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
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
- 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
- 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
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
I hope someone on here can help me out.
Hope it helped a little bit,
Thanks a lot
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