How to install Bowtie?

[nkline]

Hi,

Our lab recently installed a local version of Galaxy on Mac OS X 10.8
and can access it at localhost:8080. Now we are trying to install
Bowtie version 1 but need help getting it to work. At this point we do
not see the tool listed on the left side of the Galaxy menu. Here are
the exact steps we followed:

1. create directory /Users/administrator/galaxy-dist/tools_dependencies
2. in universe_wsgi.ini set tool_dependency_dir = tools_dependencies
3. in /etc/paths append /Users/administrator/galaxy-dist/tools_dependencies
4. create tools_dependencies/bowtie/1.0.0/bin
5. create symbolic link tools_dependencies/bowtie/default to directory in step 4
6. download Bowtie, extract it, and copy binaries to
tools_dependencies/bowtie/1.0.0/bin

Problem: Bowtie is still not appearing in menu on the left side of Galaxy

Thanks!

[Heisman]

Do you have to "make" it for what you are doing? I just installed bowtie2 today for the first time (not using galaxy though). If you look in the MANUAL it may tell you what to do to actually install it after it is downloaded.

[GenoMax]

OP is not asking about compiling bowtie. The question is about how to make bowtie option appear in the galaxy web interface.

nkline: Have you bounced (restarted) the galaxy server after you made those changes? Changes such as these require a restart of galaxy server.

[nkline]

Thank you for the quick response.

nkline: Have you bounced (restarted) the galaxy server after you made those changes? Changes such as these require a restart of galaxy server.

Yes. We also rebooted the computer but still do not see the Bowtie tool listed in the Galaxy menu.

I have a feeling that we are missing a few additional steps. For example, the official Galaxy docs (under Managed Tool Dependencies) hint at using

<requirement type="package">

tags. However, the docs do not provide background on what a

requirement

tag is nor where it should be created.

There also appears to be some data setup involved for Bowtie, as described in this doc.

Since our lab consists of mostly Biologists, we are seeking step-by-step instructions on how to properly install Bowtie in a local version of Galaxy.

Thank you for your help

[rhinoceros]

Could be helpful:

http://seqanswers.com/forums/showthread.php?t=10315

http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

[GenoMax]

This may sound strange but do you not have "map with bowtie for illumina" available under the NGS:Mapping section?

[nkline]

This may sound strange but do you not have "map with bowtie for illumina" available under the NGS:Mapping section?

Even after restarting the Galaxy server, Bowtie is still not available. Bowtie2 is available by default but is not the tool we need.

Thanks for the suggestions. Any thoughts on the links I posted earlier?

[GenoMax]

Are you checking with the galaxy developers list in parallel ([email protected])?

We do not use the "tool dependancy" method so I am not sure how to answer your question.

[nkline]

Are you checking with the galaxy developers list in parallel ([email protected])?

That was actually the first place I posted my question thinking I would receive a quick, thorough answer. I posted over a week ago and, surprisingly, have not heard back from anyone yet.

We do not use the "tool dependancy" method so I am not sure how to answer your question.

That's understandable. I sincerely appreciate your effort though in trying to help us!

[GenoMax]

Did you replicate your galaxy from mercurial repository using standard directions? If yes then I am surprised that you do not have the "map with bowtie for illumina" option under the NGS:Mapping section.

[nkline]

Did you replicate your galaxy from mercurial repository using standard directions?

Yes, we followed the official Galaxy install process.

That doc also mentions:

Some tools do have outside dependencies that cannot be provided with Galaxy for various reasons. The list of these dependencies can be found on the Admin/Tools/Tool Dependencies page.

From there, we executed the instructions in my 1st post based on portions of this Galaxy doc.

[GenoMax]

Does your "tool_conf.xml" file have default options for NGS tools? What do the XML file paths look like?

Do you not have this option in your galaxy under NGS:Mapping?

[nkline]

I have attached two screen-shots that should address your questions about our Galaxy setup.

[GenoMax]

I was able to find bowtie wrappers and associated python scripts here: https://github.com/JCVI-Cloud/galaxy...ols/sr_mapping.

You can try to put these into "sr_mapping" directory and edit the tool_conf.xml file as well. Remember to reboot the galaxy server.

[nkline]

I think we are making progress now:

1. We downloaded the Bowtie wrappers available on the Galaxy Toolshed , specifically from this page

2. Next, we placed bowtie_wrapper.py and bowtie_wrapper.xml into tools/sr_mapping

3. We edited tool_conf.xml to add this line under <section name="NGS: Mapping" id="solexa_tools"> :

<tool file="sr_mapping/bowtie_wrapper.xml" />

4. Finally, we started the Galaxy server. Under NGS: Mapping, we now see an option for "Map with Bowtie for Illumina". Clicking on the Bowtie link displays its configuration page, as usual.

Questions:

1. We installed the latest version of Bowtie version 1.0.0 Should we be using the latest version of the wrappers too? If so, from where can we download them?

2. At the top of Bowtie's config page, "Map with Bowtie for Illumina (version 1.1.2)" is displayed (please see attachment). Does this mean Bowtie version 1.1.2 is being used?

3. It looks like the next step might be to read through these two articles to install reference genomes, indexes, etc. Does that seem correct?

http://wiki.galaxyproject.org/Admin/Data%20Integration

http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

Thank you