Using Annovar in a Workflow

Question: Using Annovar in a Workflow

2.7 years ago by

France

Hello everyone,

I would like to use Annovar (developed by the devteam) in a workflow. To do so I need to specify several databases in the Annotation Databases field. Unfortunately I can't manage to find how to do it properly.

DBname1-DBname2
DBname1,DBname2
DBname1\nDBname2
many other attempt

All this things do not work since the wrapper is looking for hg19_DBname1-DBname2.txt and so on.

I think that the problem comes from the fact that the Annotation Databases selection is done through an interactif field.

I hope someone know how to select several databases, that would be really useful.

Thank you,

Christ

workflow annovar database • 1.6k views

ADD COMMENT • link •

modified 2.7 years ago by aysam.guerler ♦ 90 • written 2.7 years ago by christophe.habib • 340

Hi Jen,

I saw your reply on my email but I can't see it here anymore. Just to answer you, the wrapper does support multi-DB selection. The issue here is that it doesn't work when you include the tool in a workflow where you want to select 2 or 3 DB for annotation.

I hope someone found how to properly specify the DBs in the workflow..

Best regards,

Christ

ADD REPLY • link written 2.7 years ago by christophe.habib • 340

2.7 years ago by

aysam.guerler ♦ 90

United States

aysam.guerler ♦ 90 wrote:

Hi Christ,

Thanks for reporting this. Have you tried to separate the database by new lines like shown here: http://imgur.com/Ubtbp79.

ADD COMMENT • link modified 2.7 years ago • written 2.7 years ago by aysam.guerler ♦ 90

Yes I did, that is what I meant when I wrote DBname1 \n DBname2 ;) Here is an example of the log with exac03 and cosmic70 :

Log: tool progress
Error: the required database file /DATAS/user/galaxy/tool-data/annovarDB/hg19/hg19_exac03__cn__cosmic70.txt does not exist.
cp: impossible d'évaluer « output.hg19_multianno.vcf »: Aucun fichier ou dossier de ce type

As you see, he is looking for a file with both names instead of 2 files with the differents names.

ADD REPLY • link written 2.7 years ago by christophe.habib • 340

I confirm that is what I did in the Annotation Databases field.

ADD REPLY • link modified 2.7 years ago • written 2.7 years ago by christophe.habib • 340

when I clic on run this job again I can read this :

"An invalid option was selected for filters, 'exac03\ncosmic70', please verify."

ADD REPLY • link written 2.7 years ago by christophe.habib • 340

Can you please post the version you are using? I could not find 08b003ee9db7

ADD REPLY • link written 2.7 years ago by aysam.guerler ♦ 90

It is the revision number I have in my toolshed repository. Here is the header of the wrapper.

<tool id="table_annovar" name="ANNOVAR Annotate VCF" version="0.2">

And when I try to get update It says that it is the current version.

ADD REPLY • link modified 2.7 years ago • written 2.7 years ago by christophe.habib • 340

Thanks, and which Galaxy version you are using?

ADD REPLY • link modified 2.7 years ago • written 2.7 years ago by aysam.guerler ♦ 90

Sorry for taking this long to answer. I was on 15.01. But the issue is kind of "solved". When you observe it you need to delete the box in the workflow interface and to create it again. But this bug is not reproducible : I didn't find any clue about "when" this bug occurs on a given workflow, "why" this bug was still here when the workflow was shared and "why" delete/recreate the box solved the problem. I upgraded Galaxy to 16.01, if I observe this bug again I will let you know ! Thanks !

ADD REPLY • link written 2.6 years ago by christophe.habib • 340

Similar posts • Search »