#!/bin/csh 
#   NCBIUPDATE,   Version  09/26/14
#csh script to download GenBank files


# Example: {uses 'at' command to run a delayed batch job}
#  at 1am
#  at>gbupdate filelist &
#  at>ctrl-D  {ends the command }

#  This assumes you are in the GenBank directory.  The existing files will be 
#  replaced with the new ones, and so must be writeable.
#  Remember to include the index and documentation files in filelist.
#  When disk space is tight, edit the 'filelist' file to download files in
#  order of decreasing size.  In general, you need to have at least twice as
#  much empty space as is necessary to hold the largest file to be downloaded.
#  This can be circumvented by setting $tmpdir to /tmp, rather than ".".

#-----------------------  Set environment variables -------------


# RM_CMD - command to be used for removing files and directories
if (-e /usr/bin/rm) then
   set RM_CMD = /usr/bin/rm
else
   if (-e /bin/rm) then
      set RM_CMD = /bin/rm
   else
      set RM_CMD = rm
   endif
endif


#- - - - - - - - -  directory to store temporary files - - - - - - - - -
# Unless you are just scraping the last bytes of the
# filesystem in which GenBank is to reside, then the current working 
# directory should be fine.
set tmpdir = .

# /tmp and /var/tmp are two alternatives, if you're running out of space 
# in the target filesystem. Beware! if you max out /tmp, you will be
# interfering with the ability of everyone else on the system to
# do business as usual. /tmp on some systems can be surprisingly small,
# if it is taken from /swap.
#set tmpdir = /tmp

# On some systems, /var/tmp is an alternative place for temporary files
#set tmpdir = /var/tmp
#- - - - - - - - - - - - - - - - - - - - - -


#-----------------------  MAIN LOOP -------------

foreach file (`cat gbfiles`)
     echo '===> '$file
     if ($file:e == gz ) then
       set unzipname = $file:r
         echo '======> '$unzipname
       gunzip $file
       set basename = $unzipname:r
         if ($unzipname:e == tar ) then
             echo '=========> '$basename            
          tar xvfp $unzipname   
          set success = $status
             if ($success == 0) then
            $RM_CMD $unzipname
             else
                echo '!!! tar xvfp '$unzipname' failed' 
             endif  
         endif 
     endif

end #foreach