"Variant Annotator" reference genome
Hello, The Galaxy "Variant Annotator" tool uses this loc file : tool-data/gatk2_picard_indexes.loc This file is available in tool-data/ directory and completed but the dropdown menu of "Variant Annotator" tool is empty. more gatk2_picard_indexes.loc #This is a sample file distributed with Galaxy... oviAri1 oviAri1 Ovis:oviAri1 /bank/Galaxy/oviAri1/current/flat/picard_index/oviAri1.dict ls /bank/Galaxy/oviAri1/current/flat/picard_index/ oviAri1.dict oviAri1.fa oviAri1.fa.fai Could you please tell me where does my mistake ? Kind regards, Sarah Maman -- Sarah Maman INRA - LGC - SIGENAE Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53
Hello Sarah, Check if you not use some spaces instead of tab characters in your .loc to divise your fields. Gildas Le 10/07/2015 10:16, Sarah Maman a écrit :
Hello,
The Galaxy "Variant Annotator" tool uses this loc file : tool-data/gatk2_picard_indexes.loc
This file is available in tool-data/ directory and completed but the dropdown menu of "Variant Annotator" tool is empty.
more gatk2_picard_indexes.loc #This is a sample file distributed with Galaxy... oviAri1 oviAri1 Ovis:oviAri1 /bank/Galaxy/oviAri1/current/flat/picard_index/oviAri1.dict
ls /bank/Galaxy/oviAri1/current/flat/picard_index/ oviAri1.dict oviAri1.fa oviAri1.fa.fai
Could you please tell me where does my mistake ?
Kind regards, Sarah Maman
Hello again, My bad ! You need this : oviAri1 oviAri1 Ovis:oviAri1 /bank/Galaxy/oviAri1/current/flat/picard_index/oviAri1.fa A plus :) Gildas Le 10/07/2015 10:16, Sarah Maman a écrit :
Hello,
The Galaxy "Variant Annotator" tool uses this loc file : tool-data/gatk2_picard_indexes.loc
This file is available in tool-data/ directory and completed but the dropdown menu of "Variant Annotator" tool is empty.
more gatk2_picard_indexes.loc #This is a sample file distributed with Galaxy... oviAri1 oviAri1 Ovis:oviAri1 /bank/Galaxy/oviAri1/current/flat/picard_index/oviAri1.dict
ls /bank/Galaxy/oviAri1/current/flat/picard_index/ oviAri1.dict oviAri1.fa oviAri1.fa.fai
Could you please tell me where does my mistake ?
Kind regards, Sarah Maman
participants (2)
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Gildas Le Corguille -
Sarah Maman