Hi Sachit,

Björn answer is correct. The issue is what is a "tool". There are what
Galaxy calls "tools". Some of which are installed by default and some
of which you can install from the toolshed. There are in many cases
just wrappers to third-party tools that need to be installed and
available in the environment PATH of the user running Galaxy. Examples
of these are TopHat, Bowtie and BWA. Björn mentions in some cases the
third-party tool is automatically installed, but this is new and most
third-party tools need to be installed manually still.

If you are using Debian, thanks to the "Debian Med Team", many tools
are already available in the repositories. Both TopHat and Bowtie are.
So apt-getting them should do for you. Just remember to configure the
.loc files in Galaxy with the location of the index files. This link
will be helpful:
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup

Hope this helps,
Carlos

On Mon, Oct 8, 2012 at 6:48 AM, Sachit Adhikari
<sachit.techner...@gmail.com> wrote:
> I don't think you understood my question very well. Tophat and Bowtie are
> available by default in Galaxy. Tophat and Bowtie however is not installed
> in my operating system. Will it still work in Galaxy?
>
>
> On Mon, Oct 8, 2012 at 3:22 PM, Björn Grüning
> <bjoern.gruen...@pharmazie.uni-freiburg.de> wrote:
>>
>> Hi Sachit,
>>
>> you need to install such tools by yourself, unless you are using some
>> new tools from the toolshed. For example the ncbi-tools or BWA from the
>> toolshed are capable of installing all dependency automatically.
>> In the future the plan is to move all heavy tools to the toolshed with
>> automatic dependency and version handling, afaik.
>>
>> Regards,
>> Bjoern
>>
>> > Hello. The tools like Tophat, Bowtie etc are pre-installed in Galaxy.
>> > Are those tools must be installed in order to work in Galaxy. For
>> > example: I am using Debian machine(Don't have tophat and bowtie
>> > installed). Will tophat and bowtie work in my local galaxy? Thanks
>> > ___________________________________________________________
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>> >
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>> >
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>> >
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>>
>>
>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>   http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>   http://lists.bx.psu.edu/

___________________________________________________________
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at usegalaxy.org.  Please keep all replies on the list by
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local Galaxy instances and the Galaxy source code, please
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