📄 meme
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#!/bin/csh## $Id: meme.txt 1339 2006-09-21 19:46:28Z tbailey $# $Log$# Revision 1.8 2005/10/07 05:33:55 nadya# keep uniform name MEME_LOGS throughout scripts.## Revision 1.7 2005/10/05 06:18:35 nadya# use full path for "rm". Asssume everybody has /bin/rm.## Revision 1.6 2005/10/02 05:54:33 nadya# add sourcing meme_config.csh to set all the environment.# use variables when calling real binaries## Revision 1.5 2005/09/16 22:24:10 nadya# put temp files in LOGS## Revision 1.4 2005/08/31 04:17:13 nadya# move usage part to etc/*.doc file## Revision 1.3 2005/08/24 04:16:37 nadya# add machid## Revision 1.2 2005/08/24 00:31:04 nadya# set machid during configure step, and user variable for it## Revision 1.1.1.1 2005/07/30 01:19:40 nadya# Importing from meme-3.0.14, and adding configure/make### set the environment setenv CONF /root/etc/meme_config.cshif ( -f $CONF) then source $CONFelse echo "$CONF does not exist. Meme installation is incomplete" exit 1endif# set the mpi commandset mpicmd = ''# set the machine/OS typeset machid = linux# handle interruptsset exe_status = 0set usage = $MEME_LOGS/meme.usage.$$.tmponintr cleanup# get input argumentsset memeargs = ""set exe = "$MEME_BIN/$MEME_EXEC"set exe_check = $exeset exe_args = ""set text = 0while ("$1" != "") switch ($1) case -p: shift if ($machid == rs6000) then set exe = "poe $MEME_BIN/meme_p" set exe_check = "poe $MEME_BIN/$MEME_EXEC" set exe_args = "-nodes $1 -tasks_per_node 8" else set exe = "$mpicmd $1 $MEME_BIN/meme_p" set exe_check = "$mpicmd 1 $MEME_BIN/meme_p" endif breaksw case -text: set text = 1 breaksw case -sf: shift setenv MEME_SEQUENCE_FILE "$1" breaksw case -V: case -trace: case -print_all: case -print_w: case -print_z: case -print_ll: case -print_starts: set text = 1 default: set memeargs = "$memeargs $1" endsw shiftend# print usage message if no arguments leftif ("$memeargs" == "") then set memeargs = "$memeargs -h" set text = 1endif# add meme source directory to argumentsset memeargs = "$memeargs -dir $MEME_DIRECTORY"# check the syntax$exe_check $memeargs -check_syntax >& $usageset exe_status = $statusif ($exe_status) then goto usageendif# cat to meme2html unless -textif ($text) then $exe $memeargs $exe_args set exe_status = $statuselse set text = $MEME_LOGS/meme.text.$$.tmp $exe $memeargs $exe_args > $text set exe_status = $status if ($exe_status == 0) then $MEME_BIN/meme2html < $text set exe_status = $status else echo "<HTML><BODY><PRE>" echo "<H1>Errors occurred:</H1>" cat $text echo "</PRE></BODY></HTML>" endifendifcleanup:if (-e $usage) /bin/rm -f $usageif (-e $text) /bin/rm -f $textexit $exe_status# Describe MEME and its output format:usage:cat $MEME_DIRECTORY/etc/meme.doc >> $usagemore $usagegoto cleanup⌨️ 快捷键说明
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