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cgenomics/haplotypo

By cgenomics

•Updated almost 7 years ago

Read mapping and variant calling on phased genomes without loosing phasing information

Image
0

977

cgenomics/haplotypo repository overview

⁠Haplotypo Docker

This Dockerfile builds the Docker image to work with the Haplotypo pipeline.

⁠Download the last image version

This is our recommended option.

docker pull cgenomics/haplotypo
⁠Testing the image
docker run -it cgenomics/haplotypo python /root/src/haplotypo/bin/haplotypo.py -h
⁠Testing the image with test data

Process the data inside the image - all data will be lost at the end

docker run -v `pwd`/output/:/root/src/haplotypo/shared/output:rw -it cgenomics/haplotypo python /root/src/haplotypo/bin/haplotypo.py -o /root/src/haplotypo/shared/output -amb 0 -hapA /root/src/haplotypo/dataset/A.chr6.fa -hapB /root/src/haplotypo/dataset/B.chr6.fa -idA A_AB -idB B_AB -f1 /root/src/haplotypo/dataset/AB.chr6.1.fq.gz -f2 /root/src/haplotypo/dataset/AB.chr6.2.fq.gz -caller GATK
⁠Testing the image with your own data

Replace {mydatasetfolder} and parameters with your dataset folder path. It will be created an output folder with the result files.

docker run -v /{mydatasetfolder}/:/root/src/haplotypo/dataset:rw -it cgenomics/haplotypo \
	python /root/src/haplotypo/bin/haplotypo.py \
	-o /root/src/haplotypo/dataset/output \
	-amb 0 \
	-hapA /root/src/haplotypo/dataset/{myfileA.fa} \
	-hapB /root/src/haplotypo/dataset/{myfileB.fa} \
	-idA A_AB \
	-idB B_AB \
	-f1 /root/src/haplotypo/dataset/{myfileAB.1.fq.gz} \
	-f2 /root/src/haplotypo/dataset/{myfileAB.2.fq.gz} \
	-caller GATK
⁠Running containers

Every time you run a Docker container, it uses the Haplotypo Docker image to remake it. When the container is closed, everything in it goes away! Also, for every one of those containers you need to name it with an alias.

docker run -dit --name=your-alias -v /your/haplotypo/location:/root/src/haplotypo/shared --rm cgenomics/haplotypo`" 0 0;;
⁠Interactive session in a Haplotypo container
docker run -it cgenomics/haplotypo

⁠Find Us

⁠Authors

Cinta Pegueroles; Veronica Mixao; Laia Carreté; Manu Molina; Toni Gabaldon, PhD

⁠License

This project is licensed under the MIT License - see the LICENSE.md⁠ file for details.

Tag summary

Content type

Image

Digest

Size

1.6 GB

Last updated

almost 7 years ago

docker pull cgenomics/haplotypo