launch_all_lmer.bash 8.11 KB
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#!/bin/bash
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# Georges Kunstler 14/05/2014
# read one variable
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export LD_LIBRARY_PATH=/usr/lib64/R/library

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mkdir -p Rscript_temp
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# test parameter
nbargs=$#
echo "number of arguments="$nbargs
if [ $nbargs -ne 1 ]
then
  echo "need one and only one argument"
  echo " usage :"
  echo " ./launch_all_lmer.sh  sample.size"
  exit 100
fi


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samplesize=$1
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# "'Seed.mass'" "'Leaf.N'"
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 for trait in "'SLA'" "'Wood.density'" "'Max.height'" ; do
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# # # ALL data 0
#   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.0[1], run.lmer,$trait);print('done')\"" > Rscript_temp/all0${trait}.sh
# 	qsub Rscript_temp/all0${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.0${trait}" -q opt32G -j oe
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#   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.0[2], merge.biomes.TF = TRUE, run.lmer,$trait);print('done')\"" > Rscript_temp/all02${trait}.sh
# 	qsub Rscript_temp/all02${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.02${trait}" -q opt32G -j oe
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# # # ALL data 0b
#   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.0b[1], run.lmer,$trait);print('done')\"" > Rscript_temp/all0b${trait}.sh
# 	qsub Rscript_temp/all0b${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.0b${trait}" -q opt32G -j oe
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#   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.0b[2], merge.biomes.TF = TRUE, run.lmer,$trait);print('done')\"" > Rscript_temp/all02b${trait}.sh
# 	qsub Rscript_temp/all02b${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.02b${trait}" -q opt32G -j oe
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# # # ALL data 1
#   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.1[1], run.lmer,$trait);print('done')\"" > Rscript_temp/allf${trait}.sh
# 	qsub Rscript_temp/allf${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.f${trait}" -q opt32G -j oe
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#   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.1[2], merge.biomes.TF = TRUE, run.lmer,$trait);print('done')\"" > Rscript_temp/allf2${trait}.sh
# 	qsub Rscript_temp/allf2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.f2${trait}" -q opt32G -j oe
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# # # ALL data 1
#   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.3[1], run.lmer,$trait);print('done')\"" > Rscript_temp/allTP${trait}.sh
# 	qsub Rscript_temp/allTP${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.TP${trait}" -q opt32G -j oe
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#   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.3[2], merge.biomes.TF = TRUE, run.lmer,$trait);print('done')\"" > Rscript_temp/allTP2${trait}.sh
# 	qsub Rscript_temp/allTP2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.TP2${trait}" -q opt32G -j oe
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# # INTRA 0
  	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.0[1], run.lmer,$trait, data.type = 'intra');print('done')\"" > Rscript_temp/allINTRA0${trait}.sh
	qsub Rscript_temp/allINTRA0${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRA0${trait}" -q opt32G -j oe
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  	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.0[2], merge.biomes.TF = TRUE, run.lmer,$trait,data.type = 'intra');print('done')\"" > Rscript_temp/allINTRA02${trait}.sh
	qsub Rscript_temp/allINTRA02${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRA02${trait}" -q opt32G -j oe
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# # # INTRA 1
#   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.1[1], run.lmer,$trait, data.type = 'intra');print('done')\"" > Rscript_temp/allINTRA${trait}.sh
# 	qsub Rscript_temp/allINTRA${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRA${trait}" -q opt32G -j oe
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#   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.1[2], merge.biomes.TF = TRUE, run.lmer,$trait,data.type = 'intra');print('done')\"" > Rscript_temp/allINTRA2${trait}.sh
# 	qsub Rscript_temp/allINTRA2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRA2${trait}" -q opt32G -j oe

# # # INTRA 2
#   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.2[1], run.lmer,$trait, data.type = 'intra');print('done')\"" > Rscript_temp/allINTRAB${trait}.sh
# 	qsub Rscript_temp/allINTRAB${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRAB${trait}" -q opt32G -j oe


#   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.2[2], merge.biomes.TF = TRUE, run.lmer,$trait,data.type = 'intra');print('done')\"" > Rscript_temp/allINTRAB2${trait}.sh
# 	qsub Rscript_temp/allINTRAB2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRAB2${trait}" -q opt32G -j oe
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# # # INTRA 3
#   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.3[1], run.lmer,$trait, data.type = 'intra');print('done')\"" > Rscript_temp/allINTRAE${trait}.sh
# 	qsub Rscript_temp/allINTRAE${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRAE${trait}" -q opt32G -j oe
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#   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.intra.3[2], merge.biomes.TF = TRUE, run.lmer,$trait,data.type = 'intra');print('done')\"" > Rscript_temp/allINTRAE2${trait}.sh
# 	qsub Rscript_temp/allINTRAE2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.INTRAE2${trait}" -q opt32G -j oe
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# # # # # ecocode 3
#   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.2[1], run.lmer,$trait, data.type = 'simple');print('done')\"" > Rscript_temp/allECO${trait}.sh
# 	qsub Rscript_temp/allECO${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.ECO${trait}" -q opt32G -j oe
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#   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.2[2], run.lmer,merge.biomes.TF = TRUE,$trait, data.type = 'simple');print('done')\"" > Rscript_temp/allECO2${trait}.sh
# 	qsub Rscript_temp/allECO2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.ECO2${trait}" -q opt32G -j oe
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# # # # ecocode TP
#   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.4[1], run.lmer,$trait, data.type = 'simple');print('done')\"" > Rscript_temp/allECOTP${trait}.sh
# 	qsub Rscript_temp/allECOTP${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.ECOTP${trait}" -q opt32G -j oe
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#   	echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.4[2], run.lmer,merge.biomes.TF = TRUE,$trait, data.type = 'simple');print('done')\"" > Rscript_temp/allECOTP2${trait}.sh
# 	qsub Rscript_temp/allECOTP2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.ECOTP2${trait}" -q opt32G -j oe
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done
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