222 lines
9.6 KiB
TeX
222 lines
9.6 KiB
TeX
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\title{Processing ABI data}
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\author{Richard from a draft by John}
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\begin{document}
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\maketitle
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Before you start you need a user name and password on the Sun, and two
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subdirectories in your Sun home directories. One of these is called
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{\sf Mac-files-{\em \{your user name\}}}, and is visible from the Mac.
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This is where the raw results folder gets transferred to. The other
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is a subdirectory for your project, in which you will keep all the
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data for one cosmid and run {\sf sap}. This is called by the name of
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the cosmid (e.g. ZK637). I can help set these up.
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\section{At the Mac}
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Settings for ABI run: 14 hours, analyse all samples ({\em N.B. you
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will lose all data on the Sun for samples that were not analysed on
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the Mac}). Fill in sample names according to the following rules:
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\begin{verse}
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Each microtitre plate has a letter plus a two digit number. This
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identifier is unique to you and to a library made from a particular
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cosmid. (Fill in the index sheet on the wall to avoid conflicts.)\\
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The 96 clones in the microtitre plate are numbered a1, a2 .. h12.\\
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The sequence sample name is formed by adding a full stop, a character
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and a number. The characters in use at the present time are: s
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(single stranded), f (double stranded, forward) and r (double
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stranded, reverse). The number indicates which read this one is,
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in a series of primer walks. Thus the first, shotgun, read always ends
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in 1.\\
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e.g. a09c8.s1 is plate a09, row c, column 8, single strand, first
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(shotgun) read.\\
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If you extract a second sequence file from the same raw data file, you
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should add another letter to the name (e.g. a09c8.s1a). Another
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reaction and raw data read would be called by a different number (e.g.
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109c8.s2).
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It's a matter of personal taste whether you use upper or lower case
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letters, but I strongly recommend lower case ones for ease of UNIX typing.\\
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NB If you want to process the data on the Sun you must give the
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sample a name, even if is a test sample. Also, any spaces in the name
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will be turned into underscores by {\sf abiprocess}.\\
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\end{verse}
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After the ABI has run and processed the samples, use TOPS to transfer
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the results folder to the Sun. The results folder is called ``Results
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{\em folder\_date}'' , where the date is at the time of {\em
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termination}.
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\begin{verse}
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Select {\bf TOPS} from the pulldown desk accessory menu (apple icon in top left).\\
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Select {\bf cele} from the list of machines on the right side of the
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TOPS application.\\
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Click on {\bf open} in the central panel (or double click on {\bf cele} in previous step).\\
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Give your Sun user name and password.\\
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Click on {\bf Mac-files-{\em you}}.\\
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Select {\bf mount} from the central panel - this creates a published
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volume icon, looking a bit like a reading stand, in the place where the disk
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icons go at the right hand edge of the screen.\\
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Drag the icon for your results folder over to the published volume icon.\\
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Wait while your files get copied.\\
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Close TOPS and trash the published volume icon.\\
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\end{verse}
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Leave the results folder on the Mac until the results have been
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backed up onto tape.
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\section{At the Sun}
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Log on to a Sun (any one). Put a tape in the tape drive (currently next to
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cele at the far end of room 5036). You have to back up your data
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before {\sf abiprocess} will transfer the sequences to your project.
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Type {\sf abiprocess {\em folder\_date}}, where {\em folder\_date} is
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the date as given for the ABI results folder (i.e. with underscores
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and American ordering). You do not need to {\sf cd} anywhere before
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doing this. It will then run {\sf ted} for each sample
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for which there was a {\sf .Seq} file, i.e. for each one that was
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analysed on the Mac by the ABI software.
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For each ted run (i.e. each sequence) do the following:
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\begin{verse}
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Move the outline of the ted window to a suitable place on the screen and
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click to start (all clicks are with the left mouse button).\\
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Set the cutoffs, and edit as required. Don't waste a lot of time at
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this stage on editing. Make the right cut between 400 and 500
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usually. The additional data will be saved, and can be used later.\\
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If you want to use the sequence from this run, click on {\bf Output},
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then on {\bf OK} in the pop-up output window.\\
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Click on {\bf Quit}.
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\end{verse}
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The files you should end up with are: one file of file names {\sf {\em
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folder\_date}fn}; for each sample name in this file a sap input format
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sequence file {\em sample\_name} and a raw data file renamed to {\sf
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{\em sample\_name}RES}; and for each sample not in this list (i.e.
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those for which you didn't output a sequence in ted) a raw data file
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renamed to {\sf {\em sample\_name}FLD}.
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After processing all the samples {\sf abiprocess} requires you to back
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up the data on tape. You must have a tape loaded in the drive, with
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the door switch pulled across to the right. The tape must be
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writable, i.e. the little button at top left must be rotated so that
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the arrow points away from SAFE. You will be asked how many data sets
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have already been stored on the tape. It is possible to store many
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folders, but you have to keep track of them yourself. If you give too
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small a number you will lose data and mess things up.
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If you don't have a tape set up when you hit Return to start the
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backup, then {\sf abiprocess} will abort without giving you the chance
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to copy the data to your projet directory. However you can come back
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at any time in the future and run {\sf abiprocess} again with the same
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date to do the transfer. This will {\em not} require you to run all
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the {\sf ted}'s again.
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Similarly, you can yourself abort from {\sf abiprocess} by putting the
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cursor is in the xterm window from which you first ran {\sf
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abiprocess} and typing CTRL/C (holding down the Control key while
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pressing the C key). To be sure that you leave things in a sensible
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state, do this when inside ted, but before you output a sequence.
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Again, if you do this, you can restart at a later date by running {\sf
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abiprocess} again. You will restart with the sample that you were
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editing when you aborted.
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After backing up the results directory on tape, {\sf abiprocess} asks
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whether you want to transfer the processed data to a project, and if
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so, prompts for a project directory name. When you give this all the
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files are transferred to the project directory, and the results folder
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subdirectory of {\sf Mac-files-{\em you}} is destroyed.
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\subsection{Restoring data to the Mac from your project directory}
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If you want to restore some data to the Mac (for example to plot a
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trace) then you can use {\sf abirestore}. Run {\sf abirestore {\em
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project folder\_date}}. This creates a subdirectory {\sf
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restored.{\em folder\_date}} of your {\sf Mac\_files} directory that
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you can see from TOPS on the Mac. When you mount it all the ABI data
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files will be on top of one another in the folder window (due to the
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way I fiddled the Mac resources files -- they all get the same one!),
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so it looks like there is only one. To see them all use the finder
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options to either clean up the window or view by name.
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This only restores the successful reads (the ones you output sequence
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from in ted).
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\subsection{Restoring data from tape - and more about tape usage}
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I haven't written a script to do this yet. The following should work
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(anything after a \# sign is a comment that you don't need to type).
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\begin{verse}
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\# load the tape\\
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rlogin cele \hspace{2cm} \# if you are not already on cele\\
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cd ~/Mac-files-{\em \{your login name\}}\\
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unsetenv TAPE \hspace{2cm} \# this is a fix for something I don't understand\\
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mt fsf {\em nskip} \hspace{2cm} \# where {\em nskip} is the number of data sets to skip\\
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\hspace{3in} \# (i.e. 0 to retrieve the first folder)\\
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tar xvf /dev/rst0\\
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\# unload the tape
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\end{verse}
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You should in principle be able to get about 30 complete abi run
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folders on a tape, but there are several reasons not to go up that
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high. The first is that it will take rather a long time to wind
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forward to the right place when writing (or reading) the later ones.
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The second is that you should be backing up your entire project from
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time to time. This is done by saving everything in the project
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directory. In this case we do not bother to try to store more than
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one archive set on a tape, and so don't need the ``mt fsf'' command
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(and associated ``unsetenv TAPE''). So the following should work:
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\begin{verse}
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\# load tape and rlogin to cele if necessary
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cd ~\\
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tar cvf /dev/rst0 {\em project\_name}
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\end{verse}
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You can restore it if need be with:
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\begin{quote}
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tar xvf /dev/rst0
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\end{quote}
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or just get a listing of what it contains with
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\begin{quote}
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tar tvf /dev/rst0
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\end{quote}
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Once you have backed up the project, that tape will contain all the
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raw data files as well as the assembly data, so you can erase the tape
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you were using to store the original folders. You do this with the
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command
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\begin{quote}
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mt erase
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\end{quote}
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\subsection{For those you want to know a bit more}
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{\sf abiprocess} and {\sf abirestore} are both shell scripts,
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containing a mixture of UNIX commands and control statements. They
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can be found in {\sf /usr/local/bin} along with most other public
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local programs, such as {\sf ted}. If you want to see what they do
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you can look at them with {\sf cat} or {\sf more} or your favourite
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editor, or print them out with {\sf lpr}. In fact {\sf abiprocess}
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runs a remote shell script on cele to do the tape backup and transfer
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to project. This is called {\sf abibackup} and is also found in {\sf
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/usr/local/bin}.
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\end{document}
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