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root/owl/trunk/scripts/updateUniprot.sh
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# Line 12 | Line 12
12   CURRENT="$LOCALDIR/current"
13   DOWNLOAD="$LOCALDIR/download"
14  
15 + FORMATDB=/usr/bin/formatdb
16 +
17   #SITE="ftp://ftp.uniprot.org/pub" # US main ftp
18   SITE="ftp://ftp.ebi.ac.uk/pub" # UK mirror
19   # the swiss mirror doesn't seem to update properly, not using it anymore
# Line 97 | Line 99
99   logfile="$DOWNLOAD/formatdb.log"
100  
101   cd $DOWNLOAD
102 < formatdb -p T -o T -l $logfile -i $SPROT
103 < formatdb -p T -o T -l $logfile -i $TREMBL
104 < formatdb -p T -o T -l $logfile -i $ALL
102 > $FORMATDB -p T -o T -l $logfile -i $SPROT
103 > $FORMATDB -p T -o T -l $logfile -i $TREMBL
104 > $FORMATDB -p T -o T -l $logfile -i $ALL
105  
106   #renaming DOWNLOAD dir to uniprot version and updating current symlink
107   echo "Creating new symlink..."

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