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run.sh
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run.sh
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#######################################################
# Run #
# - - - - - - - - - - - - - - - - - - - - #
# Morteza Hosseini seyedmorteza@ua.pt #
# Diogo Pratas pratas@ua.pt #
# Armando J. Pinho ap@ua.pt #
#######################################################
#!/bin/bash
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Parameters -- set to 1 to activate, and 0 to deactivate
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
### Dataset
GET_DATASET=0 # 54 GB free disk space
DL_HUMAN_FA=0 # Download Human (FASTA) -- 3.1 GB
DL_VIRUSES_FA=0 # Download Viruses (FASTA) -- 0.3 GB
GEN_SYNTH_FA=0 # Generate synthetic dataset (FASTA) -- 2.8 GB
DL_HUMAN_FQ=0 # Download Human (FASTQ) -- 27.0 GB
DL_DENISOVA_FQ=0 # Download Denisova (FASTQ) -- 2.9 GB
GEN_SYNTH_FQ=0 # Generate synthetic dataset (FASTQ) -- 6.1 GB
DL_DENISOVA_VCF=0 # Download Denisova (VCF) -- 6.3 GB
DL_NEANDERTHAL_VCF=0 # Download Neanderthal (VCF) -- 0.8 GB
DL_HUMAN_SAM=0 # Download Human (SAM) -- 0.5 GB
DL_NEANDERTHAL_SAM=0 # Download Neanderthal (SAM) -- 1.5 GB
DL_HUMAN_BAM=0 # Download Human (BAM) -- 0.6 GB
DL_NEANDERTHAL_BAM=0 # Download Neanderthal (BAM) -- 1.3 GB
### Dependencies
INSTALL_DEPENDENCIES=0
INS_7ZIP=1 # 7zip
INS_CMAKE=1 # Cmake
INS_BOOST=0 # Boost
INS_CURL=0 # Curl
INS_VALGRIND=0 # Valgrind
INS_ZLIB=0 # Zlib
INS_SAMTOOLS=0 # Samtools
### Install methods
INSTALL_METHODS=0
# FASTA/FASTQ/VCF/SAM/BAM
INS_CRYFA=1 # Cryfa
# FASTA
INS_MFCOMPRESS=0 # MFCompress -- error: make -- executables available
INS_DELIMINATE=0 # DELIMINATE -- error: site not reachable -- exec avail.
# FASTQ
INS_FQZCOMP=0 # fqzcomp
INS_QUIP=0 # Quip
INS_DSRC=0 # DSRC
INS_FQC=0 # FQC -- error: site not reachable -- exec available
# Encryption -- FASTA/FASTQ/VCF/SAM/BAM
INS_AESCRYPT=0 # AES Crypt
### Run compression methods
RUN_METHODS_COMP=0 # 100 GB free disk space
# FASTA
RUN_CRYFA_FA=0 # Cryfa
# FASTQ
RUN_CRYFA_FQ=0 # Cryfa
# VCF
RUN_CRYFA_VCF=0 # Cryfa
# SAM
RUN_CRYFA_SAM=0 # Cryfa
# BAM
RUN_CRYFA_BAM=0 # Cryfa
# Results
RESULTS_COMP=0
### Run compression & encryption methods
RUN_METHODS_COMP_ENC=0
# FASTA -- 10 GB free disk space
RUN_GZIP_FA_AESCRYPT=0 # gzip + AES Crypt
RUN_BZIP2_FA_AESCRYPT=0 # bzip2 + AES Crypt
RUN_MFCOMPRESS_AESCRYPT=0 # MFCompress + AES Crypt
RUN_DELIMINATE_AESCRYPT=0 # DELIMINATE + AES Crypt
# FASTQ -- 50 GB free disk space
RUN_GZIP_FQ_AESCRYPT=0 # gzip + AES Crypt
RUN_BZIP2_FQ_AESCRYPT=0 # bzip2 + AES Crypt
RUN_FQZCOMP_AESCRYPT=0 # fqzcomp + AES Crypt
RUN_QUIP_AESCRYPT=0 # Quip + AES Crypt
RUN_DSRC_AESCRYPT=0 # DSRC + AES Crypt
RUN_FQC_AESCRYPT=0 # FQC + AES Crypt
# Results
RESULTS_COMP_ENC=0
### Run encryption methods
RUN_METHODS_ENC=0 # 110 GB free disk space
RUN_AESCRYPT=0 # AES Crypt
# Results
RESULTS_ENC=0
### Run Cryfa with different number of threads
RUN_CRYFA_THREADS=0
MAX_N_THR=8 # Max number of threads
CRYFA_THR_DATASET="dataset/FA/V/viruses.fasta"
# CRYFA_THR_DATASET="dataset/FQ/DS/DS-B1088_SR.fastq"
# Run
RUN_CRYFA_THR=1
# Results
RESULTS_CRYFA_THR=0
### Run different methods to explore redundancy
RUN_REDUNDANCY=0 # Cryfa, DELIMINATE, MFCompress
# Dataset (FASTA) -- archaea, bacteria, fungi, plants, viruses
GET_DATASET_REDUN=1 # 12 GB free disk space
# Run & Results
RUN_RES_REDUN=1
################################################################################
################## D O N O T C H A N G E ###################
################################################################################
. script/par.sh # Parameters
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Get dataset
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if [[ $GET_DATASET -eq 1 ]];
then
### Create a folder for dataset, if it doesn't already exist
if [[ ! -d $dataset ]]; then mkdir -p $dataset; fi
### FASTA
if [[ $DL_HUMAN_FA -eq 1 ]]; then . $script/dl_human_fa.sh; fi
if [[ $DL_VIRUSES_FA -eq 1 ]]; then . $script/dl_viruses_fa.sh; fi
if [[ $GEN_SYNTH_FA -eq 1 ]]; then . $script/gen_synth_fa.sh; fi
### FASTQ
if [[ $DL_HUMAN_FQ -eq 1 ]]; then . $script/dl_human_fq.sh; fi
if [[ $DL_DENISOVA_FQ -eq 1 ]]; then . $script/dl_denisova_fq.sh; fi
if [[ $GEN_SYNTH_FQ -eq 1 ]]; then . $script/gen_synth_fq.sh; fi
### VCF
if [[ $DL_DENISOVA_VCF -eq 1 ]]; then . $script/dl_denisova_vcf.sh; fi
if [[ $DL_NEANDERTHAL_VCF -eq 1 ]]; then . $script/dl_neanderthal_vcf.sh; fi
### SAM
if [[ $DL_HUMAN_SAM -eq 1 ]]; then . $script/dl_human_sam.sh; fi
if [[ $DL_NEANDERTHAL_SAM -eq 1 ]]; then . $script/dl_neanderthal_sam.sh; fi
### BAM
if [[ $DL_HUMAN_BAM -eq 1 ]]; then . $script/dl_human_bam.sh; fi
if [[ $DL_NEANDERTHAL_BAM -eq 1 ]]; then . $script/dl_neanderthal_bam.sh; fi
fi
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Install dependencies
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if [[ $INSTALL_DEPENDENCIES -eq 1 ]];
then
if [[ $INS_7ZIP -eq 1 ]]; then . $script/dep_7zip.sh; fi
if [[ $INS_CMAKE -eq 1 ]]; then . $script/dep_cmake.sh; fi
if [[ $INS_BOOST -eq 1 ]]; then . $script/dep_boost.sh; fi
if [[ $INS_CURL -eq 1 ]]; then . $script/dep_curl.sh; fi
if [[ $INS_VALGRIND -eq 1 ]]; then . $script/dep_valgrind.sh; fi
if [[ $INS_ZLIB -eq 1 ]]; then . $script/dep_zlib.sh; fi
if [[ $INS_SAMTOOLS -eq 1 ]]; then . $script/dep_samtools.sh; fi
fi
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Install methods
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if [[ $INSTALL_METHODS -eq 1 ]];
then
### Create a folder for programs, if it doesn't already exist
if [[ ! -d $progs ]]; then mkdir -p $progs; fi
### FASTA/FASTQ
if [[ $INS_CRYFA -eq 1 ]]; then . $script/ins_cryfa.sh; fi
if [[ $INS_AESCRYPT -eq 1 ]]; then . $script/ins_aescrypt.sh; fi
### FASTA
if [[ $INS_MFCOMPRESS -eq 1 ]]; then . $script/ins_mfcompress.sh; fi
if [[ $INS_DELIMINATE -eq 1 ]]; then . $script/ins_deliminate.sh; fi
### FASTQ
if [[ $INS_FQZCOMP -eq 1 ]]; then . $script/ins_fqzcomp.sh; fi
if [[ $INS_QUIP -eq 1 ]]; then . $script/ins_quip.sh; fi
if [[ $INS_DSRC -eq 1 ]]; then . $script/ins_dsrc.sh; fi
if [[ $INS_FQC -eq 1 ]]; then . $script/ins_fqc.sh; fi
fi
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Run compression methods
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if [[ $RUN_METHODS_COMP -eq 1 ]];
then
### Create folders for programs and results, if they don't already exist
if [[ ! -d $progs ]]; then mkdir -p $progs; fi
if [[ ! -d $result ]]; then mkdir -p $result; fi
### Check if the whole dataset is available
. $script/avail_dataset.sh;
### Compression functions
. $script/run_fn_comp.sh
### FASTA
if [[ $RUN_CRYFA_FA -eq 1 ]]; then compDecompOnDataset cryfa fa; fi
### FASTQ
if [[ $RUN_CRYFA_FQ -eq 1 ]]; then compDecompOnDataset cryfa fq; fi
### VCF
if [[ $RUN_CRYFA_VCF -eq 1 ]]; then compDecompOnDataset cryfa vcf; fi
### SAM
if [[ $RUN_CRYFA_SAM -eq 1 ]]; then compDecompOnDataset cryfa sam; fi
### BAM
if [[ $RUN_CRYFA_BAM -eq 1 ]]; then compDecompOnDataset cryfa bam; fi
### Results
if [[ $RESULTS_COMP -eq 1 ]]; then . $script/res_comp.sh; fi
fi
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Run encryption methods
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if [[ $RUN_METHODS_ENC -eq 1 ]];
then
### Create folders for programs and results, if they don't already exist
if [[ ! -d $progs ]]; then mkdir -p $progs; fi
if [[ ! -d $result ]]; then mkdir -p $result; fi
### Check if the whole dataset is available
. $script/avail_dataset.sh;
### Encryption functions
. $script/run_fn_enc.sh
### FASTA/FASTQ/VCF/SAM/BAM
if [[ $RUN_AESCRYPT -eq 1 ]]; then encDecOnDataset aescrypt; fi
### Results
if [[ $RESULTS_ENC -eq 1 ]]; then . $script/res_enc.sh; fi
fi
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Run compression+encryption methods
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if [[ $RUN_METHODS_COMP_ENC -eq 1 ]];
then
### Create folders for programs and results, if they don't already exist
if [[ ! -d $progs ]]; then mkdir -p $progs; fi
if [[ ! -d $result ]]; then mkdir -p $result; fi
### Check if the whole dataset is available
. $script/avail_dataset.sh;
### Compression+encryption functions
. $script/run_fn_comp_enc.sh
### FASTA + Encryption
if [[ $RUN_GZIP_FA_AESCRYPT -eq 1 ]]; then
compEncDecDecompOnDataset gzip fa aescrypt;
fi
if [[ $RUN_BZIP2_FA_AESCRYPT -eq 1 ]]; then
compEncDecDecompOnDataset bzip2 fa aescrypt;
fi
if [[ $RUN_MFCOMPRESS_AESCRYPT -eq 1 ]]; then
compEncDecDecompOnDataset mfcompress fa aescrypt;
fi
if [[ $RUN_DELIMINATE_AESCRYPT -eq 1 ]]; then
compEncDecDecompOnDataset delim fa aescrypt;
fi
### FASTQ + Encryption
if [[ $RUN_GZIP_FQ_AESCRYPT -eq 1 ]]; then
compEncDecDecompOnDataset gzip fq aescrypt;
fi
if [[ $RUN_BZIP2_FQ_AESCRYPT -eq 1 ]]; then
compEncDecDecompOnDataset bzip2 fq aescrypt;
fi
if [[ $RUN_FQZCOMP_AESCRYPT -eq 1 ]]; then
compEncDecDecompOnDataset fqzcomp fq aescrypt;
fi
if [[ $RUN_QUIP_AESCRYPT -eq 1 ]]; then
compEncDecDecompOnDataset quip fq aescrypt;
fi
if [[ $RUN_DSRC_AESCRYPT -eq 1 ]]; then
compEncDecDecompOnDataset dsrc fq aescrypt;
fi
if [[ $RUN_FQC_AESCRYPT -eq 1 ]]; then
compEncDecDecompOnDataset fqc fq aescrypt;
fi
### Results
if [[ $RESULTS_COMP_ENC -eq 1 ]]; then . $script/res_comp_enc.sh; fi
fi
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Run Cryfa with different number of threads
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if [[ $RUN_CRYFA_THREADS -eq 1 ]];
then
### Create a folder for results, if it doesn't already exist
if [[ ! -d $result ]]; then mkdir -p $result; fi
### Check if the dataset is available
if [[ ! -e $CRYFA_THR_DATASET ]]; then
echo "Error: The file \"$CRYFA_THR_DATASET\" is not available.";
return;
fi
### Cryfa compress/decompress function
. $script/run_fn_cryfa_thr.sh
### Run
if [[ $RUN_CRYFA_THR -eq 1 ]]; then runCryfa; fi
### Results
if [[ $RESULTS_CRYFA_THR -eq 1 ]]; then . $script/res_cryfa_thr.sh; fi
fi
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Run different methods to check exploring redundancy
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if [[ $RUN_REDUNDANCY -eq 1 ]];
then
### Create a folder for results, if it doesn't already exist
if [[ ! -d $result ]]; then mkdir -p $result; fi
### Download datasets
if [[ $GET_DATASET_REDUN -eq 1 ]]; then . $script/dl_dataset_redun.sh; fi
### Run & Results
if [[ $RUN_RES_REDUN -eq 1 ]]; then . $script/run_res_redun.sh; fi
fi