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CDS detector added

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Former-commit-id: a72f30f90d22cc3c7ff6059e0254e47911bb5af1
Former-commit-id: db0264bdbe5136b6e6dc44e4788175a257439643
This commit is contained in:
alain viari
2015-11-08 14:28:57 +01:00
parent 8dab2d56b2
commit efb9949075
17 changed files with 62 additions and 74 deletions
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33
scripts/bash_init.sh
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@ -143,27 +143,35 @@ function formatfasta {
#
#
# The absolute path to the ORG.Annote home direcotory
# The absolute path to the ORG.Annot home directory
ORG_HOME=`getAbsolutePath $(dirname ${BASH_SOURCE[0]})/..`
ORG_PORTNAME=`${ORG_HOME}/config/guess_port` # The architecture running the ORG.Annnote instance
ORG_PORTNAME=`${ORG_HOME}/config/guess_port` # The architecture running the ORG.Annot instance
BIN_DIR="${ORG_HOME}/ports/${ORG_PORTNAME}/bin" # Directory containing binaries for this port
SCRIPT_DIR="${ORG_HOME}/scripts" # Directory containing scripts utilities
PROG_DIR="$(getAbsolutePath $(dirname $0))" # Directory containing the main script file
DATA_DIR="${ORG_HOME}/data" # Directory containing reference data for the annotation
LIB_DIR="$(getAbsolutePath ${PROG_DIR}/../lib)" # Directory containing the main script libraries
CALL_DIR="$(getAbsolutePath $(pwd))" # Directory from where the main script is called
IR_DATA_DIR="${DATA_DIR}/ir" # Directory containing data related to the
# Inverted repeat strucuture
DATA_DIR="${ORG_HOME}/data" # Directory containing reference data for the annotation
IR_DATA_DIR="${DATA_DIR}/ir" # Directory containing data related to
# IRs detection
TRNA_DATA_DIR="${DATA_DIR}/trna" # Directory containing data related to
# tRNAs detection
CDS_DATA_DIR="${DATA_DIR}/trna" # Directory containing data related to
# CDSs detection
TRNA_DATA_DIR="${DATA_DIR}/trna" # Directory containing data related to the
# tRNA detection
RRNA_DATA_DIR="${DATA_DIR}/rrna" # Directory containing data related to the
# rRNA dectection
RRNA_DATA_DIR="${DATA_DIR}/rrna" # Directory containing data related to
# rRNAs detection
#
@ -179,11 +187,10 @@ RRNA_DATA_DIR="${DATA_DIR}/rrna" # Directory containing data related to the
#
# We alter the path to include the bin dir corresponding to the port
PATH="${ORG_HOME}/ports/${ORG_PORTNAME}/bin:${PATH}"
PATH="${SCRIPT_DIR}:${BIN_DIR}:${PATH}"
export PATH
# Force to basic international setting for a correction behaviour of AWK on mac with float
export LANG=C
export LC_ALL=C

20
scripts/check_port
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@ -1,20 +0,0 @@
#!/bin/csh
#
# check if port is installed
#
set ORG_HOME = `dirname $0`/..
set PORTNAME = `$ORG_HOME/config/guess_port`
if (-f $ORG_HOME/ports/$PORTNAME/bin/exonerate) then
echo "+ port $PORTNAME is correctly installed"
exit 0
endif
echo "! port $PORTNAME not installed"
echo "! Please read README.txt for proper installation"
exit 1