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Update picard version to 2.20.2 #26

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mkatsanto opened this issue Jul 2, 2019 · 1 comment
Open

Update picard version to 2.20.2 #26

mkatsanto opened this issue Jul 2, 2019 · 1 comment
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@mkatsanto
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The new version of picard is needed. There is a bug in the previous one when running MarkDuplicates with ASSUME_SORT_ORDER=queryname.

@fgypas fgypas added bug Something isn't working enhancement New feature or request labels Jul 2, 2019
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fgypas commented Jul 2, 2019

I think that commit 951be46 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?

@fgypas fgypas mentioned this issue Jul 2, 2019
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