picard 1.126 is missing R dependency

Question: picard 1.126 is missing R dependency

3.0 years ago by

Elena • 30

United Kingdom

Elena • 30 wrote:

Hello,

I was asked to set up a local instance of Galaxy which should use same software versions as Galaxy Main.

However, picard tool 1.126.0 does not have R as a dependence in toolshed. Later version 1.136.0 does and R 3.1.2 is installed as part of picard tool.

When running CollectInsertSizeMetrics under 1.126.0 local jobs fail with:

"Caused by: java.io.IOException: Cannot run program "Rscript": error=2, No such file or directory"

Same job runs fine if I switch to 1.136.0.

Could you please give me instructions how to help picard 1.126.0 find R executable?

Thank you

Elena

tool_dependency galaxy picard • 1.0k views

ADD COMMENT • link •

modified 3.0 years ago by Martin Čech ♦♦ 4.9k • written 3.0 years ago by Elena • 30

3.0 years ago by

Martin Čech ♦♦ 4.9k

United States

Martin Čech ♦♦ 4.9k wrote:

Unless you are trying to reproduce an analysis done on Picard 1.126 I would just install and use the latest (1.136). Main Galaxy will soon have it installed too.

If I understand this correctly the CollectInsertSizeMetrics tool would have never worked in 1.126 with basic installation from the TS. If you really want to run it under that version you probably need to provide the R executables in the PATH where the job is run.

ADD COMMENT • link modified 3.0 years ago • written 3.0 years ago by Martin Čech ♦♦ 4.9k

Hi Martin

Like Elena I also was running CollectInsertSizeMetrics successfully until a few days ago when I updated a few packages. I would like to getting working agin but do not really understand your instructions, could you expand on them a little. Thanks Guy

ADD REPLY • link written 3.0 years ago by Guy Reeves • 1.0k

Thank you for advise, it was solved by adding R in PATH and LIB env. variables.

Picard 1.136 has other problems further in pipeline - in AddOrReplaceReadGroup, so v1.126 is preferable because it auto-fills required parameters.

ADD REPLY • link written 3.0 years ago by Elena • 30

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