launch_all_lmer.nolog.bash 1.53 KB
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#!/bin/bash

export LD_LIBRARY_PATH=/usr/lib64/R/library

mkdir -p trait.workshop

for site in "'BCI'" "'Canada'" "'France'" "'Fushan'" "'NVS'" "'Paracou'" "'Spain'" "'US'" "'Swiss'" "'Sweden'" "'NSW'" "'Mbaiki'" "'Luquillo'" "'Japan'"; do 

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  	echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/lmer.run.nolog.R');run.models.for.set.all.traits($site,model.files.lmer.Tf.1, run.lmer,type.filling='species',std=FALSE);print('done')\"" > trait.workshop/species1$site.sh
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	qsub trait.workshop/species1$site.sh -l nodes=1:ppn=1 -N "lmerspecies1$site" -q opt32G -j oe

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  	echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/lmer.run.nolog.R');run.models.for.set.all.traits($site,model.files.lmer.Tf.2, run.lmer,type.filling='species',std=FALSE);print('done')\"" > trait.workshop/species2$site.sh
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	qsub trait.workshop/species2$site.sh -l nodes=1:ppn=1 -N "lmerspecies2$site" -q opt32G -j oe

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  	echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/lmer.run.nolog.R');run.models.for.set.all.traits($site,model.files.lmer.Tf.1, run.lmer,type.filling='genus',std=FALSE);print('done')\"" > trait.workshop/genus1$site.sh
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	qsub trait.workshop/genus1$site.sh -l nodes=1:ppn=1 -N "lmergenus1$site" -q opt32G -j oe

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  	echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/lmer.run.nolog.R');run.models.for.set.all.traits($site,model.files.lmer.Tf.2, run.lmer,type.filling='genus',std=FALSE);print('done')\"" > trait.workshop/genus2$site.sh
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	qsub trait.workshop/genus2$site.sh -l nodes=1:ppn=1 -N "lmergenus2$site" -q opt32G -j oe



done