converted to 1.6 markup
|Deletions are marked like this.||Additions are marked like this.|
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| echo "--Running bigmap.e on $str"
echo "--Running bigmap.e on $str" >> current.log
~/bin/bigmap.e < $str >> current.log
| echo "--Running bigmap on $str"
echo "--Running bigmap on $str" >> current.log
~/bin/bigmap < $str >> current.log
Support script. The current script is maintained in ~/Dropbox/Dawn-shape/scripts-limited-copy.
This will do the things needed to get a specific tiling sequence ready to be run. It figures out which landmarks and maplets are needed, copies them into the working directory, builds the make_fileT.in and does a make_script.e
- Eric Palmer
- You will need to change the "which" variable to tell it which bigmap you want to process.
There is a left, right, top and bottom variables which set the boundaries for new landmarks. These values are used to build make_fileT.in. They are of pixel value, from 50 to 950.
Executed from a working directory that has the symbolic links set (using setup.sh).
# Dec 11st, 2011 - Eric E. Palmer # Version 1.2 # This sets up a run, copying over only the files that are needed. # You must change which to match the bigmap you are using # If you want a different set of locations, then you need to change the # right, left, top, bottom # Usage: You start the script in the directory that you are going to do work in # It requires a virtual directory that is basically just sybmolic links to # the Dropbox/Dawn-Shape/Vesta (or work_generic) directory. However, it # will generate files that get copied into the working directory # Working Directory # The working directory has symbolic links to needed files (established by # using setup.sh). All other needed files are copied by this # script # Master Directory # This has a full set of files needed so we can generate bigmaps and a # place to copy things from. It is created by using setup.sh and then # update.sh dropPath=~/Dropbox/Dawn-shape # path to dropbox - localMain=/Volumes/Media/run-master # path to master directory # Ensure bigmap is given as a commandline argument if [ -z $1 ]; then echo "Usage: setupRun.sh <bigmap_name>"; echo "Example: setupRun.sh ZS0216"; exit; fi # Set variables which=$1 # first argument is set to which bigmap we are doing to do left=50 # Makescript left boundaries right=950 # Makescript right boundaries top=200 # Makescript top boundaries bottom=800 # Makescript bottom boundaries currPath=`pwd` date > current.log echo "--We are building $which from $left to $right, and $top to $bottom" echo "--We are building $which from $left to $right, and $top to $bottom" >> current.log # Setup some links and files that are needed in the local directory $dropPath/work_generic/setup.sh >> current.log if [ ! -e 'SUMFILES' ]; then ln -s $localMain/SUMFILES SUMFILES; fi #### Local # clean up old # An error with the rm is not a problem, it just means # nothing has been done previously echo "--Cleaning up previous in $currPath" echo "--Cleaning up previous in $currPath" >> current.log # rather than deleting all the old run logfiles, keep it for one more run if [ -e '001.INN' ]; then list=`ls *INN *OOT`; for i in $list do echo $i; mv $i old/; done; fi if [ -e 'LMRKLIST.TXT' ]; then mv LMRKLIST.TXT old/; fi # SPECIAL NEEDS sh rem_script.b # std rm -f TESTFILES/* # std rm -f TESTFILES1/* # std rm -f NEW_FILES/LMKFILES/* if [ -e 'NEW_FILES/LMKFILES' ]; then rmdir NEW_FILES/LMKFILES ; fi rm -f NEW_FILES/MAPFILES/* if [ -e 'NEW_FILES/MAPFILES' ]; then rmdir NEW_FILES/MAPFILES ; fi rm -f LMKFILES/* if [ -e 'LMKFILES' ]; then rmdir LMKFILES ; fi rm -f MAPFILES/* if [ -e 'MAPFILES' ]; then rmdir MAPFILES ; fi if [ -e 'LMKRLIST1.TXT' ]; then # test for a big mistake echo "#### LMRKLIST1.TXT was found. You need to delete it by hand"; echo "#### Be sure that sh EXPORT.TXT has been run" exit; fi #### Master # Deal with run-master directory cd $localMain echo "--Running update.sh in $localMain" echo "--Running update.sh in $localMain" >> current.log ./update.sh >> current.log echo "--Cleaning up previous in $localMain" >> current.log echo "--Cleaning up previous in $localMain" rm -f NEW_FILES/LMKFILES/* rm -f NEW_FILES/LMRKLIST.TXT rm -f NEW_FILES/MAPFILES/* # Get ready for new # Figure out landmarks that fall in overlap str=$dropPath/Vesta/$which.IN echo "--Running bigmap on $str" echo "--Running bigmap on $str" >> current.log ~/bin/bigmap < $str >> current.log # Cheat the system so that export.e thinks the overlap files are the # finished product of a run that need to be exported cp USED_MAPS.TXT LMRKLIST1.TXT # Build the export script and execute it (makes a tar ball of needed files) echo "--Exporting" >> current.log echo "--Exporting" ~/bin/export.e sh EXPORT.TXT # Copy files to working directory echo "--move/extract NEW_FILES.tar at $currPath" echo "--move/extract NEW_FILES.tar at $currPath" >> current.log mv NEW_FILES.tar $currPath cd $currPath tar xf NEW_FILES.tar mv NEW_FILES/* . cp $localMain/MAPFILES/$which.MAP MAPFILES/ # This must be done after the tar and mv if [ ! -e 'TESTFILES' ]; then mkdir TESTFILES; fi if [ ! -e 'TESTFILES1' ]; then mkdir TESTFILES1; fi if [ ! -e 'NEWFILES' ]; then mkdir NEWFILES; fi if [ ! -e 'NEWFILES/LMKFILES' ]; then mkdir NEWFILES/LMKFILES; fi if [ ! -e 'NEWFILES/MAPFILES' ]; then mkdir NEWFILES/MAPFILES; fi echo "--Building make_scriptT.in" >> current.log echo "--Building make_scriptT.in" # Backup the old, just in case if [ -e 'make_script.in' ]; then mv make_script.in old/ ; fi # Set headers echo "& cp MAPFILES/$which.MAP MAPFILES/XXXXXX.MAP" > make_scriptT.in echo "XXXXXX" >> make_scriptT.in echo "XXX050.SEED" >> make_scriptT.in x=$left # Loop to build the locations of the landmarks make_scriptT.in while [ $x -le $right ]; do y=$top while [ $y -le $bottom ]; do echo "$x, $y" >> make_scriptT.in let y=y+50 done let x=x+50 done echo "END" >> make_scriptT.in # Build the script and prepare it to be run ~/bin/make_scriptT.e chmod a+x run_script.b echo "" echo "Now you can run it by using:" echo "./run_script.b &" echo "" # All done echo "Done with setupRun.sh" >> current.log date >> current.log