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#!/bin/sh
usage() {
cat <<EOF
this script must be executed from the top-level directory of the
EMBOSS Explorer distribution.
EOF
exit 1
}
prompt() {
echo -e "$1\n\t(default is $2)"
read INPUT
eval $3=${INPUT:-$2}
}
echo installing EMBOSS Explorer perl modules...
echo
perl Makefile.PL && make && make install || exit
echo installing EMBOSS Explorer GUI components...
echo
echo I need to collect some information in order to install EMBOSS Explorer:
EMBOSS_PREFIX=`embossversion -full 2>/dev/null | awk '/^InstallDirectory/ { print $2 }'`
prompt "Where was EMBOSS installed?" ${EMBOSS_PREFIX:-/usr/local} EMBOSS_PREFIX
# TODO something fancy to guess the web root?
prompt "Where should the EMBOSS Explorer HTML files be installed?" /var/www/html/emboss HTML_PATH
OUTPUT_PATH=$HTML_PATH/output
prompt "What is the URL prefix corresponding to the HTML directory above?" /emboss HTML_URL
OUTPUT_URL=$HTML_URL/output
prompt "Where should the EMBOSS Explorer CGI script be installed?" /var/www/cgi-bin/emboss CGI_PATH
if [ -d $CGI_PATH ]
then
CGI_DIR=$CGI_PATH
CGI_PATH=$CGI_DIR/emboss
else
CGI_DIR=${CGI_PATH%/*}
fi
prompt "What is the complete URL corresponding to the CGI script '$CGI_PATH'?" /cgi-bin/emboss CGI_URL
# munge EMBOSS::GUI::Conf according to the information above...
CONF_MODULE=`perl -MEMBOSS::GUI::Conf -e 'print $INC{"EMBOSS/GUI/Conf.pm"}'`
perl -pi -e "
\$HTML_PATH = '$HTML_PATH'; s/(?<=HTML_PATH = \")[^\"]*/\$HTML_PATH/;
\$HTML_URL='$HTML_URL'; s/(?<=HTML_URL = \")[^\"]*/\$HTML_URL/;
\$OUTPUT_PATH = '$OUTPUT_PATH'; s/(?<=OUTPUT_PATH = \")[^\"]*/\$OUTPUT_PATH/;
\$OUTPUT_URL='$OUTPUT_URL'; s/(?<=OUTPUT_URL = \")[^\"]*/\$OUTPUT_URL/;
\$EMBOSS_PREFIX='$EMBOSS_PREFIX'; s/(?<=EMBOSS_PREFIX = \")[^\"]*/\$EMBOSS_PREFIX/;
" $CONF_MODULE
# install HTML and CGI files...
[ -d html ] || usage
echo installing HTML files to $HTML_PATH...
if [ -d $HTML_PATH ]
then
cp -rp html/* $HTML_PATH
else
cp -rp html $HTML_PATH
fi
echo creating HTML index file at $HTML_PATH/index.html...
echo "<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Frameset//EN\"
\"http://www.w3.org/TR/xhtml1/DTD/xhtml1-frameset.dtd\">
<html xmlns='http://www.w3.org/1999/xhtml' xml:lang='en' lang='en'>
<head>
<title>EMBOSS Explorer</title>
</head>
<frameset cols=\"170, *\">
<frame src=\"$CGI_URL/menu\" name=\"menu\" />
<frame src=\"$CGI_URL/intro\" name=\"main\" />
</frameset>
</html>" >$HTML_PATH/index.html
echo creating output directory at $OUTPUT_PATH...
[ -d $OUTPUT_PATH ] || mkdir $OUTPUT_PATH
#echo creating .htaccess file in $OUTPUT_PATH/.htaccess...
#echo "Header add Cache-Control: no-cache" >>$OUTPUT_PATH/.htaccess
echo installing CGI script to $CGI_PATH...
cp cgi/emboss $CGI_PATH
# copy support files used in the program manuals...
echo copying manual support files to $HTML_PATH/manual...
[ -d $HTML_PATH/manual ] || mkdir $HTML_PATH/manual
# EMBOSS 3
find $EMBOSS_PREFIX/share/EMBOSS/doc/programs/html -type f ! -name '*.html' -exec cp {} $HTML_PATH/manual \;
# EMBOSS 4
find $EMBOSS_PREFIX/share/EMBOSS/doc/html/emboss/apps -type f ! -name '*.html' -exec cp {} $HTML_PATH/manual \;
# fix permissions...
echo fixing permissions...
find $HTML_PATH -type d -exec chmod a+rx {} \; -o -type f -exec chmod a+r {} \;
chmod a+rwx $OUTPUT_PATH
chmod a+rx $CGI_PATH
# TODO mention cron script in bin directory, when it exists...
CRON="0 4 * * * find $OUTPUT_PATH -type d -mindepth 1 -maxdepth 1 -atime 1 -exec rm -rf {} \;"
# mention location of configuration file and things that can be changed (list
# of excluded applications, mostly...)
cat <<EOF
EMBOSS Explorer is installed. Visit $CGI_URL to test it out.
Site configuration (including a list of applications to be excluded from
public access) is stored in the EMBOSS::GUI::Conf module (located at $CONF_MODULE).
The main style sheet, which can be edited to customize the appearance of
EMBOSS Explorer is $HTML_PATH/style/emboss.css. If you prefer the look and
feel of the old EMBOSS GUI, you can use $HTML_PATH/style/classic.css
instead (the style sheet is specified in the EMBOSS::GUI::Conf module).
EMBOSS Explorer generates temporary output files every time an application is
used. Depending on the tasks being performed, these output files can consume
space fairly quickly. The old output can be cleaned up on a regular basis by
adding a task to the root user's crontab. The following example runs every
morning at 0400 and removes all output files that have not been accessed in
the last 24 hours:
0 4 * * * find $OUTPUT_PATH -type d -mindepth 1 -maxdepth 1 -atime 1 -exec rm -rf {} \;
Please report any errors or strange occurrences using the bug tracker at
http://sourceforge.net/tracker/?func=add&group_id=124389&atid=699414
EOF
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