Nope, it still isn't working. I deleted tophat2, package_tophat2 and 
package_samtools and then reinstalled tophat2 from Galaxy main. Here are what I 
think are the relevant installed packages:

tophat2
package_tophat2_2_0_9
package_samtools_0_1_18

Any other advice would be appreciated.

> On Feb 23, 2015, at 8:23 AM, Saket Choudhary <sake...@gmail.com> wrote:
> 
> On 22 February 2015 at 23:17, Michael Thon <mike.t...@gmail.com> wrote:
>> bam_index_build2() not yet
> 
> Hi Michael,
> 
> This seems to be related to this:
> https://github.com/samtools/samtools/issues/199
> 
> You should probably switch to samtools 0.1.19
> 
> Saket

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