Hi Bjoern,
Please find the bowtie2 and bowtie .loc files. In the paster.log file I see 
these entries for bowtie

galaxy.tools.data DEBUG 2014-03-04 10:14:11,048 Loaded tool data table 
'bowtie_indexes'
galaxy.tools.data DEBUG 2014-03-04 10:14:11,051 Loading another instance of 
data table 'bowtie_indexes', attempting to merge content.
galaxy.tools.parameters.dynamic_options WARNING 2014-03-04 10:14:33,335 Data 
table named 'bowtie2_indexes' is required by tool but not configured

And ls -l /global/referenceData/databases/bowtie2/hg19 is 
drwxr-xr-x 2 ralla cgrl      2048 Sep 10 11:14 .
drwxr-xr-x 3 ralla cgrl      2048 Sep 10 11:06 ..
-rw-rw-r-- 1 ralla cgrl 960018873 May  2  2012 hg19.1.bt2
-rw-rw-r-- 1 ralla cgrl 716863572 May  2  2012 hg19.2.bt2
-rw-rw-r-- 1 ralla cgrl      3833 May  2  2012 hg19.3.bt2
-rw-rw-r-- 1 ralla cgrl 716863565 May  2  2012 hg19.4.bt2
-rw-rw-r-- 1 ralla cgrl 960018873 May  2  2012 hg19.rev.1.bt2
-rw-rw-r-- 1 ralla cgrl 716863572 May  2  2012 hg19.rev.2.bt2

and ls -l /global/referenceData/databases/bowtie/hg19 is
drwxr-xr-x 2 ralla cgrl      2048 Mar  4 10:07 .
drwxr-xr-x 3 ralla cgrl      2048 Nov 30  2012 ..
-rw-rw-r-- 1 ralla cgrl 821725563 Nov 13  2009 hg19.1.ebwt
-rw-rw-r-- 1 ralla cgrl 357667968 Nov 13  2009 hg19.2.ebwt
-rw-rw-r-- 1 ralla cgrl      3284 Nov 13  2009 hg19.3.ebwt
-rw-rw-r-- 1 ralla cgrl 715335926 Nov 13  2009 hg19.4.ebwt
lrwxrwxrwx 1 ralla cgrl        45 Aug 21  2013 hg19.fa -> 
/global/referenceData/genomes/hs/hg19/hg19.fa
-rw-rw-r-- 1 ralla cgrl 821725563 Nov 13  2009 hg19.rev.1.ebwt
-rw-rw-r-- 1 ralla cgrl 357667968 Nov 13  2009 hg19.rev.2.ebwt

Thanks for looking into this.
Ravi.
On Mar 4, 2014, at 9:13 AM, Björn Grüning <bjoern.gruen...@gmail.com> wrote:

> Hi Ravi,
> 
> can you attach the loc file, do you see anything in the Galaxy log files 
> about bowtie2, try grepping for "bowtie2".
> 
> Cheers,
> Bjoern
> 
> Am 04.03.2014 18:07, schrieb Ravi Alla:
>> Hi Bjoern,
>> Thank you for your clarifications. I have tried installing bowtie2 using 
>> both variations, once with both wrapper and dependencies and once with only 
>> wrapper (since I have dependencies installed on the system). In either case 
>> even after editing the .loc file I cannot see the indices in galaxy. I tried 
>> the same edits to .loc file with bwa and the indices show right up, but not 
>> with bowtie2 and even bowtie for that matter. I really don't know what to do 
>> about this.
>> Thanks
>> Ravi
>> On Mar 4, 2014, at 3:06 AM, Björn Grüning <bjoern.gruen...@gmail.com> wrote:
>> 
>>> Hi Ravi,
>>> 
>>>> Hi guys,
>>>> I am new to galaxy and am in the process of setting it up on a cluster 
>>>> with some help. I am trying to install bowtie2 to my local galaxy through 
>>>> the toolshed. I have a few questions.
>>>> 
>>>> - Which bowtie2 should I install? When I search for bowtie2 a bunch of 
>>>> results come up?
>>> 
>>> Only two, or? Please make sure you are using the main toolshed. bowtie2 and 
>>> package_bowtie2_2_1_0 are connected together. One is the binary and the 
>>> other contains the wrapper. Use devteam respositories is always a good 
>>> choice.
>>> 
>>>> - What are repository dependencies? Why would I need these if bowtie2 is 
>>>> already installed on my system?
>>> 
>>> repository dependecies containing all dependencies of your wrappers, that 
>>> can be some binaries, but also R, Perl, python libraries that are needed to 
>>> execute your wrappers. We recommend you to use the dependencies because 
>>> then you have full control over all your used versions (wrapper, 
>>> dependencies, tool) and that enables reproducibility. To put in other 
>>> words: With the toolshed you can have different tool and wrappers versions 
>>> with different dependencies at the same time.
>>> 
>>>> - I have been installing bowtie2 by unchecking the repository dependencies 
>>>> and tool dependencies boxes. Is this correct?
>>> 
>>> It will work, if you have a system installed version. But you need to take 
>>> care about binary updates by your own. And reproducibility of your results 
>>> is not guaranteed.
>>> 
>>>> - Finally when I install bowtie2 this way it creates 2 bowtie2_indices.loc 
>>>> files, one in galaxy/tool-data and the other in 
>>>> shed_tools/toolshed.g2.gx.psu.edu/dev/bowtie2, which one do I need to edit 
>>>> to point to my index files? No matter which one I change I can't seem to 
>>>> see the indices.
>>> 
>>> That is strange. Are you sure you don't have a spelling mistake in it. It 
>>> should be the bowtie2_indices.los I think. I will CC Greg, he is one of the 
>>> Tool Shed Developers and should know more about it.
>>> Please do not forget to restart your Galaxy instance once you have update 
>>> the *loc files.
>>> 
>>>> I hope someone on here can help me out.
>>> 
>>> Hope it helped a little bit,
>>> Bjoern
>>> 
>>>> Thanks a lot
>>>> Ravi.
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