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

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