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Fix repeatmodeler recipe #19137

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merged 8 commits into from
Dec 13, 2019
Merged

Fix repeatmodeler recipe #19137

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b7c313d
fix bug mixing up DIR and PRGM paths
Juke34 Dec 6, 2019
479e788
increment build
Juke34 Dec 6, 2019
ea16c54
fix path to different RepeatModeler tools, add RepeatPeps.lib.psq if …
Juke34 Dec 9, 2019
76398b8
sed has to be done after creation
Juke34 Dec 9, 2019
fa12f08
remove maleblastDB has to be done in the RepeatMasker recipe
Juke34 Dec 9, 2019
92f38d6
forgot to export the new paths of the tools
Juke34 Dec 9, 2019
1434fb9
include minimum test data, even if not recommended
Juke34 Dec 9, 2019
34fafe5
Update run_test.sh
Juke34 Dec 10, 2019
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29 changes: 25 additions & 4 deletions recipes/repeatmodeler/RepModelConfig.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -104,21 +104,42 @@ BEGIN
## ============
## Tandem Repeat Finder program.
##
$TRF_PRGM = $ENV{'TRF_DIR'};

$TRF_DIR = $ENV{'TRF_DIR'};
$TRF_PRGM = "$TRF_DIR/trf";
##
## NSEG Location
## =============
## Location of the NCBI nseg program
$NSEG_PRGM = $ENV{'NSEG_DIR'};

$NSEG_DIR = $ENV{'NSEG_DIR'};
$NSEG_PRGM = "$NSEG_DIR/nseg";
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##
## RepeatScout Location
## ====================
## Alkes Price RepeatScout DeNovo Repeat Finder
##
$RSCOUT_DIR = $ENV{'RSCOUT_DIR'};

##
## Refiner Location
## ====================
##
$REFINER_DIR = $ENV{'REFINER_DIR'};
$REFINER_PRGM = "$REFINER_DIR/Refiner";

##
## Refiner Location
## ====================
##
$TRFMASK_DIR = $ENV{'TRFMASK_DIR'};
$TRFMASK_PRGM = "$TRFMASK_DIR/TRFMask";

##
## Refiner Location
## ====================
##
$REPEATCLASSIFIER_DIR = $ENV{'REPEATCLASSIFIER_DIR'};
$REPEATCLASSIFIER_PRGM = "$REPEATCLASSIFIER_DIR/RepeatClassifier";

##
## Turns on debugging in all RepeatModeler modules/scripts
##
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19 changes: 18 additions & 1 deletion recipes/repeatmodeler/build.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,20 @@ mkdir -p ${PREFIX}/bin
mkdir -p ${RM_DIR}
cp -r * ${RM_DIR}

# Hack J. Dainat - fix path to access the tools through the wrapper in the bin
if [[ "$OSTYPE" == "darwin"* ]]; then
sed -i '' 's/REPEATMODELER_DIR\/Refiner/REFINER_PRGM/' ${RM_DIR}/RepeatModeler
sed -i '' 's/REPEATMODELER_DIR\/TRFMask/TRFMASK_PRGM/' ${RM_DIR}/RepeatModeler
sed -i '' 's/REPEATMODELER_DIR\/RepeatClassifier/REPEATCLASSIFIER_PRGM/' ${RM_DIR}/RepeatModeler
sed -i '' 's/REPEATMODELER_DIR\/TRFMask/TRFMASK_PRGM/' ${RM_DIR}/RepeatClassifier
else
sed -i 's/REPEATMODELER_DIR\/Refiner/REFINER_PRGM/' ${RM_DIR}/RepeatModeler
sed -i 's/REPEATMODELER_DIR\/TRFMask/TRFMASK_PRGM/' ${RM_DIR}/RepeatModeler
sed -i 's/REPEATMODELER_DIR\/RepeatClassifier/REPEATCLASSIFIER_PRGM/' ${RM_DIR}/RepeatModeler
sed -i 's/REPEATMODELER_DIR\/TRFMask/TRFMASK_PRGM/' ${RM_DIR}/RepeatClassifier
fi
# END HACK

# Copy edited config file for auto configuration
cp ${RECIPE_DIR}/RepModelConfig.pm ${RM_DIR}/RepModelConfig.pm

Expand All @@ -17,12 +31,15 @@ cat <<END >>${PREFIX}/bin/RepeatModeler
#!/bin/bash
REPEATMODELER_DIR=${PREFIX}/share/RepeatModeler
REPEATMASKER_DIR=${PREFIX}/share/RepeatMasker
REFINER_DIR=${PREFIX}/bin
TRFMASK_DIR=${PREFIX}/bin
REPEATCLASSIFIER_DIR=${PREFIX}/bin
TRF_DIR=${PREFIX}/bin
RMBLAST_DIR=${PREFIX}/bin
RECON_DIR=${PREFIX}/bin
RSCOUT_DIR=${PREFIX}/bin
NSEG_DIR=${PREFIX}/bin
export REPEATMODELER_DIR REPEATMASKER_DIR TRF_DIR RMBLAST_DIR RECON_DIR RSCOUT_DIR NSEG_DIR
export REPEATMODELER_DIR REPEATMASKER_DIR REFINER_DIR TRFMASK_DIR REPEATCLASSIFIER_DIR TRF_DIR RMBLAST_DIR RECON_DIR RSCOUT_DIR NSEG_DIR
NAME=\$(basename \$0)
perl ${RM_DIR}/\${NAME} \$@
END
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5 changes: 4 additions & 1 deletion recipes/repeatmodeler/meta.yaml
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Expand Up @@ -7,7 +7,7 @@ source:
md5: c148b4b56bb3fbd4e9ba88ac8736baa3

build:
number: 1
number: 2
skip: True #[osx]

requirements:
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Expand All @@ -24,7 +24,10 @@ requirements:
- perl-text-soundex

test:
files:
- test.fa
commands:
# (see run_test.sh )
- RepeatModeler > /dev/null

about:
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11 changes: 11 additions & 0 deletions recipes/repeatmodeler/run_test.sh
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Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
#!/bin/sh
set -x -e

# build the db with BuildDatabase
BuildDatabase -engine ncbi -name db test.fa 2> /dev/null

# run repeat modeler
RepeatModeler -engine ncbi -database db 2> /dev/null

# check the result
test -s RM_*/consensi.fa
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