Commit e046ef88 by Eric Coissac

integrate options in the main script

parent 128f0656
......@@ -41,20 +41,28 @@ pkg.make:: pkg.expand
export LDFLAGS="$(LDFLAGS)" && \
cd $(PKGDIR) && \
./configure --prefix=$(PRTPATH) $(CONFIGURE_OPTIONS))
$(MAKE) -C $(PKGDIR)
(export PATH="$(PRTPATH_BIN):$$PATH" && \
export PKG_CONFIG=$(PKG_CONFIG) && \
export CC="$(CC)" && \
export CXX="$(CXX)" && \
export CPP="$(CPP)" && \
export CXXPP="$(CXXPP)" && \
export CFLAGS="$(CFLAGS)" && \
export LDFLAGS="$(LDFLAGS)" && \
$(MAKE) $(MAKEOPTIONS) -C $(PKGDIR))
pkg.install:: pkg.make
$(MAKE) -C $(PKGDIR) install
$(MAKE) $(MAKEOPTIONS) -C $(PKGDIR) install
pkg:: pkg.install
@echo "+++++++++++ package $(PKG) done"
test::
(! test -d $(PKGDIR)) || $(MAKE) -C $(PKGDIR) test
(! test -d $(PKGDIR)) || $(MAKE) $(MAKEOPTIONS) -C $(PKGDIR) test
clean::
(! test -d $(PKGDIR)) || $(MAKE) -C $(PKGDIR) clean
(! test -d $(PKGDIR)) || $(MAKE) $(MAKEOPTIONS) -C $(PKGDIR) clean
portclean::
(! test -d $(PKGDIR)) || $(MAKE) -C $(PKGDIR) distclean
(! test -d $(PKGDIR)) || $(MAKE) $(MAKEOPTIONS) -C $(PKGDIR) distclean
(! test -d $(PKGDIR)) || \rm -r $(PKGDIR)
......@@ -14,6 +14,48 @@
THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
source "${THIS_DIR}/scripts/bash_init.sh"
#
# Management of options
#
taxid="no"
normalization="yes"
irdetection="yes"
# options may be followed by one colon to indicate they have a required argument
if ! options=$(getopt -o t:ih -l ncbi-taxid:,no-ir-detection,help -- "$@")
then
# something went wrong, getopt will put out an error message for us
exit 1
fi
set -- $options
while [ $# -gt 0 ]
do
case $1 in
-t|--ncbi-taxid) taxid="$2" ; shift;;
-i|--no-ir-detection) irdetection="no" ;;
-h|--help) echo "Usage:" ;
echo " $0 "'[-t|--ncbi-taxid ###] [-n|--no-normalization] \'
echo " [-i|--no-ir-detection] [-h|--help] <FASTAFILE>"
echo
echo "Options:"
echo ' -t ### | --ncbi-taxid ###'
echo ' ### represents the ncbi taxid associated to the sequence'
echo
echo ' -i | --no-ir-detection'
echo ' Does not look for inverted repeats in the plastid genome'
exit 0;;
(--) shift; break;;
(-*) echo "$0: error - unrecognized option $1" 1>&2; exit 1;;
(*) break;;
esac
shift
done
#############################
pushTmpDir ORG.organnot
if [[ ! "$1" =~ ^/ ]]; then
......@@ -27,15 +69,19 @@ pushTmpDir ORG.organnot
rm -f ${LOG}
openLogFile ${LOG}
loginfo "Normalizing the structure of the Chloroplast sequence..."
loginfo " LSC + IRB + SSC + IRA"
${PROG_DIR}/detectors/normalize/bin/go_normalize.sh ${QUERY} > "${RESULTS}.norm.fasta"
loginfo "Done."
loginfo "Annotating the Inverted repeats and Single copies (LSC and SSC)..."
${PROG_DIR}/detectors/ir/bin/go_ir.sh "${RESULTS}.norm.fasta" > "${RESULTS}.annot"
loginfo "Done."
if [ "$irdetection"=="yes" ]; then
loginfo "Normalizing the structure of the Chloroplast sequence..."
loginfo " LSC + IRB + SSC + IRA"
${PROG_DIR}/detectors/normalize/bin/go_normalize.sh ${QUERY} > "${RESULTS}.norm.fasta"
loginfo "Done."
loginfo "Annotating the Inverted repeats and Single copies (LSC and SSC)..."
${PROG_DIR}/detectors/ir/bin/go_ir.sh "${RESULTS}.norm.fasta" > "${RESULTS}.annot"
loginfo "Done."
fi
loginfo "Annotating the tRNA..."
${PROG_DIR}/detectors/trna/bin/go_trna.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
......
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