How to run pipeline:
singularity run -H $HOME:/home/$USER --app [appname] --bind [directory_info] container_name.simg
Path to genome in container needs to be: '/genomes/test/Sequence/Bowtie2Index/genome' -or- '/genomes/spike/dm6/Sequence/Bowtie2Index/genome' -or- '/genomes/spike/sacCer3/Sequence/Bowtie2Index/genome' -or- '/genomes/STAR/[STAR index files]' -or- '/genomes/anno/[gtf or gff annotation file]'
For Baker Cluster Users: directory to mount for fly spike-in is: /gpfs0/home/gdlessnicklab/share/trails/genomes/Drosophila_melanogaster/UCSC directory to mount for yeast spike-in is: /gpfs0/home/gdlessnicklab/share/trails/genomes/Saccharomyces_cerevisiae/UCSC directory to mount for E. coli spike-in is: /gpfs0/home/gdlessnicklab/share/trails/genomes/Escherichia_coli_K_12_DH10B/NCBI directory to mount for hg19 is: /reference/homo_sapiens/hg19/ucsc_assembly/illumina_download/
The correct bind commands for test and spike are as follows: --bind /reference/homo_sapiens/hg19/ucsc_assembly/illumina_download/:/genomes/test --bind /gpfs0/home/gdlessnicklab/share/trails/genomes/Escherichia_coli_K_12_DH10B/NCBI:/genomes/spike
To run interactive terminal in container
singularity shell -H $HOME:/home/$USER --bind [directory_info] appalachian_hg19.simg
To run command from a program in the container
singularity exec -H $HOME:/home/$USER --bind [directory_info] appalachian_hg19.simg [command information]
##Be sure to bind your data, your genome, and any script files you may want to run
Apps: cutnrun_full : full pipeline from fastqc to mapped bam, bed, normalized bedgraph, and normalized bigwig with mapping qc using plotFingerprint from deeptools - bowtie2 alignment assumes 150 bp PE reads and allows dovetail and overlap in alignment cutntag : full pipeline from fastqc to mapped bam, bed, normalized bedgraph, and normalized bigwig with mapping qc using plotFingerprint from deeptools - bowtie2 alignment assumes 150 bp PE reads and allows dovetail and overlap in alignment cutnrun_hardtrim : full pipeline from fastqc to mapped bam, bed, normalized bedgraph, and normalized bigwig with mapping qc using plotFingerprint from deeptools - bowtie2 alignment. First step trims 150 bp reads from HiSeq to 60 bp. cutntag_hardtrim : full pipeline from fastqc to mapped bam, bed, normalized bedgraph, and normalized bigwig with mapping qc using plotFingerprint from deeptools - bowtie2 alignment. First step trims 150 bp reads from HiSeq to 60 bp. fastqc_pre : FastQC pre-trim trim_qc : Fastq trimming with Trim Galore and FastQC post trim bowtie2_alignment : Alignment for CUT&RUN samples; insert 10 bp-700 bp, assumes paired end 150 bp reads, makes bams/beds/bg/bw with no spike in. bams : Generate downstream files for starting at bams using same pipeline - assumes hg19 alignment mapqc_fingerprint : Use deeptools to assess enrichment quality
Data should be stored in a "project" directory with a sub-directory called "fastq". The "fastq" subdirectory should have all of your paired end fastq or fastq.gz files. Then the correct bind for data is: --bind /path_to/project/:/data