/usr/share/logol/convert2gff.sh is in logol 1.6.10-1build1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | #!/bin/bash
# ARGS:
# Mandatory input file name
# Mandatory output file name
#
#
# Installation directory
export REALDIR="$(readlink -f $0)"
export LOGOL_HOME="$(dirname "$REALDIR" )"
echo "calling convert2fasta with parameters "$*
java -Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -classpath $LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.2.jar org.irisa.genouest.logol.utils.converter.GFFConverter $*
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