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zavolanlab / Dockerfiles

Dockerfile repository of the Zavolan Lab
Apache License 2.0
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Update picard version to 2.20.2 #26

Open mkatsanto opened 5 years ago

mkatsanto commented 5 years ago

The new version of picard is needed. There is a bug in the previous one when running MarkDuplicates with ASSUME_SORT_ORDER=queryname.

fgypas commented 5 years ago

I think that commit 951be46a22fd8ada9fb570348b7abae4d568af46 fixes the issue. Works with both docker and singularity.

Docker:

docker pull zavolab/picard:2.20.2
docker run -d -t zavolab/picard:2.20.2
docker ps # find container id
docker exec c6a9f1df4358 java -jar /usr/local/bin/picard.jar --help

Singularity:

singularity pull docker://zavolab/picard:2.20.2
singularity exec picard-2.20.2.simg java -jar /usr/local/bin/picard.jar --help

@mkatsanto Can you please try the MarkDuplicates with ASSUME_SORT_ORDER=queryname and let me know if it works as expected?