tools version (eg: cufflinks) and bowtie indices file

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tools version (eg: cufflinks) and bowtie indices file

elchia
Hi there


1. Why is it that even after installing cufflinks 2.1.1 from the toolshed, it doesn't get reflected when I clicked on the tool from the side panel? It still shows 0.0.5 and 0.0.7. Think it's the same with others too (eg: bowtie)
2. I've modified the bowtie_indices.loc file under tool-data but the entries doesn't get reflected on the Map with Bowtie for Illumina (select a reference genome). I did the same for the bowtie2_indices.loc file and this one got reflected under Bowtie2.

Been a little frustrating. Can anyone please advise?

Many thanks.

Best regards
liz







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Re: tools version (eg: cufflinks) and bowtie indices file

Björn Grüning-3
Hi Elizabeth,

Am 09.11.2014 um 20:26 schrieb Elizabeth Chia:
> Hi there
>
> 1. Why is it that even after installing cufflinks 2.1.1 from the toolshed,
> it doesn't get reflected when I clicked on the tool from the side panel? It
> still shows 0.0.5 and 0.0.7. Think it's the same with others too (eg:
> bowtie)

The Galaxy tool versions do not correspond to the cufflinks program
version. I think 0.0.7 is the most recent version.

> 2. I've modified the bowtie_indices.loc file under tool-data but the
> entries doesn't get reflected on the Map with Bowtie for Illumina (select a
> reference genome). I did the same for the bowtie2_indices.loc file and this
> one got reflected under Bowtie2.

Have you installed data_managers?
Please have also a look at:
https://wiki.galaxyproject.org/Admin/DataIntegration

Hope this helps a little bit,
Bjoern

> Been a little frustrating. Can anyone please advise?
>
> Many thanks.
>
> Best regards
> liz
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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