petadimensionlab/docker_igv_batch repository overview

⁠Docker_IGV_batch

これはIGV（batchスクリプト作成用）のdockerイメージです / This is a docker image for IGV.(For batch script creation) また、samtoolsも使用できます / Can also samtools this docker　image.

⁠1.Usage

⁠docker pull image

docker pull petadimensionlab/docker_igv_batch

⁠docker run

docker run -it --name container_name -v /yourlocal_dir:/condir --rm petadimensionlab/docker_igv_batch

Copy your "bam file" , "bed file" and "sampleID list text" into the "/yourlocal_dir" .

example ""sampleID list text""data = https://github.com/petadimensionlab/Docker_IGV_batch/blob/master/SRR_Acc_List.txt⁠

⁠Run python into this docker

# python3 /tmp/igv_samtools_docker.py

• igv_samtools_docker.py = Samtools sorting and indexing

# python3 tmp/igv_batch_docker.py

• igv_batch_docker.py = Create an IGV batch scrip

All execution result is output to the "/yourlocal_dir".

⁠Running IGV with a batch file

can load a batch file by using " Tools > Run Batch Script ".

Manual page here = https://software.broadinstitute.org/software/igv/batch⁠

⁠exit docker

/ # exit