update: gmap_build

Status: Beta

Brought to you by: amcpherson

update: gmap_build

Forum: deFuse Help

Creator: Simon Potter

Created: 2013-12-16

Updated: 2014-06-28

Simon Potter - 2013-12-16

Newer releases of gmap now use gmap_build over gmap_setup -

http://research-pub.gene.com/gmap/

I've made changes to scripts/create_reference_dataset.pl (which appear to work), but I'd prefer not to do this. Is it possible to get an official update to the defuse source to reflect this change, or at least a patch?

Thanks,

Simon

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Andrew - 2014-01-23

I will try to do this as soon as possible.
Andrew

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Wayne - 2014-03-01

Hi Andrew,

I'm having the same issue with gmap_setup being replaced by gmap_build. Is there an update or patch for this yet?

Thanks!

Wayne

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Kipp - 2014-03-14

A quick workaround is to use an older version of gmap. gmap-2013-03-31 worked for me.

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Andrew - 2014-06-19

This should be fixed in the development branch on bitbucket:
https://bitbucket.org/dranew/defuse

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Andrew - 2014-06-28

i have added a 0.6.2 release that fixes this.

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