that identifies the instrument, eg
-# ctd_jc032_001_ctm.cnv
-#
-#
-# The initial foreach command will need to be modified for each cruise.
-#cd data
-#cd ctd
-# modded bak di368
-# modded bak jr302 8 jun 2014 to use rsync
-cd
-cd cruise/data
-cd ctd
-cd BOTTLE_OXY 
-
-#rsync -av jcrfs_oxy/* .
-
-
-
-foreach i (`ls unc/JR302OXY???.csv`)
-#echo $i
-set num = `echo $i | awk '{print substr($1,13,3)}'`
-set cruise = 'jr302'
-#echo $num
-
-set linkfile = oxy_${cruise}_${num}_unc.csv
-#echo $linkfile
-
-if (! -e $linkfile) then
-  echo Making link $linkfile for raw file $i
-  ln -s $i $linkfile
-endif
-end

synclists

-#!/bin/csh 
-# jr302 bak
-cd
-cd data
-cd ctd
-#rsync -av samlist_jr302_???_co2.csv ../legwork/jr302_co2
-#rsync -av samlist_jr302_???_ch4.csv ../legwork/jr302_ch4
-#rsync -av samlist_jr302_???_nuts.csv ../legwork/jr302_nut
-#rsync -av startend_jr302_??? ../legwork/jr302_surfactant
-# jr302 at end of crusie when legwork is no longer available
-rsync -av samlist_jr302_???_co2.csv ../from_legwork/jr302_co2
-rsync -av samlist_jr302_???_ch4.csv ../from_legwork/jr302_ch4
-rsync -av samlist_jr302_???_nuts.csv ../from_legwork/jr302_nut
-rsync -av startend_jr302_??? ../from_legwork/jr302_surfactant

vmadcp_linkscript

-#!/bin/csh -f
-#
-#foreach i (`ls rawdata/*JC32*`)
-
-# overhaul on jr302 may 2014, to fit with new python codas
-# may need modification on cook/discovery to handle os75 and os150
-cd /local/users/pstar/cruise/data/vmadcp/
-
-echo "synchronising raw data"
-rsync -av ../jcrfs/current/adcp/ jr17001_os75/vmdas_data/
-# jcrfs is link to raw data on jrlb
-
-echo "making links to individual sequence directories"
-cd jr17001_os75/vmdas_data
-foreach i (`ls *.*`) # list all *.* to avoid collecting N1R directory
-set num = `echo $i | awk -F'.' '{print substr($1,length($1)-9,3)}'`
-
-set linkdir = rawdata{$num}
-
-if (! -e $linkdir) then
-  echo making $linkdir
-  mkdir $linkdir
-endif
-
-set rfile = $i
-set lfile = $i
-cd $linkdir
-if (! -e $lfile) then
-  echo linking ${lfile} to ${rfile}
-  ln -s ../${rfile} ${lfile}
-endif
-cd ..
-
-end

vmadcp_linkscript_jc145

-#!/bin/csh -f
-#
-# This script assumes that a mount to adcp data has been setup and files are named like
-# /local/users/pstar/cruise/data/vmadcp/jc145_os75/rawraw/OS075_JC145004_000000.ENR  
-# or mostly
-# /local/users/pstar/cruise/data/vmadcp/jc145_os75/rawraw/ADCP75_BTon_nosync010_000000.ENR
-# note unfortunately on this cruise the names didn't change for BToff files, 
-# however BT status is determined separately
-#
-# Go through loop once for each adcp
-
-set cruise = jc145
-set CRUISE = JC145
-    
-foreach adp ('75' '150')
-  echo $adp
-  cd /local/users/pstar/cruise/data/vmadcp
-  cd ${cruise}_os${adp}
-
-  echo "Synchronising raw data for the $adp"
-  rsync -av /mnt/adcp${adp}/${CRUISE}/raw_data/ rawraw
-
-# --------------------------------------------------
-# These next steps were needed as naming of files was not correct
-  cd rawdata
-  foreach fl (`ls ../rawraw/ADCP${adp}_BT*`)
-    set bb = `echo $fl | awk '{print substr($1,length($1)-13,length($1))}'`
-    set fl2 = OS${adp}_JC145_${bb}
-    if (! -e $fl2) then
-      ln -s $fl $fl2
-    endif
-  end
-  cd ..
-# --------------------------------------------------
-
-end
-
-#JC145 only: now deal with the initial (transit) files, one sequence at a time because
-#the sequences will have to be renumbered
-cd /local/users/pstar/cruise/data/vmadcp/jc145_os75/rawdata
-foreach fl (`ls ../rawraw/OS75_JC145001*`)
-  set bb = `echo $fl | awk '{print substr($1,length($1)-9,length($1))}'`
-  set fl2 = OS75_JC145_901_${bb}
-  if (! -e $fl2) then
-    ln -s $fl $fl2
-  endif
-end
-foreach fl (`ls ../rawraw/OS75_JC145002*`)
-  set bb = `echo $fl | awk '{print substr($1,length($1)-9,length($1))}'`
-  set fl2 = OS75_JC145_902_${bb}
-  if (! -e $fl2) then
-    ln -s $fl $fl2
-  endif
-end
-cd /local/users/pstar/cruise/data/vmadcp/jc145_os150/rawdata
-foreach fl (`ls ../rawraw/OS150_JC145001*`)
-  set bb = `echo $fl | awk '{print substr($1,length($1)-9,length($1))}'`
-  set fl2 = OS150_JC145_901_${bb}
-  if (! -e $fl2) then
-    ln -s $fl $fl2
-  endif
-end
-foreach fl (`ls ../rawraw/OS150_JC145002*`)
-  set bb = `echo $fl | awk '{print substr($1,length($1)-9,length($1))}'`
-  set fl2 = OS150_JC145_902_${bb}
-  if (! -e $fl2) then
-    ln -s $fl $fl2
-  endif
-end

vmadcp_linkscript_jc145a

-#!/bin/csh -f
-#
-# This script assumes that a mount to adcp data has been setup and files are named like
-# /local/users/pstar/Acoustics/OS75kHz/raw_data/OS075_DY039004_000000.ENR  
-# /local/users/pstar/Acoustics/OS150kHz/raw_data/OS150_DY039002_000000.LOG
-# Works on dy039 might may need to modify on next cruise
-#
-# Go through loop once for each adcp
-foreach adp ('75' '150')
-  cd /local/users/pstar/cruise/data
-  cd va$adp
-  if ($adp == '75') then  
-	  set adpx = '075'
-	  echo $adpx
-  else if ($adp == '150') then
-	  set adpx = '150'
-	  echo $adpx
-  endif  
-
-  echo "Synchronising raw data for the v$adp"
-#  rsync -av /local/users/pstar/Acoustics/OS${adp}kHz/raw_data/OS${adpx}* rawdata
-  rsync -av /mnt/adcp${adp}/JC145/raw_data/OS* rawraw
-
-# --------------------------------------------------
-# These next steps were needed as nameing of files was not correct and need to add an extra underscore
-  cd rawdata
-  foreach fl (`ls ../rawraw/*`)
-    #set aa = `echo $fl | awk '{print substr($1,11,11)}'`
-    set aa = `echo $fl | awk '{print substr($1,11,length($1)-24)}'`
-    #set bb = `echo $fl | awk '{print substr($1,22,14)}'`
-    set bb = `echo $fl | awk '{print substr($1,length($1)-13,length($1))}'`
-    set fl2 = ${aa}_${bb}
-    echo $fl
-    echo $fl2
-    if (! -e $fl2) then
-      ln -s $fl $fl2
-    endif
-  end
-  cd ..
-# --------------------------------------------------
-
-  echo "Creating directories for OS$adp"
-  foreach i (`ls rawdata/*`)
-    set num = `echo $i | awk -F'_' '{print substr($3,length($3)-2,3)}'`
-# Extract file extension, e.g. for i = rawdata/OS150_DY039005_000000.ENX, num = 'ENR'
-    set fname = `echo $i | awk '{print substr($1,9,26)}'`
-    set movedir = rawdata{$num}
-
-# Create new directory like 'rawdataENX' if does nto already exist
-   if (! -e $movedir) then
-     echo making $movedir
-     mkdir $movedir
-   endif
-
-# Now create links from new directories to original files in rawdata with corresponding suffix
-   set rfile = ../${i}
-   set lfile = ${movedir}/${fname}
-   if (! -e ${lfile}) then
-     echo linking ${lfile} to ${rfile}
-     ln -s ${rfile} ${lfile}
-   endif
-   end
-end
-
-

vmadcp_linkscript_jr302

-#!/bin/csh -f
-#
-#foreach i (`ls rawdata/*JC32*`)
-
-# overhaul on jr302 may 2014, to fit with new python codas
-# may need modification on cook/discovery to handle os75 and os150
-cd /local/users/pstar/cruise/data/vmadcp
-
-echo "synchronising raw data"
-rsync -av jcrfs_adcp75/* raw_os75
-# jcrfs_adcp75 is link to raw data on jrlb
-# raw_os75 is link to directory in codas_shared available in virtual box.
-# raw_os75 -> codas_shared/vmdas_data/jr281_os75      so raw directory must already be configured in codas_shared
-
-echo "making links in old codas directory"
-foreach i (`ls raw_os75/*.*`) # list all *.* to avoid collecting N1R directory
-#set num = `echo $i | awk -F'_' '{print substr($2,length($2)-2,3)}'`
-# this extracts the file extension, e.g. for i = rawdata/D344os150001_000000.ENR, num is then set as ENR, ZBS 19.10.2009
-set num = `echo $i | awk -F'.' '{print substr($1,length($1)-9,3)}'`
-set fname = `echo $i | awk '{print substr($1,10,19)}'` # start at char 10 allows for removing raw_os75/ 
-
-cd /local/users/pstar/cruise/data/vmadcp/v75
-
-set linkdir = rawdata{$num}
-
-if (! -e $linkdir) then
-  echo making $linkdir
-  mkdir $linkdir
-endif
-
-
-set rfile = ../../${i}
-set lfile = ${linkdir}/${fname}
-if (! -e ${lfile}) then
-  echo linking ${lfile} to ${rfile}
-  ln -s ${rfile} ${lfile}
-endif
-
-end

vmadcp_movescript

-#!/bin/csh -f
-#
-#foreach i (`ls rawdata/*JC32*`)
-foreach i (`ls rawdata/*`)
-#set num = `echo $i | awk -F'_' '{print substr($2,length($2)-2,3)}'`
-# this extracts the file extension, e.g. for i = rawdata/D344os150001_000000.ENR, num is then set as ENR, ZBS 19.10.2009
-set num = `echo $i | awk -F'.' '{print substr($1,length($1)-9,3)}'`
-
-set movedir = rawdata{$num}
-
-if (! -e $movedir) then
-  echo making $movedir
-  mkdir $movedir
-endif
-
-echo moving $i to $movedir
-mv {$i} {$movedir}
-
-end

vmadcp_movescript_150khz

-#!/bin/csh -f
-#
-#foreach i (`ls rawdata/*JC32*`)
-foreach i (`ls rawdata/*`)
-#set num = `echo $i | awk -F'_' '{print substr($2,length($2)-2,3)}'`
-# this extracts the file extension, e.g. for i = rawdata/D344os150001_000000.ENR, num is then set as ENR, ZBS 19.10.2009
-set num = `echo $i | awk -F'.' '{print substr($1,length($1)-9,3)}'`
-
-set movedir = rawdata{$num}
-
-if (! -e $movedir) then
-  echo making $movedir
-  mkdir $movedir
-endif
-
-echo moving $i to $movedir
-mv {$i} {$movedir}
-
-end

vmadcp_movescript_75khz

-#!/bin/csh -f
-#
-#foreach i (`ls rawdata/*JC32*`)
-foreach i (`ls rawdata/*`)
-#set num = `echo $i | awk -F'_' '{print substr($2,length($2)-2,3)}'`
-# this extracts the file extension, e.g. for i = rawdata/D344os150001_000000.ENR, num is then set as ENR, ZBS 19.10.2009
-set num = `echo $i | awk -F'.' '{print substr($1,length($1)-9,3)}'`
-
-set movedir = rawdata{$num}
-
-if (! -e $movedir) then
-  echo making $movedir
-  mkdir $movedir
-endif
-
-echo moving $i to $movedir
-mv {$i} {$movedir}
-
-end