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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