Commit 974280ac authored by Georges Kunstler's avatar Georges Kunstler
Browse files

test directory issue with qsub

parent 3b9752b9
......@@ -4,19 +4,21 @@ export LD_LIBRARY_PATH=/usr/lib64/R/library
mkdir -p Rscript_temp
pwd
for trait in "'SLA'" "'Leaf.N'" "'Wood.density'" "'Max.height'" "'Seed.mass'"; do
echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait);print('done')\"" > Rscript_temp/gdata1$trait.sh
echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); print(getwd());print('done')\"" > Rscript_temp/gdata1$trait.sh
qsub Rscript_temp/gdata1$trait.sh -l nodes=1:ppn=1,mem=8gb -N "gdata1$trait" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, cat.TF=TRUE);print('done')\"" > Rscript_temp/gdata2$trait.sh
# qsub Rscript_temp/gdata2$trait.sh -l nodes=1:ppn=1,mem=8gb -N "gdata2$trait" -q opt32G -j oe
# # echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, cat.TF=TRUE);print('done')\"" > Rscript_temp/gdata2$trait.sh
# # qsub Rscript_temp/gdata2$trait.sh -l nodes=1:ppn=1,mem=8gb -N "gdata2$trait" -q opt32G -j oe
echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, fname = 'data.all.log.rds');print('done')\"" > Rscript_temp/gdata3$trait.sh
qsub Rscript_temp/gdata3$trait.sh -l nodes=1:ppn=1,mem=8gb -N "gdata3$trait" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, fname = 'data.all.log.rds');print('done')\"" > Rscript_temp/gdata3$trait.sh
# qsub Rscript_temp/gdata3$trait.sh -l nodes=1:ppn=1,mem=8gb -N "gdata3$trait" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, cat.TF=TRUE, fname = 'data.all.log.rds');print('done')\"" > Rscript_temp/gdata4$trait.sh
# qsub Rscript_temp/gdata4$trait.sh -l nodes=1:ppn=1,mem=8gb -N "gdata4$trait" -q opt32G -j oe
# # echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, cat.TF=TRUE, fname = 'data.all.log.rds');print('done')\"" > Rscript_temp/gdata4$trait.sh
# # qsub Rscript_temp/gdata4$trait.sh -l nodes=1:ppn=1,mem=8gb -N "gdata4$trait" -q opt32G -j oe
done
#!/bin/bash
pwd
export LD_LIBRARY_PATH=/usr/lib64/R/library
# export LD_LIBRARY_PATH=/usr/lib64/R/library
mkdir -p Rscript_temp
# mkdir -p Rscript_temp
for trait in "'SLA'" "'Leaf.N'" "'Wood.density'" "'Max.height'" "'Seed.mass'"; do
# for trait in "'SLA'" "'Leaf.N'" "'Wood.density'" "'Max.height'" "'Seed.mass'"; do
echo "Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait);print('done')\"" > Rscript_temp/gdata1$trait.sh
bash Rscript_temp/gdata1$trait.sh
# echo "Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait);print('done')\"" > Rscript_temp/gdata1$trait.sh
# bash Rscript_temp/gdata1$trait.sh
echo "Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, cat.TF=TRUE);print('done')\"" > Rscript_temp/gdata2$trait.sh
bash Rscript_temp/gdata2$trait.sh
# echo "Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, cat.TF=TRUE);print('done')\"" > Rscript_temp/gdata2$trait.sh
# bash Rscript_temp/gdata2$trait.sh
echo "Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, fname = 'data.all.csv');print('done')\"" > Rscript_temp/gdata3$trait.sh
bash Rscript_temp/gdata3$trait.sh
# echo "Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, fname = 'data.all.csv');print('done')\"" > Rscript_temp/gdata3$trait.sh
# bash Rscript_temp/gdata3$trait.sh
echo "Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, cat.TF=TRUE, fname = 'data.all.csv');print('done')\"" > Rscript_temp/gdata4$trait.sh
bash Rscript_temp/gdata4$trait.sh
# echo "Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, cat.TF=TRUE, fname = 'data.all.csv');print('done')\"" > Rscript_temp/gdata4$trait.sh
# bash Rscript_temp/gdata4$trait.sh
done
# done
......@@ -4,13 +4,15 @@ export LD_LIBRARY_PATH=/usr/lib64/R/library
mkdir -p Rscript_temp
for trait in "SLA" "Leaf.N" "Wood.density" "Max.height" "Seed.mass"; do
pwd
for trait in "SLA" "Leaf.N" "Wood.density" "Max.height" "Seed.mass"; do
Rscript -e "source('R/analysis/lmer.run.R');load.and.save.data.for.lmer('$trait')"
Rscript -e "print(getwd()); source('R/analysis/lmer.run.R')"
# ; load.and.save.data.for.lmer('$trait')
Rscript -e "source('R/analysis/lmer.run.R');load.and.save.data.for.lmer('$trait', fname = 'data.all.log.rds')"
# Rscript -e "source('R/analysis/lmer.run.R'); load.and.save.data.for.lmer('$trait', fname = 'data.all.log.rds')"
done
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