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.gruening@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. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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