/TimeLapse-docker

Primary LanguageShell

TimeLapse Docker

This is a dockerized version of TimeLapse pipeline. Work is still in progress.

Build

To build the image from scratch, install docker and clone the repository. Then run:

cd TimeLapse-docker
docker build --platform=linux/amd64 -t timelapse . --build-arg GIT_NAME={NET_ID} --build-arg GIT_PWD={NET_ID_PASSWORD}

Where {NET_ID} and {NET_ID_PASSWORD} are your credetials to log in into TimeLapse Git repository.

Run

To run the image, first endure that all .fastq files are in their separate directories named after the respecitve sample and they are all placed in ./fastq directory. In addition, required are: 1) genome sequence in .fasta file format, 2) genome annotation as .gtf file, 3) hisat-3n genome index files.

Image can be then run as docker run -it <parameters> -v ${PWD}:/data timelapse

Or from prebuit image from Docker Hub docker run -it <parameters> -v ${PWD}:/data machyna/timelapse

List of Parameters

    SAMPLES              - comma-separated list of all sample and control names
    CONTROLS             - comma-separated list of -s4U control name(s)
    PREFIX               - avoid typing repetitive part of sample names e.g. \"Sample_*\" (default: none)
    GENOME               - species [Hs, Mm, Dm]  (default: Mm)
    FORMAT               - reads format [PE, SE, NU]  (default: PE)
    READS                - reads strandness [FR, RF, F]  (default: RF)
    MUT_TRACKS           - Mutation type(s) to analyze [TC, GA, TC,GA] (default: TC)
    STL                  - experiment is STL (default: off)
    MUT_POS              - call mutations by absolute genomic location (default: TRUE)
    BIGWIG               - Make additional .bigWig track files (default: TRUE)
    CHR_TAG              - add chr prefix to chromosome names during alignment (default: FALSE)
    SPIKEIN_NAME         - common string identifying spikein names in .gtf file
    FASTA                - path to genome fasta file
    GTF                  - path to gtf genome annotation file
    INDEX                - path to aligner genome index (HISAT-3N)
    CPUS                 - number of cpus used by pipeline or Slurm jobs [int] (default: 10)
    MEM                  - memory used by Slurm jobs [intG](default: 20G)

e.g.

docker run -it -e SAMPLES=LC210501_1in,LC210501_2A \
               -e CONTROLS=LC210501_1in \
               -e SPECIES=Hs\
               -e CPUS=10 \
               -e MEM=20G \
               -e FORMAT=PE \
               -e MUT_TRACKS=TC \
               -e FASTA=genome/GRCh38_dm6_dm.fa \
               -e GTF=genome/GRCh38_dm6_dm.gtf \
               -e INDEX=genome/GRCh38_dm6_dm \
               -v ${PWD}:/data \
               timelapse