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Commit f9fa314e authored by Dillenn Terumalai's avatar Dillenn Terumalai :speech_balloon:
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Merge branch 'dev' into 'master' 

Version 1.9.0

See merge request SPSP/transfer-tool!11
parents bec294d9 5fad2416
Branches
Tags v1.9.0
1 merge request!11Version 1.9.0
Pipeline #2085 passed
Stage: deploy
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......@@ -2,7 +2,7 @@
# SPSP transfer-tool is developed and maintained by SIB. For more information, please contact spsp-support@sib.swiss
VERSION="1.8.0" # bumped to support spsp --help, spsp --version
VERSION="1.9.0" # bumped to support spsp --help, spsp --version
# Define colors that are used in the help screen
......@@ -23,7 +23,7 @@ UNAMEOUT="$(uname -s)"
case "${UNAMEOUT}" in
Linux*) MACHINE=linux ;;
Darwin*) MACHINE=mac ;;
*) MACHINE="UNKNOWN"
*) MACHINE="UNKNOWN" ;;
esac
if [ "$MACHINE" == "UNKNOWN" ]; then
......@@ -59,7 +59,7 @@ showHelp() {
commands="${COL_LYELLOW}Commands:\n${COL_RESET}"
commands="$commands auto Automatically run the commands to Compress, Hash, Encrypt & Transfer, add --no-archive option to delete the files after the transfer\n"
commands="$commands help Shows help screen\n"
commands="$commands test Dry run with fake generated files with report\n"
commands="$commands test Fake run with fake generated files\n"
commands="$commands cleanup Clean the following directories: logs, sent, viruses, bacteria and .outbox\n"
options="${COL_LYELLOW}Options:\n${COL_RESET}"
......@@ -84,7 +84,6 @@ compressFolder() {
tar -czf $1.tar.gz $1
}
hashFile() {
$SHACMD "$1" >"$1".sha256
}
......@@ -235,7 +234,7 @@ autoMode() {
if [ -d "$DIRECTORY" ] && [ "$DIRECTORY" != $OUTBOX ] && [ "$DIRECTORY" != $SENT ] && [ "$DIRECTORY" != $LOGS ]; then
for FILE in "$DIRECTORY"/*; do
if [[ -f $FILE && $FILE != *.@(fasta|fa|fasta.gz|fa.gz|fasta.xz|fa.xz|fastq|fastq.gz|cram|bam|csv|tsv|csv.gz|tsv.gz|vcf|xls|xlsx) ]]; then
if [[ -f $FILE && $FILE != *.@(fasta|fa|fasta.gz|fa.gz|fasta.xz|fa.xz|fastq|fastq.gz|cram|bam|cram.gz|bam.gz|csv|tsv|csv.gz|tsv.gz|vcf|xls|xlsx) ]]; then
((ERRORS = ERRORS + 1))
((STEP_ERRORS = STEP_ERRORS + 1))
echo "[$(date +"%T")] local.ERROR: Unsupported format ($FILE)" >>"../$LOGFILE"
......@@ -243,10 +242,10 @@ autoMode() {
fi
done
if ls "$DIRECTORY"/*.fa* 1> /dev/null 2>&1 || ls "$DIRECTORY"/*.*am 1> /dev/null 2>&1 || ls "$DIRECTORY"/*.*sv* 1> /dev/null 2>&1 || ls "$DIRECTORY"/*.vcf 1> /dev/null 2>&1 && ls "$DIRECTORY"/*.xls* 1> /dev/null 2>&1; then
if ls "$DIRECTORY"/*.fa* 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.*am 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.*sv* 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.vcf 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.xls* 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.*.gz 1>/dev/null 2>&1; then
if [[ "$*" == *--fake* ]] || [[ "$*" == *-F* ]]; then
compressFolder "$DIRECTORY"
compressFolder "$DIRECTORY" 2>>"../$ERRORLOGFILE"
if [ -f "$DIRECTORY.tar.gz" ]; then
echo "[$(date +"%T")] local.SUCCESS: $DIRECTORY has been successfully compress into $DIRECTORY.tar.gz" >>"../$LOGFILE"
else
......@@ -258,7 +257,7 @@ autoMode() {
else
ARCHIVENAME=$(date +"%Y%m%d%H%M")
mv $DIRECTORY $ARCHIVENAME
compressFolder "$ARCHIVENAME"
compressFolder "$ARCHIVENAME" 2>>"../$ERRORLOGFILE"
if [ -f "$ARCHIVENAME.tar.gz" ]; then
echo "[$(date +"%T")] local.SUCCESS: $ARCHIVENAME has been successfully compress into $DIRECTORY.tar.gz" >>"../$LOGFILE"
else
......@@ -289,16 +288,16 @@ autoMode() {
fi
done
cd ..;
cd ..
cd $BACTERIA;
cd $BACTERIA
for DIRECTORY in ./*; do
if [ -d "$DIRECTORY" ] && [ "$DIRECTORY" != $OUTBOX ] && [ "$DIRECTORY" != $SENT ] && [ "$DIRECTORY" != $LOGS ]; then
for FILE in "$DIRECTORY"/*; do
if [[ -f $FILE && $FILE != *.@(fasta|fa|fasta.gz|fa.gz|fasta.xz|fa.xz|fastq|fastq.gz|cram|bam|csv|tsv|csv.gz|tsv.gz|vcf|xls|xlsx) ]]; then
if [[ -f $FILE && $FILE != *.@(fasta|fa|fasta.gz|fa.gz|fasta.xz|fa.xz|fastq|fastq.gz|cram|bam|cram.gz|bam.gz|csv|tsv|csv.gz|tsv.gz|vcf|xls|xlsx) ]]; then
((ERRORS = ERRORS + 1))
((STEP_ERRORS = STEP_ERRORS + 1))
echo "[$(date +"%T")] local.ERROR: Unsupported format ($FILE)" >>"../$LOGFILE"
......@@ -306,7 +305,7 @@ autoMode() {
fi
done
if ls "$DIRECTORY"/*.fa* 1> /dev/null 2>&1 || ls "$DIRECTORY"/*.*am 1> /dev/null 2>&1 || ls "$DIRECTORY"/*.*sv* 1> /dev/null 2>&1 || ls "$DIRECTORY"/*.vcf 1> /dev/null 2>&1 && ls "$DIRECTORY"/*.xls* 1> /dev/null 2>&1; then
if ls "$DIRECTORY"/*.fa* 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.*am 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.*sv* 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.vcf 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.xls* 1>/dev/null 2>&1 || ls "$DIRECTORY"/*.*.gz 1>/dev/null 2>&1; then
if [[ "$*" == *--fake* ]] || [[ "$*" == *-F* ]]; then
compressFolder "$DIRECTORY"
......@@ -351,7 +350,7 @@ autoMode() {
fi
done
cd ..;
cd ..
if [[ $STEP_ERRORS > 0 ]]; then
printf "${BACK_RED} ERROR ${COL_RESET}\n"
......@@ -363,7 +362,7 @@ autoMode() {
printf " - Hashing and encrypting the archives... "
cd $OUTBOX/$VIRUSES;
cd $OUTBOX/$VIRUSES
for FILE in *.*; do
if [ -f "$FILE" ]; then
......@@ -394,7 +393,7 @@ autoMode() {
fi
done
cd ../$BACTERIA;
cd ../$BACTERIA
for FILE in *.*; do
if [ -f "$FILE" ]; then
......@@ -434,11 +433,11 @@ autoMode() {
printf " - Transferring the encrypted archives... "
cd ../$VIRUSES;
cd ../$VIRUSES
for FILE in *.*; do
if [ -f "$FILE" ]; then
echo put "$FILE" | sftp -q -b- "${SFTP_URL}/$VIRUSES" 1> /dev/null
echo put "$FILE" | sftp -q -b- "${SFTP_URL}/$VIRUSES" 1>/dev/null 2>>"../../$ERRORLOGFILE"
((SUCCESS = SUCCESS + 1))
echo "[$(date +"%T")] local.SUCCESS: $FILE has been successfully transferred to the remote server" >>"../../$LOGFILE"
if [[ "$*" == *--no-archive* ]] || [[ "$*" == *-NA* ]]; then
......@@ -448,19 +447,14 @@ autoMode() {
mv "$FILE" ../../$SENT
echo "[$(date +"%T")] local.SUCCESS: $FILE successfully moved to $SENT folder" >>"../../$LOGFILE"
fi
else
((ERRORS=ERRORS+1))
((STEP_ERRORS=STEP_ERRORS+1))
echo "[$(date +"%T")] local.ERROR: Transfer of $FILE failed" >> "../../$LOGFILE"
echo "[$(date +"%F %T")] local.ERROR: Transfer of $FILE failed" >> "../../$ERRORLOGFILE"
fi
done
cd ../$BACTERIA;
cd ../$BACTERIA
for FILE in *.*; do
if [ -f "$FILE" ]; then
echo put "$FILE" | sftp -q -b- -o LogLevel=QUIET "${SFTP_URL}/$BACTERIA" 1> /dev/null
echo put "$FILE" | sftp -q -b- -o LogLevel=QUIET "${SFTP_URL}/$BACTERIA" 1>/dev/null 2>>"../../$ERRORLOGFILE"
((SUCCESS = SUCCESS + 1))
echo "[$(date +"%T")] local.SUCCESS: $FILE has been successfully transferred to the remote server" >>"../../$LOGFILE"
if [[ "$*" == *--no-archive* ]] || [[ "$*" == *-NA* ]]; then
......@@ -470,11 +464,6 @@ autoMode() {
mv "$FILE" ../../$SENT
echo "[$(date +"%T")] local.SUCCESS: $FILE successfully moved to $SENT folder" >>"../../$LOGFILE"
fi
else
((ERRORS=ERRORS+1))
((STEP_ERRORS=STEP_ERRORS+1))
echo "[$(date +"%T")] local.ERROR: Transfer of $FILE failed" >> "../../$LOGFILE"
echo "[$(date +"%F %T")] local.ERROR: Transfer of $FILE failed" >> "../../$ERRORLOGFILE"
fi
done
......@@ -504,90 +493,309 @@ generateFakeFiles() {
VIRUSES=viruses
BACTERIA=bacteria
#We generate the fake folders with their fake files
if [ ! -d "$VIRUSES/fake-viruses" ]; then
mkdir -p $VIRUSES/fake-viruses
if [ ! -d "$VIRUSES/fake-viruses-xlsx" ]; then
mkdir -p $VIRUSES/fake-viruses-xlsx
fi
rm -rf ./$VIRUSES/fake-viruses-xlsx/*
truncate -s 5M ./$VIRUSES/fake-viruses-xlsx/fake-viruses.xlsx
if [ ! -d "$VIRUSES/fake-viruses-xls" ]; then
mkdir -p $VIRUSES/fake-viruses-xls
fi
rm -rf ./$VIRUSES/fake-viruses-xls/*
truncate -s 5M ./$VIRUSES/fake-viruses-xls/fake-viruses.xls
if [ ! -d "$VIRUSES/fake-viruses-fasta" ]; then
mkdir -p $VIRUSES/fake-viruses-fasta
fi
rm -rf ./$VIRUSES/fake-viruses-fasta/*
truncate -s 100M ./$VIRUSES/fake-viruses-fasta/fake-viruses.fasta
if [ ! -d "$VIRUSES/fake-viruses-fa" ]; then
mkdir -p $VIRUSES/fake-viruses-fa
fi
rm -rf ./$VIRUSES/fake-viruses-fa/*
truncate -s 100M ./$VIRUSES/fake-viruses-fa/fake-viruses.fa
if [ ! -d "$VIRUSES/fake-viruses-fasta-gz" ]; then
mkdir -p $VIRUSES/fake-viruses-fasta-gz
fi
rm -rf ./$VIRUSES/fake-viruses-fasta-gz/*
truncate -s 100M ./$VIRUSES/fake-viruses-fasta-gz/fake-viruses.fasta.gz
if [ ! -d "$VIRUSES/fake-viruses-fa-gz" ]; then
mkdir -p $VIRUSES/fake-viruses-fa-gz
fi
rm -rf ./$VIRUSES/fake-viruses-fa-gz/*
truncate -s 100M ./$VIRUSES/fake-viruses-fa-gz/fake-viruses.fa.gz
if [ ! -d "$VIRUSES/fake-viruses-fasta-xz" ]; then
mkdir -p $VIRUSES/fake-viruses-fasta-xz
fi
rm -rf ./$VIRUSES/fake-viruses-fasta-xz/*
truncate -s 100M ./$VIRUSES/fake-viruses-fasta-xz/fake-viruses.fasta.xz
if [ ! -d "$VIRUSES/fake-viruses-fa-xz" ]; then
mkdir -p $VIRUSES/fake-viruses-fa-xz
fi
rm -rf ./$VIRUSES/fake-viruses-fa-xz/*
truncate -s 100M ./$VIRUSES/fake-viruses-fa-xz/fake-viruses.fa.xz
if [ ! -d "$VIRUSES/fake-viruses-fastq" ]; then
mkdir -p $VIRUSES/fake-viruses-fastq
fi
rm -rf ./$VIRUSES/fake-viruses-fastq/*
truncate -s 100M ./$VIRUSES/fake-viruses-fastq/fake-viruses.fastq
if [ ! -d "$VIRUSES/fake-viruses-fastq-gz" ]; then
mkdir -p $VIRUSES/fake-viruses-fastq-gz
fi
rm -rf ./$VIRUSES/fake-viruses/*
rm -rf ./$VIRUSES/fake-viruses-fastq-gz/*
truncate -s 5M ./$VIRUSES/fake-viruses/fake-viruses.xlsx
truncate -s 100M ./$VIRUSES/fake-viruses-fastq-gz/fake-viruses.fastq.gz
truncate -s 5M ./$VIRUSES/fake-viruses/fake-viruses.xls
if [ ! -d "$VIRUSES/fake-viruses-cram" ]; then
mkdir -p $VIRUSES/fake-viruses-cram
fi
rm -rf ./$VIRUSES/fake-viruses-cram/*
truncate -s 100M ./$VIRUSES/fake-viruses/fake-viruses.fasta
truncate -s 100M ./$VIRUSES/fake-viruses-cram/fake-viruses.cram
truncate -s 100M ./$VIRUSES/fake-viruses/fake-viruses.fa
if [ ! -d "$VIRUSES/fake-viruses-bam" ]; then
mkdir -p $VIRUSES/fake-viruses-bam
fi
truncate -s 100M ./$VIRUSES/fake-viruses/fake-viruses.fasta.gz
rm -rf ./$VIRUSES/fake-viruses-bam/*
truncate -s 100M ./$VIRUSES/fake-viruses/fake-viruses.fa.gz
truncate -s 100M ./$VIRUSES/fake-viruses-bam/fake-viruses.bam
truncate -s 100M ./$VIRUSES/fake-viruses/fake-viruses.fasta.xz
if [ ! -d "$VIRUSES/fake-viruses-cram-gz" ]; then
mkdir -p $VIRUSES/fake-viruses-cram-gz
fi
truncate -s 100M ./$VIRUSES/fake-viruses/fake-viruses.fa.xz
rm -rf ./$VIRUSES/fake-viruses-cram-gz/*
truncate -s 100M ./$VIRUSES/fake-viruses/fake-viruses.fastq
truncate -s 100M ./$VIRUSES/fake-viruses-cram-gz/fake-viruses.cram.gz
truncate -s 100M ./$VIRUSES/fake-viruses/fake-viruses.fastq
if [ ! -d "$VIRUSES/fake-viruses-bam-gz" ]; then
mkdir -p $VIRUSES/fake-viruses-bam-gz
fi
truncate -s 100M ./$VIRUSES/fake-viruses/fake-viruses.fastq.gz
rm -rf ./$VIRUSES/fake-viruses-bam-gz/*
truncate -s 100M ./$VIRUSES/fake-viruses/fake-viruses.cram
truncate -s 100M ./$VIRUSES/fake-viruses-bam-gz/fake-viruses.bam.gz
truncate -s 100M ./$VIRUSES/fake-viruses/fake-viruses.bam
if [ ! -d "$VIRUSES/fake-viruses-csv" ]; then
mkdir -p $VIRUSES/fake-viruses-csv
fi
truncate -s 100M ./$VIRUSES/fake-viruses/fake-viruses.csv
rm -rf ./$VIRUSES/fake-viruses-csv/*
truncate -s 100M ./$VIRUSES/fake-viruses/fake-viruses.tsv
truncate -s 100M ./$VIRUSES/fake-viruses-csv/fake-viruses.csv
truncate -s 100M ./$VIRUSES/fake-viruses/fake-viruses.csv.gz
if [ ! -d "$VIRUSES/fake-viruses-tsv" ]; then
mkdir -p $VIRUSES/fake-viruses-tsv
fi
truncate -s 100M ./$VIRUSES/fake-viruses/fake-viruses.tsv.gz
rm -rf ./$VIRUSES/fake-viruses-tsv/*
truncate -s 100M ./$VIRUSES/fake-viruses/fake-viruses.vcf
truncate -s 100M ./$VIRUSES/fake-viruses-tsv/fake-viruses.tsv
if [ ! -d "$BACTERIA/fake-bacteria" ]; then
mkdir -p $BACTERIA/fake-bacteria
if [ ! -d "$VIRUSES/fake-viruses-csv-gz" ]; then
mkdir -p $VIRUSES/fake-viruses-csv-gz
fi
rm -rf ./$BACTERIA/fake-bacteria/*
rm -rf ./$VIRUSES/fake-viruses-csv-gz/*
truncate -s 5M ./$BACTERIA/fake-bacteria/fake-bacteria.xlsx
truncate -s 100M ./$VIRUSES/fake-viruses-csv-gz/fake-viruses.csv.gz
truncate -s 5M ./$BACTERIA/fake-bacteria/fake-bacteria.xls
if [ ! -d "$VIRUSES/fake-viruses-tsv-gz" ]; then
mkdir -p $VIRUSES/fake-viruses-tsv-gz
fi
truncate -s 100M ./$BACTERIA/fake-bacteria/fake-bacteria.fasta
rm -rf ./$VIRUSES/fake-viruses-tsv-gz/*
truncate -s 100M ./$BACTERIA/fake-bacteria/fake-bacteria.fa
truncate -s 100M ./$VIRUSES/fake-viruses-tsv-gz/fake-viruses.tsv.gz
truncate -s 100M ./$BACTERIA/fake-bacteria/fake-bacteria.fasta.gz
if [ ! -d "$VIRUSES/fake-viruses-vcf" ]; then
mkdir -p $VIRUSES/fake-viruses-vcf
fi
truncate -s 100M ./$BACTERIA/fake-bacteria/fake-bacteria.fa.gz
rm -rf ./$VIRUSES/fake-viruses-vcf/*
truncate -s 100M ./$BACTERIA/fake-bacteria/fake-bacteria.fasta.xz
truncate -s 100M ./$VIRUSES/fake-viruses-vcf/fake-viruses.vcf
truncate -s 100M ./$BACTERIA/fake-bacteria/fake-bacteria.fa.xz
if [ ! -d "$BACTERIA/fake-bacteria-xlsx" ]; then
mkdir -p $BACTERIA/fake-bacteria-xlsx
fi
truncate -s 100M ./$BACTERIA/fake-bacteria/fake-bacteria.fastq
rm -rf ./$BACTERIA/fake-bacteria-xlsx/*
truncate -s 100M ./$BACTERIA/fake-bacteria/fake-bacteria.fastq
truncate -s 5M ./$BACTERIA/fake-bacteria-xlsx/fake-bacteria.xlsx
truncate -s 100M ./$BACTERIA/fake-bacteria/fake-bacteria.fastq.gz
if [ ! -d "$BACTERIA/fake-bacteria-xls" ]; then
mkdir -p $BACTERIA/fake-bacteria-xls
fi
truncate -s 100M ./$BACTERIA/fake-bacteria/fake-bacteria.cram
rm -rf ./$BACTERIA/fake-bacteria-xls/*
truncate -s 100M ./$BACTERIA/fake-bacteria/fake-bacteria.bam
truncate -s 5M ./$BACTERIA/fake-bacteria-xls/fake-bacteria.xls
truncate -s 100M ./$BACTERIA/fake-bacteria/fake-bacteria.csv
if [ ! -d "$BACTERIA/fake-bacteria-fasta" ]; then
mkdir -p $BACTERIA/fake-bacteria-fasta
fi
truncate -s 100M ./$BACTERIA/fake-bacteria/fake-bacteria.tsv
rm -rf ./$BACTERIA/fake-bacteria-fasta/*
truncate -s 100M ./$BACTERIA/fake-bacteria-fasta/fake-bacteria.fasta
if [ ! -d "$BACTERIA/fake-bacteria-fa" ]; then
mkdir -p $BACTERIA/fake-bacteria-fa
fi
truncate -s 100M ./$BACTERIA/fake-bacteria/fake-bacteria.csv.gz
rm -rf ./$BACTERIA/fake-bacteria-fa/*
truncate -s 100M ./$BACTERIA/fake-bacteria-fa/fake-bacteria.fa
if [ ! -d "$BACTERIA/fake-bacteria-fasta-gz" ]; then
mkdir -p $BACTERIA/fake-bacteria-fasta-gz
fi
rm -rf ./$BACTERIA/fake-bacteria-fasta-gz/*
truncate -s 100M ./$BACTERIA/fake-bacteria-fasta-gz/fake-bacteria.fasta.gz
if [ ! -d "$BACTERIA/fake-bacteria-fa-gz" ]; then
mkdir -p $BACTERIA/fake-bacteria-fa-gz
fi
rm -rf ./$BACTERIA/fake-bacteria-fa-gz/*
truncate -s 100M ./$BACTERIA/fake-bacteria-fa-gz/fake-bacteria.fa.gz
if [ ! -d "$BACTERIA/fake-bacteria-fasta-xz" ]; then
mkdir -p $BACTERIA/fake-bacteria-fasta-xz
fi
rm -rf ./$BACTERIA/fake-bacteria-fasta-xz/*
truncate -s 100M ./$BACTERIA/fake-bacteria-fasta-xz/fake-bacteria.fasta.xz
if [ ! -d "$BACTERIA/fake-bacteria-fa-xz" ]; then
mkdir -p $BACTERIA/fake-bacteria-fa-xz
fi
rm -rf ./$BACTERIA/fake-bacteria-fa-xz/*
truncate -s 100M ./$BACTERIA/fake-bacteria-fa-xz/fake-bacteria.fa.xz
if [ ! -d "$BACTERIA/fake-bacteria-fastq" ]; then
mkdir -p $BACTERIA/fake-bacteria-fastq
fi
rm -rf ./$BACTERIA/fake-bacteria-fastq/*
truncate -s 100M ./$BACTERIA/fake-bacteria-fastq/fake-bacteria.fastq
if [ ! -d "$BACTERIA/fake-bacteria-fastq-gz" ]; then
mkdir -p $BACTERIA/fake-bacteria-fastq-gz
fi
rm -rf ./$BACTERIA/fake-bacteria-fastq-gz/*
truncate -s 100M ./$BACTERIA/fake-bacteria-fastq-gz/fake-bacteria.fastq.gz
if [ ! -d "$BACTERIA/fake-bacteria-cram" ]; then
mkdir -p $BACTERIA/fake-bacteria-cram
fi
rm -rf ./$BACTERIA/fake-bacteria-cram/*
truncate -s 100M ./$BACTERIA/fake-bacteria-cram/fake-bacteria.cram
if [ ! -d "$BACTERIA/fake-bacteria-bam" ]; then
mkdir -p $BACTERIA/fake-bacteria-bam
fi
rm -rf ./$BACTERIA/fake-bacteria-bam/*
truncate -s 100M ./$BACTERIA/fake-bacteria-bam/fake-bacteria.bam
if [ ! -d "$BACTERIA/fake-bacteria-cram-gz" ]; then
mkdir -p $BACTERIA/fake-bacteria-cram-gz
fi
rm -rf ./$BACTERIA/fake-bacteria-cram-gz/*
truncate -s 100M ./$BACTERIA/fake-bacteria-cram-gz/fake-bacteria.cram.gz
if [ ! -d "$BACTERIA/fake-bacteria-bam-gz" ]; then
mkdir -p $BACTERIA/fake-bacteria-bam-gz
fi
rm -rf ./$BACTERIA/fake-bacteria-bam-gz/*
truncate -s 100M ./$BACTERIA/fake-bacteria-bam-gz/fake-bacteria.bam.gz
if [ ! -d "$BACTERIA/fake-bacteria-csv" ]; then
mkdir -p $BACTERIA/fake-bacteria-csv
fi
rm -rf ./$BACTERIA/fake-bacteria-csv/*
truncate -s 100M ./$BACTERIA/fake-bacteria-csv/fake-bacteria.csv
if [ ! -d "$BACTERIA/fake-bacteria-tsv" ]; then
mkdir -p $BACTERIA/fake-bacteria-tsv
fi
rm -rf ./$BACTERIA/fake-bacteria-tsv/*
truncate -s 100M ./$BACTERIA/fake-bacteria-tsv/fake-bacteria.tsv
if [ ! -d "$BACTERIA/fake-bacteria-csv-gz" ]; then
mkdir -p $BACTERIA/fake-bacteria-csv-gz
fi
rm -rf ./$BACTERIA/fake-bacteria-csv-gz/*
truncate -s 100M ./$BACTERIA/fake-bacteria-csv-gz/fake-bacteria.csv.gz
if [ ! -d "$BACTERIA/fake-bacteria-tsv-gz" ]; then
mkdir -p $BACTERIA/fake-bacteria-tsv-gz
fi
rm -rf ./$BACTERIA/fake-bacteria-tsv-gz/*
truncate -s 100M ./$BACTERIA/fake-bacteria-tsv-gz/fake-bacteria.tsv.gz
if [ ! -d "$BACTERIA/fake-bacteria-vcf" ]; then
mkdir -p $BACTERIA/fake-bacteria-vcf
fi
truncate -s 100M ./$BACTERIA/fake-bacteria/fake-bacteria.tsv.gz
rm -rf ./$BACTERIA/fake-bacteria-vcf/*
truncate -s 100M ./$BACTERIA/fake-bacteria/fake-bacteria.vcf
truncate -s 100M ./$BACTERIA/fake-bacteria-vcf/fake-bacteria.vcf
autoMode --fake --no-archive
......@@ -610,8 +818,7 @@ if [ $# -gt 0 ]; then
while [ "$answer" = false ]; do
read -r -p "Please type laboratory/institution identifier: " identifier
read -r -p "Is $identifier correct?[y/n] " -n 1
if [[ $REPLY =~ ^[Yy]$ ]]
then
if [[ $REPLY =~ ^[Yy]$ ]]; then
echo "ID=$identifier" >.env
echo 'HOST=spsp.sib.swiss' >>.env
echo 'SFTP_URL=${ID}@${HOST}:data' >>.env
......
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