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UPPMAX

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Shintaro Katayama edited this page Feb 16, 2016 · 40 revisions

Run on UPPMAX

Installation

git clone -b v3dev https://github.com/shka/STRTprep.git STRTprep3.test
cd STRTprep3.test
bin/install_uppmax.sh

Protocol

  • Step 1: (Copy pre-build indexes, or) build indexes of reference genome and transcriptome, like as
sbatch -A bXXXXXXX -t 12:00:00 -p core -n 1 <<EOF
#!/usr/bin/env bash
. bin/setup_uppmax.sh
bin/index_hg19_ercc92_ynbA_u13369.sh
bin/index_refGene.sh hg19 src/ebwt/hg19_ercc92_ynbA_u13369/ref
EOF
  • Step 2: Edit conf.yaml and src/samples.csv
  • Step 3: Run preprocessing and quality-check as follows, then check out/byGene/samples.xls 
sbatch -A bXXXXXXX -t 24:00:00 -p node -n 16 <<EOF
#!/usr/bin/env bash
. bin/setup_uppmax.sh
rake -m -j 16 qc
EOF
  • Step 4: Run differential expression tests as follows, then check out/byGene/diffexp.xls and analyze more further!
sbatch -A bXXXXXXX -t 24:00:00 -p node -n 16 <<EOF
#!/usr/bin/env bash
. bin/setup_uppmax.sh
rake gene
EOF
  • [v3dev] Step 5: Add "CLASS.TFE" column for classification of samples into src/samples.csv table, run differential expression tests, based on transcription-start-regions, then check out/byTFE/diffexp.xls and analyze more further!
sbatch -A bXXXXXXX -t 24:00:00 -p node -n 16 <<EOF
#!/usr/bin/env bash
. bin/setup_uppmax.sh
rake
EOF
  • Tips 1: If the job will finish within one hour but require much memory (ex. addition of one differential expression test), , you can use devel queue instead of node, which can run a job up to one hour for development/test purpose. For example,
sbatch -A bXXXXXXX -t 1:00:00 -p devel -n 16 <<EOF
#!/usr/bin/env bash
. bin/setup_uppmax.sh
rake gene
EOF
  • Tips 2: If the job will finish soon and require only a few memory (ex. update of plugins without new differential expression tests), you don't need submit as a job - you can run it directly as follows.
. bin/setup_uppmax.sh; rake gene

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