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ORG.Asm
ORG.Annotate
Commits
e046ef88
Commit
e046ef88
authored
Dec 18, 2015
by
Eric Coissac
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integrate options in the main script
parent
128f0656
Changes
2
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2 changed files
with
67 additions
and
13 deletions
+67
-13
config/targets/package.targ
config/targets/package.targ
+13
-5
org-annotate.sh
org-annotate.sh
+54
-8
No files found.
config/targets/package.targ
View file @
e046ef88
...
...
@@ -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)
org-annotate.sh
View file @
e046ef88
...
...
@@ -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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