/
reprocess.sh
83 lines (66 loc) · 1.83 KB
/
reprocess.sh
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#!/bin/bash
set -e
cd "$(dirname "$0")"
STUDY_TMI=10317
STUDY_META_16S_FECAL=11358.850.2024.11937.11993.10581.10352.10249
STUDY_META_16S_MIXED=2136.10052.10333.11724.11874.1189.1774.550
TYPE_16S=16S
TYPE_WGS=WGS
HUMAN_GUT=human-gut
HUMAN_SKIN=human-skin
HUMAN_ORAL=human-oral
HUMAN_MIXED=human-gut.human-oral.human-skin
mkdir -p ../results
pushd ../results
datetag=$(date +"%d%b%Y")
if [[ -d ${datetag} ]];
then
echo "${datetag} result set already exists!"
exit 1
fi
mkdir ${datetag}
rm -f current
ln -s ${datetag} current
mkdir -p ${datetag}/${HUMAN_GUT}
mkdir -p ${datetag}/${HUMAN_SKIN}
mkdir -p ${datetag}/${HUMAN_ORAL}
mkdir -p ${datetag}/${HUMAN_MIXED}
popd
# Microsetta WGS specific
export TMI_DATATYPE=$TYPE_WGS
export ENV_PACKAGE=$HUMAN_GUT
export STUDIES=$STUDY_TMI
export TMI_TITLE="Microsetta WGS fecal samples"
export TMI_NAME=tmi-gut-WGS
sh submit_all.sh
# Microsetta 16S specific
export TMI_DATATYPE=$TYPE_16S
export ENV_PACKAGE=$HUMAN_SKIN
export STUDIES=$STUDY_TMI
export TMI_TITLE="Microsetta 16S skin samples"
export TMI_NAME=tmi-skin-16S
sh submit_all.sh
export ENV_PACKAGE=$HUMAN_ORAL
export STUDIES=$STUDY_TMI
export TMI_TITLE="Microsetta 16S oral samples"
export TMI_NAME=tmi-oral-16S
sh submit_all.sh
export ENV_PACKAGE=$HUMAN_GUT
export STUDIES=$STUDY_TMI
export TMI_TITLE="Microsetta 16S fecal samples"
export TMI_NAME=tmi-gut-16S
sh submit_all.sh
# Multipop gut 16S
export TMI_DATATYPE=$TYPE_16S
export ENV_PACKAGE=$HUMAN_GUT
export STUDIES=${STUDY_TMI}.${STUDY_META_16S_FECAL}
export TMI_TITLE="Meta-analysis 16S fecal samples"
export TMI_NAME=meta-gut-16S
sh submit_all.sh
# Multibody site 16S
export TMI_DATATYPE=$TYPE_16S
export ENV_PACKAGE=$HUMAN_MIXED
export STUDIES=${STUDY_TMI}.${STUDY_META_16S_MIXED}
export TMI_TITLE="Meta-analysis 16S multi-bodysite samples"
export TMI_NAME=meta-mixed-16S
sh submit_all.sh