Picard AddOrReplaceReadGroups fails when Auto-assign is used

[jennaj]

Tool version:

Development repository: https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard
Link to this repository: https://toolshed.g2.bx.psu.edu/view/devteam/picard/00fe2ff64467

Issue:

Auto-assign does not have a default value for the tag PU. This causes the tool to fail.

Solution:

Place a default value for the option Platform unit (PU) on the tool form. Meta tag is RUPG, the second value for the option on tool form.

RGPU=String
PU=String Read Group platform unit (eg. run barcode) Required.

Impact:

All usage, including that at http://usegalaxy.org. Note that a current Coursera class/workflow uses the Auto-assign option and it is confusing students/tool users.

Work-around until fix:

Add in any single word (no spaces) alphanumeric value into the tool form for RU (PU=String). Example "Test" works. Or, add a specific value when it is known.

Error when bug icon is clicked on:

Dataset generation errors
Dataset 12: AddOrReplaceReadGroups on data 7: BAM with replaced/modified readgroups

Tool execution generated the following error message:
Fatal error: Exit code 1 ()
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch -Xmx7680m -Xms256m
ERROR: Option 'RGPU' is required.

USAGE: AddOrReplaceReadGroups [options]

Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#AddOrReplaceReadGroups

Replaces all read groups in the INPUT file with a single new read group and assigns all reads to this read group in the OUTPUT BAM
Version: 1.136(f187319bf8bbde56892d5b5a1ce3fc0529b71a49_1436805856)

Options:

--help
-h Displays options specific to this tool.

--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.

--version Displays program version.

INPUT=String
I=String Input file (bam or sam or a GA4GH url). Required.

OUTPUT=File
O=File Output file (bam or sam). Required.

SORT_ORDER=SortOrder
SO=SortOrder Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT.
Default value: null. Possible values: {unsorted, queryname, coordinate, duplicate}

RGID=String
ID=String Read Group ID Default value: 1. This option can be set to 'null' to clear the default
value.

RGLB=String
LB=String Read Group Library Required.

RGPL=String
PL=String Read Group platform (e.g. illumina, solid) Required.

RGPU=String
PU=String Read Group platform unit (eg. run barcode) Required.

RGSM=String
SM=String Read Group sample name Required.

RGCN=String
CN=String Read Group sequencing center name Default value: null.

RGDS=String
DS=String Read Group description Default value: null.

RGDT=Iso8601Date
DT=Iso8601Date Read Group run date Default value: null.

RGPI=Integer
PI=Integer Read Group predicted insert size Default value: null.

RGPG=String
PG=String Read Group program group Default value: null.

RGPM=String
PM=String Read Group platform model Default value: null.

Possibly introduced with this tool change ??:

#92

cc @galaxyproject/guac

[jennaj]

Closing as a duplicate is now under tools-iuc galaxyproject/tools-iuc#1736

[jennaj]

Status: galaxyproject/tools-iuc#1736 (comment)