Automated installation of EMBOSS and EMBASSY

Once you have installed EMBOSS and got it to work you have solved the hardest part of the struggle. Updating EMBOSS as new releases appear^5.1 can be quite tedious. UNIX is designed for the lazy, so here is our lazy man's guide to always having an up to the minute EMBOSS installation.

The following script can be run manually (it should probably be `

source

d' rather than executed directly) or can be fired off with cron (in the early hours of the morning is a good time). It assumes you are installing EMBOSS outside the source directory and have write permissions to do so.

EMBOSS will update EMBOSS distributed files but will not alter or overwrite your own datafiles^5.2or your

emboss.default

.

# This script should be sourced, not run.
# EMBOSS UPDATE.
# it assumes \$packages_dir/EMBOSS is a symbolic link to 
# \$mirror_dir/emboss.open-bio.org/pub/EMBOSS
#

#site specific variables: season according to taste..

set mirror_dir=('/ftp/mirrors')
set packages_dir=('/site/newprog')
set emboss_config_options=\
('--prefix=/site/prog/emboss --with-pngdriver=/site/lib')

# Now the script proper

set oldpwd=`pwd`

cd \$mirror_dir
echo 'updating EMBOSS'
if ( `wget -m 'ftp://emboss.open-bio.org/pub/EMBOSS' |& \
  tail -1 | awk '/^Downloaded:/{print \$5}'` != "0" ) then 

    cd \${packages_dir}/EMBOSS
    echo 'new EMBOSS programs found .. installing'
    set latest_emboss=`ls -t EMBOSS*|head -1`

    cd \$packages_dir
    rm -Rf EMBOSS-*
    tar zxf EMBOSS/\$latest_emboss
    set emboss_dir=`ls -dt EMBOSS-*[^z]|head -1`

#the next line is necessary on our system but may not be for yours.
    setenv LD_LIBRARYN32_PATH /site/lib

    cd \$emboss_dir

# If you have any site specific changes to the source code 
# that you want to include, copy them in here

    ./configure \$emboss_config_options &&\
    make && \
    make install

#Now unpack and build EMBASSY

    mkdir embassy
    cd embassy

#Unpack and build each package one at a time

    foreach embassadir ( `ls ../../EMBOSS/*gz |grep -v E
MBOSS-` )

	tar zxf \$embassadir
	set embassadir_arch=\$embassadir:t
	set embassadir_root=\$embassadir_arch:r

	cd \$embassadir_root:r
	./configure  \$emboss_config_options &&\
	make && \
	make install

	cd ..
    end
else
    echo 'No new version of EMBOSS available'
endif

cd \$oldpwd