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HumanCellAtlas / skylab

Soon to be deprecated in favor of broadinstitute/warp github repo. Previously: Secondary analysis pipelines
BSD 3-Clause "New" or "Revised" License
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Can't access /usr/picard/picard.jar when using singularity #286

Closed evan-wehi closed 4 years ago

evan-wehi commented 4 years ago

Optimus.wdl fails with the following error:

[First 300 bytes]:Error: Unable to access jarfile /usr/picard/picard.jar

when running this task: https://github.com/HumanCellAtlas/skylab/blob/master/library/tasks/FastqToUBam.wdl

The reason seems to be that, in the docker image, the file is only readable by root:

$ ls -l /usr/picard/picard.jar 
-rw------- 1 root root 11815043 Aug 17  2017 /usr/picard/picard.jar

Because I'm running in a multitenanted HPC environment, I'm using singularity and so I run as a regular user and can't access this file.

It is possible to fix the image so that this file is readable by all users?

kbergin commented 4 years ago

I have transferred this issue to our new repository (in progress of being set up). We've heard this issue again recently, and have filed a ticket in our backlog to address.

Thanks