diff --git a/akeake/backup_core_local b/akeake/backup_core_local
new file mode 100755
index 0000000000000000000000000000000000000000..d939013f508ffb90c88de8c946cdca6141f7c2d5
--- /dev/null
+++ b/akeake/backup_core_local
@@ -0,0 +1,50 @@
+#!/bin/csh
+# DAS adapt from previous version for remote sync
+
+if ($#argv != 4) then
+ echo Wrong number of arguements
+else
+ echo - root_path = $1
+ echo - sync_dir = $2
+ echo - back_dir = $3
+ echo - backuplog = $4
+endif
+
+set root_path = $1
+set sync_dir = $2
+set back_dir = $3
+set backuplog = $4
+
+if (-e $back_dir) then
+ echo $back_dir exists
+ exit
+else
+ mkdir $back_dir
+endif
+
+if (-e $sync_dir) then
+ echo ' '
+else
+ echo $sync_dir does not exist
+ exit
+endif
+
+# Sync all of the cruise directory
+echo Going to sync: $root_path
+echo to: $sync_dir,
+echo backup changed files to $back_dir
+echo and record in logfile $backuplog,
+echo ' '
+echo ------------- >> $backuplog
+echo Syncing $root_path to $sync_dir >> $backuplog
+echo Start `date` >> $backuplog
+
+rsync -v -a --delete -b --backup-dir=$back_dir $root_path $sync_dir
+
+set how_much1 = `du -sm $sync_dir`
+set how_much2 = `du -sm $back_dir`
+echo done copying
+echo Finish `date` >> $backuplog
+echo Total size '(Mb)': $how_much1 >> $backuplog
+echo Total size '(Mb)': $how_much2 >> $backuplog
+echo ------------- >> $backuplog
diff --git a/akeake/mstar_backup b/akeake/mstar_backup
new file mode 100755
index 0000000000000000000000000000000000000000..f1ec7ec712f85570293749de88f277c716654726
--- /dev/null
+++ b/akeake/mstar_backup
@@ -0,0 +1,118 @@
+#!/bin/csh
+# Backup script for use on RAPID cruises
+# Data is copied to an external connected to main workstation
+# Drive mounted in /media
+#
+# This version by DAS Updated Tue 28th 2017. Edited previous verions used
+# for remote backup on RAPID cruises
+# 1) syncs data from "cruise" directory, and creates a bakup of all changed files
+# 2) syncs data from "rapid/osnap" directory, and creates a bakup of all changed files
+# 3) syncs data from "Desktop" directory, and creates a bakup of all changed files
+# When change for a new cruise need to change
+# - drive names
+# - $root
+# - $cru
+
+# Variables for pathnames
+set cru = jc145
+set CRU = JC145
+set root = /local/users/pstar/rpdmoc/
+set rapiddir = rapid # Could be osnap
+set usersdir = users
+
+# Which drive are we using and is it there?
+echo ' '
+echo `date` ' Starting backup'
+echo ' '
+echo -n 'Which disk are you using? Enter '1', '2', or '0': '
+set drq = $<
+echo $drq
+if ($drq == 1) then
+ set drive_name = ${CRU}_back_1
+else if ($drq == 2) then
+ set drive_name = ${CRU}_back_22
+else if ($drq == 0) then
+ set drive_name = ${CRU}_back
+else
+ echo 'Input not recognised'
+ exit
+endif
+
+# Drive pathname
+set drive_path = '/media/'${drive_name}
+
+if (-e ${drive_path}) then
+ echo Drive connected
+else
+ echo ${drive_path} ' Does not seem to be there'
+# exit
+endif
+
+# Create a logfile for the backup
+set now = `date +%Y%m%d%H%M%S`
+set backuplog = ${drive_path}/backup_logs/backup_log_${now}
+if (-e $backuplog) then
+ echo $backuplog exists
+ exit
+else
+ touch $backuplog
+endif
+
+# -----------------------------------------------------------------
+# First backup the cruise directory
+set root_path_cru = ${root}${cru}
+set sync_cru = ${drive_path}/cruise_${cru}_sync_$drq
+set back_cru = ${drive_path}/cruise_${cru}_back_$drq/backup_${now}
+
+# Call the main routine
+# ----------------------------------------------------
+backup_core_local $root_path_cru $sync_cru $back_cru $backuplog
+# ----------------------------------------------------
+
+# --------------------------------------------------------------------
+# Sync all of the RAPID directory
+set now = `date +%Y%m%d%H%M%S`
+set root_path_rap = $root$rapiddir
+set sync_rap = ${drive_path}/${rapiddir}_${cru}_sync_$drq
+set back_rap = ${drive_path}/${rapiddir}_${cru}_back_$drq/backup_${now}
+
+# Call the main routine
+# ----------------------------------------------------
+backup_core_local $root_path_rap $sync_rap $back_rap $backuplog
+# ----------------------------------------------------
+
+# --------------------------------------------------------------------
+# Sync all of the RAPID directory
+set now = `date +%Y%m%d%H%M%S`
+set root_path_users = $root$usersdir
+set sync_users = ${drive_path}/${usersdir}_${cru}_sync_$drq
+set back_users = ${drive_path}/${usersdir}_${cru}_back_$drq/backup_${now}
+
+# Call the main routine
+# ----------------------------------------------------
+backup_core_local $root_path_users $sync_users $back_users $backuplog
+# ----------------------------------------------------
+
+# --------------------------------------------------------------------
+# Sync all of the Desktop/dy054 directory
+set now = `date +%Y%m%d%H%M%S`
+set deskdir = '../Desktop'
+set root_path_desk = $root$deskdir
+set sync_desk = ${drive_path}/desk_${cru}_sync_$drq
+set back_desk = ${drive_path}/desk_${cru}_back_$drq/backup_${now}
+
+# Call the main routine
+# ----------------------------------------------------
+backup_core_local $root_path_desk $sync_desk $back_desk $backuplog
+# ----------------------------------------------------
+
+# ------------------------------------------------------------------
+# And finally copy log of backup to oceanus
+set olog = /backup_logs
+
+# Don't want to time out on password so check ok now
+echo 'Press return to copy:' $backuplog $root_path_desk$olog
+set qqq = $<
+scp $backuplog $root_path_cru$olog
+echo ' '
+echo `date` - Backup finished
diff --git a/akeake/rapid_sync_from_noc b/akeake/rapid_sync_from_noc
new file mode 100755
index 0000000000000000000000000000000000000000..11170b3e5058e5e79871f015b5ec970951130379
--- /dev/null
+++ b/akeake/rapid_sync_from_noc
@@ -0,0 +1,21 @@
+#!/bin/csh
+
+# Where we will copy from
+set remote_fs = 'surman@neyman:'
+set fromDir = '/noc/mpoc/rpdmoc/'
+#
+set local_path = '/local/users/pstar/rpdmoc'
+# Edit following to make list of things to copy
+set dirs2copy = 'doc_library bathym_data tide_model hydro CTD_archive jc145 dy039 jc103 d382 jc064 rapid mocha_ab1403 mocha_ab1705 mocha_ab1209 mocha_ab1104 waveglider_telem_trial_2018 Florida_Straits'
+
+# The now loop through the list
+foreach dd ($dirs2copy)
+ echo --- $fromDir$dd ---
+ set from_path = $remote_fs$fromDir$dd
+
+ rsync -v -a $from_path $local_path
+ echo done copying
+ echo Finish `date`
+
+ echo -------------
+end
diff --git a/akeake/rmate b/akeake/rmate
new file mode 100755
index 0000000000000000000000000000000000000000..a813b0a4a83ea04a5b0ebee727cb410789ca53b8
--- /dev/null
+++ b/akeake/rmate
@@ -0,0 +1,228 @@
+#!/usr/bin/env ruby
+# encoding: UTF-8
+
+$VERBOSE = true # -w
+$KCODE = "U" if RUBY_VERSION < "1.9" # -KU
+
+require 'optparse'
+require 'socket'
+require 'tempfile'
+require 'yaml'
+require 'fileutils'
+
+module Rmate
+ DATE = "2017-02-10"
+ VERSION = "1.5.9"
+ VERSION_STRING = "rmate version #{Rmate::VERSION} (#{Rmate::DATE})"
+
+ class Settings
+ attr_accessor :host, :port, :unixsocket, :wait, :force, :verbose, :lines, :names, :types
+
+ def initialize
+ @host, @port, @unixsocket = 'localhost', 52698, '~/.rmate.socket'
+
+ @wait = false
+ @force = false
+ @verbose = false
+ @lines = []
+ @names = []
+ @types = []
+
+ read_disk_settings
+
+ @host = ENV['RMATE_HOST'].to_s if ENV.has_key? 'RMATE_HOST'
+ @port = ENV['RMATE_PORT'].to_i if ENV.has_key? 'RMATE_PORT'
+ @unixsocket = ENV['RMATE_UNIXSOCKET'].to_s if ENV.has_key? 'RMATE_UNIXSOCKET'
+
+ parse_cli_options
+
+ @host = parse_ssh_connection if @host == 'auto'
+ end
+
+ def read_disk_settings
+ [ "/etc/rmate.rc", "/usr/local/etc/rmate.rc", "~/.rmate.rc"].each do |current_file|
+ file = File.expand_path current_file
+ if File.exist? file
+ params = YAML::load(File.open(file))
+ @host = params["host"] unless params["host"].nil?
+ @port = params["port"] unless params["port"].nil?
+ @unixsocket = params["unixsocket"] unless params["unixsocket"].nil?
+ end
+ end
+ end
+
+ def parse_cli_options
+ OptionParser.new do |o|
+ o.on( '--host=name', "Connect to host.", "Use 'auto' to detect the host from SSH.", "Defaults to #{@host}.") { |v| @host = v }
+ o.on('-s', '--unixsocket=name', "UNIX socket path.", "Takes precedence over host/port if the file exists", \
+ "Default #{@unixsocket}") { |v| @unixsocket = v }
+ o.on('-p', '--port=#', Integer, "Port number to use for connection.", "Defaults to #{@port}.") { |v| @port = v }
+ o.on('-w', '--[no-]wait', 'Wait for file to be closed by TextMate.') { |v| @wait = v }
+ o.on('-l', '--line [NUMBER]', 'Place caret on line [NUMBER] after loading file.') { |v| @lines <<= v }
+ o.on('-m', '--name [NAME]', 'The display name shown in TextMate.') { |v| @names <<= v }
+ o.on('-t', '--type [TYPE]', 'Treat file as having [TYPE].') { |v| @types <<= v }
+ o.on('-f', '--force', 'Open even if the file is not writable.') { |v| @force = v }
+ o.on('-v', '--verbose', 'Verbose logging messages.') { |v| @verbose = v }
+ o.on_tail('-h', '--help', 'Show this message.') { puts o; exit }
+ o.on_tail( '--version', 'Show version.') { puts VERSION_STRING; exit }
+ o.parse!
+ end
+ end
+
+ def parse_ssh_connection
+ ENV['SSH_CONNECTION'].nil? ? 'localhost' : ENV['SSH_CONNECTION'].split(' ').first
+ end
+ end
+
+ class Command
+ def initialize(name)
+ @command = name
+ @variables = {}
+ @data = nil
+ @size = nil
+ end
+
+ def []=(name, value)
+ @variables[name] = value
+ end
+
+ def read_file(path)
+ @size = File.size(path)
+ @data = File.open(path, "rb") { |io| io.read(@size) }
+ end
+
+ def read_stdin
+ @data = $stdin.read
+ @size = @data.bytesize
+ end
+
+ def send(socket)
+ socket.puts @command
+ @variables.each_pair do |name, value|
+ value = 'yes' if value === true
+ socket.puts "#{name}: #{value}"
+ end
+ if @data
+ socket.puts "data: #{@size}"
+ socket.puts @data
+ end
+ socket.puts
+ end
+ end
+
+ module_function
+
+ def handle_save(socket, variables, data)
+ path = variables["token"]
+ if File.writable?(path) || !File.exist?(path)
+ $stderr.puts "Saving #{path}" if $settings.verbose
+ begin
+ backup_path = "#{path}~"
+ backup_path = "#{backup_path}~" while File.exist? backup_path
+ FileUtils.cp(path, backup_path, :preserve => true) if File.exist?(path)
+ open(path, 'wb') { |file| file << data }
+ File.unlink(backup_path) if File.exist? backup_path
+ rescue
+ # TODO We probably want some way to notify the server app that the save failed
+ $stderr.puts "Save failed! #{$!}" if $settings.verbose
+ end
+ else
+ $stderr.puts "Skipping save, file not writable." if $settings.verbose
+ end
+ end
+
+ def handle_close(socket, variables, data)
+ path = variables["token"]
+ $stderr.puts "Closed #{path}" if $settings.verbose
+ end
+
+ def handle_cmd(socket)
+ cmd = socket.readline.chomp
+
+ variables = {}
+ data = ""
+
+ while line = socket.readline.chomp
+ break if line.empty?
+ name, value = line.split(': ', 2)
+ variables[name] = value
+ data << socket.read(value.to_i) if name == "data"
+ end
+ variables.delete("data")
+
+ case cmd
+ when "save" then handle_save(socket, variables, data)
+ when "close" then handle_close(socket, variables, data)
+ else abort "Received unknown command “#{cmd}â€, exiting."
+ end
+ end
+
+ def connect_and_handle_cmds(host, port, unixsocketpath, cmds)
+ socket = nil
+ unixsocketpath = File.expand_path(unixsocketpath) unless unixsocketpath.nil?
+ if unixsocketpath.nil? || !File.exist?(unixsocketpath)
+ $stderr.puts "Using TCP socket to connect: ‘#{host}:#{port}’" if $settings.verbose
+ begin
+ socket = TCPSocket.new(host, port)
+ rescue Exception => e
+ abort "Error connecting to ‘#{host}:#{port}’: #{e.message}"
+ end
+ else
+ $stderr.puts "Using UNIX socket to connect: ‘#{unixsocketpath}’" if $settings.verbose
+ socket = UNIXSocket.new(unixsocketpath)
+ end
+ server_info = socket.readline.chomp
+ $stderr.puts "Connect: ‘#{server_info}’" if $settings.verbose
+
+ cmds.each { |cmd| cmd.send(socket) }
+
+ socket.puts "."
+ handle_cmd(socket) while !socket.eof?
+ socket.close
+ $stderr.puts "Done" if $settings.verbose
+ end
+end
+
+## MAIN
+
+$settings = Rmate::Settings.new
+
+## Parse arguments.
+cmds = []
+
+ARGV << '-' if ARGV.empty? and (!$stdin.tty? or $settings.wait)
+
+ARGV.each_index do |idx|
+ path = ARGV[idx]
+ if path == '-'
+ $stderr.puts "Reading from stdin, press ^D to stop" if $stdin.tty?
+ else
+ abort "'#{path}' is a directory! Aborting." if File.directory? path
+ abort "File #{path} is not writable! Use -f/--force to open anyway." unless $settings.force or File.writable? path or not File.exist? path
+ $stderr.puts "File #{path} is not writable. Opening anyway." if not File.writable? path and File.exist? path and $settings.verbose
+ end
+ cmd = Rmate::Command.new("open")
+ cmd['display-name'] = "#{Socket.gethostname}:untitled (stdin)" if path == '-'
+ cmd['display-name'] = "#{Socket.gethostname}:#{path}" unless path == '-'
+ cmd['display-name'] = $settings.names[idx] if $settings.names.length > idx
+ cmd['real-path'] = File.expand_path(path) unless path == '-'
+ cmd['data-on-save'] = true
+ cmd['re-activate'] = true
+ cmd['token'] = path
+ cmd['selection'] = $settings.lines[idx] if $settings.lines.length > idx
+ cmd['file-type'] = 'txt' if path == '-'
+ cmd['file-type'] = $settings.types[idx] if $settings.types.length > idx
+ cmd.read_stdin if path == '-'
+ cmd.read_file(path) if path != '-' and File.exist? path
+ cmd['data'] = "0" unless path == '-' or File.exist? path
+ cmds << cmd
+end
+
+unless $settings.wait
+ pid = fork do
+ Rmate::connect_and_handle_cmds($settings.host, $settings.port, $settings.unixsocket, cmds)
+ end
+ Process.detach(pid)
+else
+ Rmate::connect_and_handle_cmds($settings.host, $settings.port, $settings.unixsocket, cmds)
+end
diff --git a/akeake/sync_2_data_from_noc b/akeake/sync_2_data_from_noc
new file mode 100755
index 0000000000000000000000000000000000000000..83928cd098b1d84ee1d020f3533445fc697cb2a3
--- /dev/null
+++ b/akeake/sync_2_data_from_noc
@@ -0,0 +1,25 @@
+#!/bin/csh
+
+# Where we will copy from
+set remote_fs = 'surman@neyman:'
+set fromDir = '/noc/mpoc/rpdmoc/'
+#
+set local_path = '/data/pstar'
+# Edit following to make list of things to copy
+set dirs2copy = 'cd170 cd177 d279 d304 d324 d333.tar d334 d344 d345 d346 d359 en517 kn182 kn200-4 oc459 p343 p345 rb0602 rb0701 rb0901 rb1009 rb1201 sj0614 sj08'
+
+# The now loop through the list
+foreach dd ($dirs2copy)
+ echo --- $fromDir$dd ---
+ set from_path = $remote_fs$fromDir$dd
+
+ rsync -v -a $from_path $local_path
+ echo done copying
+ echo Finish `date`
+
+ echo -------------
+end
+
+rsync -a -v ${remote_fs}/noc/mpoc/drake/jc159/backup_20180411170013/ ${local_path}/jc159
+
+rsync -a -v --exclude 'bim' ${remote_fs}/noc/mpoc/rpdmoc/users ${local_path}
diff --git a/commands/mstar_dotlogin b/commands/mstar_dotlogin
index ccd5386e21b05775da50354a2995a48bd341df1b..5ef699e34d251ec1a5a526ed47851b3b1bfa8aa8 100755
--- a/commands/mstar_dotlogin
+++ b/commands/mstar_dotlogin
@@ -1,9 +1,8 @@
-#
# Clean up by DAS September 2018
# Almsot all in .cshrc not sure need anything here
#
# This script executed on each login - will be after .cshrc
# Load modules - these will be put at front of path
# #module load matlab/2015b
-module load matlab/2011a
+module load matlab/2011b
#module load anaconda2
diff --git a/mexec_cruise_backup b/mexec_cruise_backup
index 6f6020abf1d6b740b91931882c53bb82bed3b7a6..b6499b1572319107958cf0799b83d53c365c4b90 100755
--- a/mexec_cruise_backup
+++ b/mexec_cruise_backup
@@ -56,11 +56,15 @@ echo Date `date` >> $backuplog
echo start copying mexec software >> $backuplog
echo ------ >> $backuplog
cd $root
-rsync -a sw/mexec/ ${backupdir}/
+rsync -a ~/programs/mexec_v3 ${backupdir}/
echo ------------- >> $backuplog
echo Date `date` >> $backuplog
echo done copying mexec software >> $backuplog
echo ------ >> $backuplog
+rsync -a ~/programs/mexec-exec ${backupdir}/
+echo ------------ >> $backuplog
+echo Date `date` >> $backuplog
+echo done copying mexec shell scripts >> $backuplog
# backup everything in data
echo ------------- >> $backuplog
@@ -68,13 +72,13 @@ echo Date `date` >> $backuplog
echo start copy to disk of data >> $backuplog
echo ------ >> $backuplog
cd $root
-rsync -aL --exclude legwork --exclude scs_raw --exclude jcrfs --exclude netcdf_files_rawdir_ship data ${backupdir}
+rsync -aL --exclude legwork --exclude scs_raw --exclude jcrfs --exclude netcdf_files_rawdir_ship --exclude from_public data ${backupdir}
echo ------------- >> $backuplog
echo Date `date` >> $backuplog
echo done copy to disk of data >> $backuplog
echo ------ >> $backuplog
-echo general_sw, legdata and legwork not backed up
+echo general_sw, legdata, legwork, public, scs/techsas raw not backed up
popd
diff --git a/uhdas_00_linkmerge b/uhdas_00_linkmerge
index 432fc1dd142375101ea5397d408078f94d9ca78f..1b202d24fd78fe96b8abd5ff6f501cdd42ba1f12 100755
--- a/uhdas_00_linkmerge
+++ b/uhdas_00_linkmerge
@@ -3,15 +3,12 @@
# bak in Amsterdam before start of jc184 uhdas trial
# 3 July 2019
#
-# 1) rsync uhdas data from uhdas server to local machine
+# prepare for reprocessing of single-ping data (i.e. running
+# quick_adcp.py)
+# make links to contents of atsea and copy over config files
+# as a starting point
#
-# 2) ensure postprocessing directories exist
-#
-# If the script hasn't been run recently, there will
-# be a lot of files to sync across. The processing on the uhdas
-# server updates plenty of things in routine processing every few minutes.
-# If the script is then immediately run again, there will be a few files
-# that are updated every ping.
+# run after uhdas_01!
#
# List of cruise segments to be processed is found in
# ~/cruise/data/vmadcp/cruise_segments
diff --git a/uhdas_01_syncraw b/uhdas_01_syncraw
index 1bdcc173bc0f888652edc8812a855722cb14f9aa..a024b98910d18dee7fe74bff106ce267352f3628 100755
--- a/uhdas_01_syncraw
+++ b/uhdas_01_syncraw
@@ -3,7 +3,7 @@
# bak in Amsterdam before start of jc184 uhdas trial
# 3 July 2019
#
-# 1) rsync uhdas data from uhdas server to local machine
+# 1) rsync uhdas data from uhdas server to local machine directory atsea
#
# 2) ensure postprocessing directories exist
#
diff --git a/uhdas_02_sync_postprocessing_from_raw b/uhdas_02_sync_postprocessing_from_raw
index ceb78f04eb95010bbf627ee7f9fbe2ebf8c56dce..7e299f3504b3b7379ed02b857b8953e03b16e398 100755
--- a/uhdas_02_sync_postprocessing_from_raw
+++ b/uhdas_02_sync_postprocessing_from_raw
@@ -3,7 +3,8 @@
# bak in Amsterdam before start of jc184 uhdas trial
# 3 July 2019
#
-# 1) rsync proc directory from the local atsea copy to the editing directory
+# 1) rsync proc directory from the local atsea copy to the
+# editing directory, postprocessing/proc_editing
#
# If the script hasn't been run recently, there will
# be a lot of files to sync across. The processing on the uhdas