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@bretonics
Last active Dec 15, 2019
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Bash Functions
# .bash_functions - User bash functions
# Template from https://gist.github.com/bretonics/894d8c2d1d4813c36b7d36e9a97aedd6
#-------------------------------------------------------------------------------
# SYSTEM
mkcd() {
mkdir $1; cd $1
}
get-git-branch() {
git branch 2> /dev/null | sed -e '/^[^*]/d' -e 's/* \(.*\)/ (\1)/'
}
#-------------------------------------------------------------------------------
# QSUB
submit_cr() {
# Pre-Flight Run Checks
if [ $# -ne 1 ]; then
echo "No argument passed. Needs 1 argument, a simple format CSV file."
echo "Usage: qsub cellranger.qsub [simple.csv]"
kill -9 $$
fi
}
projects() {
if [ $# == 0 ]
then
echo "Usage: projects [project names]"
else
args=("$@")
for project in ${args[@]}; do
if [ ! -e $project ]; then
mkdir $project
else
echo -e "Folder $project ${RED}exists${NC}"
fi
echo "Copying templates to $project..."
# Copy report
if [ ! -e ${project}/${project}_report.docx ]; then
cp "../Templates/Microarray report template.docx" ${project}/${project}_report.docx
else
echo -e "\t${project}/${project}_report.docx ${RED}exists${NC}"
fi
# Copy analysis
if [ ! -e ${project}/${project}_analysis.xlsx ]; then
cp ../Templates/microarray_pairwise_comparison.xlsx ${project}/${project}_analysis.xlsx
else
echo -e "\t${project}/${project}_analysis.xlsx ${RED}exists${NC}"
fi
# Copy GSEA
if [ ! -e ${project}/${project}_GSEA.xlsx ]; then
cp ../Templates/GSEA_template.xlsx ${project}/${project}_GSEA.xlsx
else
echo -e "\t${project}/${project}_GSEA.xlsx ${RED}exists${NC}"
fi
done
# Move to project folder
if [ ${#args[@]} == 1 ]; then
cd ${project}
fi
fi
}
sync-project() {
if [ $# == 0 ]; then
echo "Usage: sync-project [project folder name(s)]"
else
parent=$(basename $(pwd))
projects=("$@")
for project in ${projects[@]}; do
command="rsync -avzhce ssh -u --progress --exclude cache --exclude MAKE_FASTQS_CS --exclude SC_RNA_COUNTER_CS --exclude SC_VDJ_ASSEMBLER_CS --exclude *fastq.gz --exclude *bam* scsdata@scc4.bu.edu:~/scscore/Analysis/${parent}/${project}/ ${project}"
echo -e "\nRunning command: ${command}\n"
$command
done
fi
}
Rrender() {
if [ $# == 0 ]; then
echo "Usage: Rrender [file.Rmd] [qsub options (optional)]"
echo "Qsub rmarkdown file to render"
else
project=${1}; shift
options=$@
name=$(basename $(dirname `pwd`))
date=$(basename `pwd`)
qsub -N "${name}_${date}_report" -m beas ${options[@]} ~/bin/render "${project}"
fi
}
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