cd -place_in_your_local_computer
git clone https://github.com/PLStenger/Coral_block_colonisation.git

git pull

cd 99_softwares/
conda install -c bioconda fastqc
conda install -c bioconda trimmomatic
conda install -c bioconda multiqc

sysctl hw.ncpu
> hw.ncpu: 4

# Put you in your working directory
cd /scratch_vol1/fungi/Coral_block_colonisation/00_scripts


# For run all pipeline, lunch only this command line : 
time nohup bash 000_run_all_pipeline_in_one_script.sh &> 000_run_all_pipeline_in_one_script.out

# For run pipeline step by step, lunch :
# Run the first script for check the quality of your data and then for choosing the good cleanning parameters
time nohup bash 01_quality_check_by_FastQC.sh &> 01_quality_check_by_FastQC.out

    real	2m29.904s
    user	3m14.842s
    sys	    0m14.673s

# Go out of the folder
cd ..

# Go in the "02_quality_check" folder
cd 02_quality_check

# Run multiqc for synthetized information
multiqc .

# Go out of the folder
cd ..

# Go in the script folder
cd 00_script

# Run the second script for cleaned your data
time nohup bash 02_trimmomatic_q30.sh &> 02_trimmomatic_q30.out

    real	1m12.017s
    user	1m31.466s
    sys	    0m8.983s

# Run the third script for checking the quality of your cleaned data 
time nohup bash 03_check_quality_of_cleaned_data.sh &> 03_check_quality_of_cleaned_data.out

    real	5m5.974s
    user	5m42.971s
    sys	    0m27.492s
    
# Go out of the folder
cd ..

# Go in the "04_quality_check" folder
cd 04_quality_check

# Run multiqc for synthetized information
multiqc .

# Go out of the folder
cd ..

# Go in the script folder
cd 00_script

# Try to deal with the V1V3 - V3V4 situation :
time nohup bash 04_fastq-cat.sh &> 04_fastq-cat.out

    real	0m1.264s
    user	0m0.039s
    sys	    0m0.692s

# Import the data in QIIME2 format
time nohup bash 05_qiime2_import_PE.sh &> 05_qiime2_import_PE.out

    real	1m56.160s
    user	0m55.588s
    sys	    0m11.154s

# Run the Denoise
time nohup bash 06_qiime2_denoise_PE.sh &> 06_qiime2_denoise_PE.out
    real	66m29.579s
    user	129m35.661s
    sys	    4m17.156s

# Run the tree construction
time nohup bash 07_qiime2_tree_PE.sh &> 07_qiime2_tree_PE.out
    real	8m29.501s
    user	2m23.194s
    sys	0m20.178s

# Run the rarefaction
time nohup bash 08_qiime2_rarefaction_PE.sh &> 08_qiime2_rarefaction_PE.out
    real	1m15.788s
    user	0m28.194s
    sys	       0m8.118s
    
# For obtainning better plots, run this script on your computer :    
08_qiime2_rarefaction_PE_plots.R

time nohup bash 09_qiime2_calculate_and_explore_diversity_metrics_PE.sh &> 09_qiime2_calculate_and_explore_diversity_metrics_PE.out
    real	59m0.552s
    user	7m23.905s
    sys	1m51.603s

time nohup bash 10_qiime2_assign_taxonomy_PE.sh &> 10_qiime2_assign_taxonomy_PE.out
    real	82m44.469s
    user	74m58.003s
    sys	    1m21.506s
time nohup bash 11_core_biom_PE.sh &> 11_core_biom_PE.out

Run "12_FunGuild.sh" localy please

time nohup bash 13_PICRUSt2.sh &> 13_PICRUSt2.out


time nohup bash 99_junk.sh &> 99_junk.out