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#!/bin/csh
# for running under cygwin
# with EMBOSS under ~/devemboss
# and emboss-ms under ~/emboss-ms
# cd ~/
# save data files
setenv EMBOSS_DATA ~/devemboss/emboss/data
cd ~/datafiles
echo "Updating datafiles from ~/datafiles/*"
echo "AAINDEX (nakai)"
rm ~/devemboss/emboss/data/AAINDEX/[a-z]*[0-9]
aaindexextract nakai/aaindex1 -auto
echo "JASPAR"
rm -rf ~/devemboss/emboss/data/JASPAR_*/*.pfm
rm -rf ~/devemboss/emboss/data/JASPAR_*/matrix_list.txt
jaspextract jaspar/all_data/FlatFileDir -auto
echo "PRINTS"
rm ~/devemboss/emboss/data/PRINTS/PR*
rm ~/devemboss/emboss/data/PRINTS/prints.mat
printsextract prints/prints[0-9]*.dat -auto
echo "PROSITE"
rm ~/devemboss/emboss/data/PROSITE/PS*
rm ~/devemboss/emboss/data/PROSITE/prosite.lines
prosextract prosite -auto
echo "REBASE"
rm ~/devemboss/emboss/data/REBASE/emboss*.*
rebaseextract rebase/withrefm.[0-9]* rebase/proto.[0-9]* -auto
echo "TRANSFAC"
rm ~/devemboss/emboss/data/tf*
tfextract transfac/site.dat -auto
cd ~/devemboss/scripts
# make sure protection is set correctly on external .exe files
chmod ugo+x ~/devemboss/win32/exes/*.exe
# compile the bundlewin executable
gcc -o bundlewin -O2 bundlewin.c
# set the default location of Visual C++ libraries
setenv vc100files /home/emboss/emboss-ms/redist/vc100
setenv vc90files /home/emboss/emboss-ms/redist/vc90
setenv vc80files /home/emboss/emboss-ms/redist/vc80
if(-d ~/membossdev/win32build) then
rm -rf ~/membossdev/win32build
endif
if (-s ~/membossdev/memboss-dev.zip) then
rm ~/membossdev/memboss-dev.zip
endif
# run and accept default (see above) VC++ library locations
./bundlewin /home/emboss/devemboss /home/emboss/membossdev
echo "when ready, unpack with"
echo "cd ~/membossdev"
echo "rename or remove memboss-dev directory"
echo "unzip -q ~/membossdev/memboss-dev.zip"
echo "or unzip in windows by opening the memboss-dev.zip file"
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