Memory requirement? Picard missing tool dependencies

3.4 years ago by

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The minimum recommended memory for Galaxy is 8 GB, but most start with 16 GB and then scale up from there as needed. The requirements of the tool when used line-command will be about the same as when run when wrapped in Galaxy.

Install Picard from the Main Tool Shed with managed dependencies (the default).

Best, Jen, Galaxy team

ADD COMMENT • link written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks, but I searched in the tool shed and found three picard available, and all of them has the same missing tool dependencies problem after I installed them.

Another matter is that is it true that the galaxy won't be able take advantage of a multi-core system, and only able to scale by using multiple processes?

ADD REPLY • link written 3.4 years ago by Marc • 30

Hi Marc, often you can just install that particular dependency by clicking on the respective dependency that is listed by the installed tool, otherwise reinstalling or repairing often also helps. In addition, in the main toolshed, there seems to be one picard package, which is updated and maintained by the galaxy devteam, https://toolshed.g2.bx.psu.edu/repository?repository_id=c45d6c51a4fcfc6c.

For the multicore question read this: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Advanced_configuration and https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Using_a_compute_cluster . Basically, you should not have any problems utilizing all the compute power you have available.

ADD REPLY • link written 3.4 years ago by Jelle Scholtalbers • 360

Hi Jelle, thanks. By the way, do you know that if there is a problem in the gatk2 installation on local galaxy now? cause the installation just stuck at the status of cloning. And at the manage installed tool shed dependencies, the status is Unable to get information from the Tool Shed

ADD REPLY • link written 3.4 years ago by Marc • 30

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