Setup conda environments

1. install rnaseq on sage

   #-- version 2 --
   conda install -c conda-forge mamba
   mamba create -n rnaseq -c conda-forge -c bioconda -c defaults python fastqc trim-galore star hisat2 picard csvtk preseq rseqc samtools
   conda activate rnaseq
   pip3 install deeptools
   pip3 install multiqc
   mamba install -c conda-forge -c bioconda -c defaults -c r stringtie subread gffread r-data.table r-gplots bioconductor-dupradar bioconductor-edger
   #(rnaseq) [jhuang@sage ~]$ which nextflow
   #/usr/local/bin/nextflow
   conda install -c bionconda fq
   mamba install -c bioconda ucsc-bedclip ucsc-bedgraphtobigwig
   mamba install -c bioconda rsem
   mamba install -c bioconda salmon
   mamba install -c conda-forge -c bioconda -c defaults -c r r-data.table r-gplots bioconductor-dupradar bioconductor-edger bioconductor-deseq2
   mamba install -c conda-forge openjdk=17
   conda install -c bioconda bedtools qualimap
   #under R
   install.packages("BiocManager")
   BiocManager::install("tximport")
   BiocManager::install("tximeta")        
   install.packages("optparse")            
   install.packages(“pheatmap”)
   (rnaseq2) [jhuang@sage Data_Soeren_RNA-seq_2023]$ nextflow run rnaseq/main.nf --input samplesheet.csv    --outdir results_GRCh38 --genome GRCh38   -profile test_full -resume --max_memory 300.GB --max_time 2400.h --save_reference --aligner star_salmon  --skip_deseq2_qc
   (rnaseq) nextflow run rnaseq/main.nf --input samplesheet.csv --outdir results_1585 --fasta 1585.fasta --gtf 1585_m_.gtf -profile test_full -resume --max_memory 200.GB --max_time 2400.h --save_reference --aligner star_salmon   --skip_rseqc --skip_dupradar --skip_preseq --skip_biotype_qc --skip_deseq2_qc --min_mapped_reads 0
   #--gtf_extra_attributes gene_name
   
   #-- version 1 --
   #conda env create -f ~/Tools/rnaseq/environment.yml
   conda create -n rnaseq -c conda-forge -c bioconda -c defaults python=3.6 fastqc trim-galore star=2.6.1d hisat2
   conda activate rnaseq
   conda install -c conda-forge -c bioconda -c defaults picard csvtk preseq rseqc samtools
   pip3 install deeptools
   pip3 install multiqc
   conda install -c bioconda stringtie subread gffread
   conda install -c conda-forge -c bioconda -c defaults -c r r-data.table r-gplots
   conda install -c conda-forge -c bioconda -c defaults -c r bioconductor-dupradar bioconductor-edger
   conda install nextflow=20.04
   

2. install chipseq

   conda create -n chipseq -c conda-forge -c bioconda -c defaults -c r python=3.9 fastqc cutadapt trim-galore bwa samtools 
   conda activate chipseq
   conda install picard bedtools phantompeakqualtools 
   conda install -c conda-forge -c bioconda -c defaults -c r r-base 
   #ERROR_SINCE_R_NGSPLOT_ONLY_FOR_PYTHON2 conda install -c conda-forge -c bioconda -c defaults -c r r-ngsplot
   sudo apt install macs
   conda install -c bioconda multiqc
   pip3 install deeptools
   conda install nextflow=20.04
   
   #conda env chipseq2 is still NOT working.
   conda create -n chipseq2 -c conda-forge -c bioconda -c defaults python=2.7 fastqc cutadapt trim-galore bwa samtools 
   conda activate chipseq2
   conda install -c conda-forge -c bioconda -c defaults picard bedtools phantompeakqualtools 
   conda install -c conda-forge -c bioconda -c defaults -c r deeptools r-base r-ngsplot macs multiqc
   conda install -c conda-forge -c bioconda -c defaults -c r r-ade4 r-assertthat r-base r-bh r-biocmanager r-bit r-bit64 r-bitops r-blob r-catools r-codetools r-crayon r-curl r-dbi r-digest r-domc r-foreach r-formatr r-futile.logger r-futile.options r-glue r-hms r-httr r-hwriter r-idr r-iterators r-jsonlite r-lambda.r r-lattice r-latticeextra r-lazyeval r-magrittr r-mass r-matrix r-matrixstats r-memoise r-mime r-openssl r-pkgconfig r-plogr r-prettyunits r-progress r-r6 r-rcolorbrewer r-rcpp r-rcurl r-rlang r-rsqlite r-segmented r-seqinr r-snow r-spp r-stringi r-stringr r-survival r-venndiagram r-xml
   conda install -c conda-forge -c bioconda -c defaults -c r bioconductor-annotationdbi bioconductor-annotationfilter bioconductor-biobase bioconductor-biocgenerics bioconductor-biocparallel bioconductor-biomart bioconductor-biostrings bioconductor-bsgenome bioconductor-chippeakanno bioconductor-delayedarray bioconductor-ensembldb bioconductor-genomeinfodb bioconductor-genomeinfodbdata bioconductor-genomicalignments bioconductor-genomicfeatures bioconductor-genomicranges bioconductor-go.db bioconductor-graph bioconductor-iranges bioconductor-limma bioconductor-multtest bioconductor-protgenerics bioconductor-rbgl bioconductor-regioner bioconductor-rsamtools bioconductor-rsubread bioconductor-rtracklayer bioconductor-s4vectors bioconductor-shortread bioconductor-summarizedexperiment bioconductor-xvector bioconductor-zlibbioc
   conda install nextflow=20.04
   
   #first_try
   (chipseq) nextflow run NGI-ChIPseq/main.nf --reads '/home/jhuang/DATA/Data_Denise_LT_DNA_Binding/enhancer_analysis/Raw_Data/*.fastq.gz' --genome hg38 --macsconfig macs.config --saveReference --saveAlignedIntermediates --singleEnd --blacklist_filtering -profile standard --project NHDF_enhancer_analysis_hg38 -resume
   #--notrim
   (chipseq) nextflow run NGI-ChIPseq/main.nf --reads '/home/jhuang/DATA/Data_Denise_LT_DNA_Binding/enhancer_analysis/Raw_Data/*.fastq.gz' --genome hg38 --macsconfig macs.config --saveAlignedIntermediates --notrim --saveTrimmed --singleEnd --blacklist_filtering -profile standard --project NHDF_enhancer_analysis_hg38 -resume
   #test
   (chipseq) nextflow run NGI-ChIPseq/main.nf --reads '/home/jhuang/DATA/Data_Denise_LT_DNA_Binding/Raw_Data/p783_*.fastq.gz' --genome hg38 --macsconfig macs.config --saveReference --saveAlignedIntermediates --singleEnd --blacklist_filtering -profile standard --project NHDF_enhancer_analysis_hg38 -resume
   

3. install spandx

   conda create --name spandx2 python=3.8
   conda activate spandx2
   conda install -c conda-forge -c bioconda -c defaults art trimmomatic bwa bedtools=2.28.0 seqtk pindel mosdepth samtools=1.9 picard gatk4 snpeff=4.3.1t nextflow=22 fasttree
   #[genbank copying]
   mkdir ~/miniconda3/envs/spandx2/share/snpeff-4.3.1t-5/data/WA_plasmid
   cp WA_plasmid.gb ~/miniconda3/envs/spandx2/share/snpeff-4.3.1t-5/data/WA_plasmid/genes.gbk
   vim ~/miniconda3/envs/spandx2/share/snpeff-4.3.1t-5/snpEff.config
   /home/jhuang/miniconda3/envs/spandx2/bin/snpEff build -genbank WA_plasmid      -d
   
   nextflow run spandx/main.nf --fastq "Raw_Data_RNAseq_K331A_d8_SPANDx/*.fastq.gz" --ref LT_wt.fasta --annotation --database LT_wildtype --pairing SE -resume
   (spandx2) nextflow run spandx/main.nf --fastq "raw_data/*_R{1,2}.fastq.gz" --ref WA_chr.fasta --annotation --database WA_chr -resume
   (spandx2) nextflow run spandx/main.nf --fastq "raw_data/*_R{1,2}.fastq.gz" --ref WA_plasmid.fasta --annotation --database WA_plasmid -resume
   #Note that the files in variants contain only SNPs, but the files in snippy contain SNPs+INDELs which can be used to consensus the results of SPANDx, resulting in the final results of SNPs+INDELs.
   ~/DATA/Data_Benjamin_Yersinia_SNP/variants_WA_chr$ vim snippy.core.vcf
   ~/DATA/Data_Benjamin_Yersinia_SNP/snippy_WA_chr/Wacton_S96/Wacton_S96.txt
   ~/DATA/Data_Benjamin_Yersinia_SNP/snippy_WA_chr/Wacton_S96/Wacton_S96.filt.vcf
   
   #FOLLOWING INSTALLATION CANNOT FINISH CALCULATION --> MAYBE IT NOW WORKS, BUT NEEDS TO GIVE AT LEAST SAMPLES, AS SAME AS IN SPANDX2
   conda create --name spandx python=3.8
   #conda install -c conda-forge -c bioconda -c defaults art trimmomatic bwa bedtools seqtk pindel mosdepth samtools picard gatk4 snpeff nextflow fasttree
   #-->picard-3.0.0-1, gatk4-4.4.0.0-0, snpeff-5.1-2, trimmomatic-0.39-2 installed!
   #DEBUG1: Due to using snpeff-5.1-2 by deleting the option '-t' in all 'snpEff eff -t ...' since '-t' is not a option in the new version.
   #DEBUG2: Don't login spandx after login base, since in the case the env uses /home/jhuang/anaconda3/bin/java.
   #  - /usr/bin/java: openjdk version "11.0.18" 2023-01-17
   #  - /home/jhuang/anaconda3/bin/java: openjdk version "1.8.0_152-release"
   #  - /home/jhuang/anaconda3/envs/spandx/bin/java: openjdk version "17.0.3-internal" 2022-04-19
   #DEBUG3: using '-' instead of '_'
   #  mv V_8_2_4_p600_d8_DonorI.fastq.gz    control-d8-DI.fastq.gz
   

4. install bengal3_ac3

   conda create -n bengal3_ac3 python=3.6
   conda activate bengal3_ac3
   conda install -c conda-forge -c bioconda -c defaults  prokka 
   conda install -c conda-forge -c bioconda -c defaults  shovill mlst 
   conda install -c conda-forge -c bioconda -c defaults  trimmomatic fastqc    
   conda install -c conda-forge -c bioconda -c defaults  roary
   conda install -c conda-forge -c bioconda -c defaults  snippy
   conda install -c conda-forge -c bioconda -c defaults  fasttree raxml-ng  
   conda install -c conda-forge -c bioconda -c defaults  gubbins snp-sites
   conda install -c conda-forge -c bioconda -c defaults openjdk=11
   TODO: snippy is still NOT working in hamm, we have to run the modul  "variants_calling" on hamburg.
   

5. install qiime1

   conda create -n qiime1 -c bioconda qiime
   

6. export environments

   #!/bin/bash
   
   # Get a list of conda environments
   env_list=$(conda env list | awk '{print $1}' | tail -n +4)
   
   # Iterate through each environment and export it to a YAML file
   for env in $env_list; do
       echo "conda activate $env"
       echo "conda env export > \"${env}_exported.yml\""
       echo "conda deactivate"
   done
   
   #conda create --name spandx2 --clone spandx
   #conda env remove --name spandx
   
   #conda activate spandx
   #conda env export > spandx.yml
   #rsync -a -P *.yml xxx@xxx:~/xxx/xxx
   #conda env create -f spandx.yml
   
   conda activate base
   conda env export > "base_exported.yml"
   conda deactivate
   conda activate HLCA_mapping_env
   conda env export > "HLCA_mapping_env_exported.yml"
   conda deactivate
   conda activate assembly2
   conda env export > "assembly2_exported.yml"
   conda deactivate
   conda activate bac3
   conda env export > "bac3_exported.yml"
   conda deactivate
   conda activate bactopia
   conda env export > "bactopia_exported.yml"
   conda deactivate
   

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