Hi, I am upgrading to the newest version of dysgu and I have the following error w

Yes of course. There is an example shown on dockerhub page: <a href="https://hub.docke

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Error - pip3 dysgu installation about dysgu HOT 5 CLOSED

kcleal commented on May 20, 2024

Error - pip3 dysgu installation

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Comments (5)

kcleal commented on May 20, 2024 1

Yes of course. There is an example shown on dockerhub page: https://hub.docker.com/repository/docker/kcleal/dysgu/

An example workflow using docker:

# Make an 'input_folder', put your bam file and reference genome inside:

.
├── input_folder
│    ├──sample.bam
│    ├── reference.fasta
│    └── reference.fasta.fai
└── ...

# Make an 'output_folder':

mkdir output_folder

# Set up docker:

docker pull kcleal/dysgu
docker run -it \
     --mount src="${PWD}"/input_folder,target=/input_folder,type=bind \
     --mount src="${PWD}"/output_folder,target=/output_folder,type=bind \
     kcleal/dysgu
cd input_folder

# Run dysgu:

dysgu run reference.fasta wd sample.bam > ../output_folder/sample.vcf

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kcleal commented on May 20, 2024

Hi @KristinaGagalova,
As you say, it looks like the gcc-5 command is not working. Its possible your system has an older version of gcc that is functional, this may help https://askubuntu.com/questions/26498/how-to-choose-the-default-gcc-and-g-version
If you have docker installed that might also work.

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