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gkno / gkno_launcher

The gkno launcher for executing tools or pipelines
MIT License
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tangram pipeline failed #37

Open kspham opened 9 years ago

kspham commented 9 years ago

It seems that the pipeline configuration of tangram is not correct?

./gkno pipe fastq-tangram -r resources/homo_sapiens/current/human_reference_v37_decoys.fa -mr resources/homo_sapiens/current/mobile_element_sequences.fa -q /raid/sonpham/pairs/originalbam/fastq/pe/LID115260_MERGE1_1.fastq -q2 /raid/sonpham/pairs/originalbam/fastq/pe/LID115260_MERGE1_2.fastq -srh 50 -sr moblist -rg chr1

Output:

ERROR: Invalid attribute in pipeline configuration file: help group

DETAILS: The configuration file for pipeline 'fastq-tangram' contains the general attribute 'help group'. This is an unrecognised attribute which is not permitted. The general attributes allowed in a pipeline configuration file are:

     categories:    <type 'list'>, required = True
     description:   <type 'str'>, required = True
     developmental: <type 'bool'>, required = False
     hide in help:  <type 'bool'>, required = False
     nodes: <type 'list'>, required = True
     parameter sets:    <type 'list'>, required = True
     tasks: <type 'dict'>, required = True

     Please remove or correct the invalid attribute in the configuration file.

TERMINATED: Errors in configurationClass. See specific error messages above for resolution.

kspham commented 9 years ago

here is the used version of gkno

University of Utah gkno package

version: 1.61.0 date: January 2015

git commit: 640386124c025095c87140376ff907e4f8850f82

AlistairNWard commented 9 years ago

Hi Son,

This is indeed an error in the configuration file. I am working on a new release of gkno that will hopefully be out next week. This should make life simpler and I will make sure that this pipeline is working in the new release. I will announce the new release via our Twitter feed (@gknoProject). Please bug me if you don't see the release.

Al

On Thu, Feb 19, 2015 at 3:58 PM, Son Pham notifications@github.com wrote:

here is the used version of gkno

University of Utah gkno package

version: 1.61.0 date: January 2015 git commit: 6403861 https://github.com/gkno/gkno_launcher/commit/640386124c025095c87140376ff907e4f8850f82

— Reply to this email directly or view it on GitHub https://github.com/gkno/gkno_launcher/issues/37#issuecomment-75134531.

kspham commented 9 years ago

Thank you, Alistair!