GALAXY local setup - bowtie

[stoker]

Dear all,
I have working local galaxy-dist on my machine and I would like to attach bowtie and tophat to it. The reference indexes setup is ok already, i can select between them in bowtie menu. However, when i execute the bowtie it says:

An error occurred running this job: Error aligning sequence. /bin/sh: bowtie: command not found

I guess still my galaxy is not connected with bowtie properly.
Any ideas how could I update galaxy with proper paths to have it working?

[benjamin.rodriguez]

Same error

I'm having the same error... It would be great if someone could help in this.

[stoker]

Solved,
Enter the /bin directory, and create there a soft link to bowtie (Bowtie will become a system command)
You can make it with ln -s /your/path/to/bowtie/bowtie bowtie

[tujchl]

you can try to put all bowtie excutive file into system bin folder, and error could be solved

[jgoecks]

Hi all,

Galaxy does not include Bowtie in its distribution. You'll need to download and install Bowtie in order to run it using Galaxy. More information about installing Bowtie for Galaxy can be found here:

https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup

Also, questions about local Galaxy installs are best sent to the galaxy-dev mailing list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

Galaxy developers and others who run local installations participate on the list.

Best,
J.
Galaxy Team

[lvcosme]

oh permissions

I am trying to set it up, but I keep getting this error message:
ln: creating symbolic link `bowtie': Permission denied

I changed the permission of bowtie folders and files but keep getting same problem. I looked up on linux forums about symbolic permissions but could not find and answer. Did anyone have same problem?
Thank you.
Luciano

[stoker]

You need to login as root (su command).

[ihara920]

Dear all,
I also have local galaxy installed on my machine and I would like to run bowtie-tophat-cufflinks work flow. At the first step of running bowtie, I am wondering how to add my own reference genome sequences to the selction menu. Where is a proper directory?
Thank you in advance.

Kunio

[jgoecks]

All,

You'll need to put Bowtie--and other tools that you want to use--in your user's path. Something like:

% bash
% export PATH=$PATH:/path/to/bowtie/

should do the trick on most systems. That said, you'll probably want to set up and run Galaxy under a dedicated user.

We encourage all users setting up a local instance to direct their questions to the galaxy-dev mailing list and/or search the archive for answers:

http://wiki.g2.bx.psu.edu/Support

http://wiki.g2.bx.psu.edu/Admin

Good luck,
J.

[ihara920]

Thank for your reply, J!

All progarm is completely set up as galaxy which is dedicated user.
And test run is successful, but I do not understand how to add my own reference genome. As your instruction, I will ask my question to the galaxy-dev mailing list.

Many thanks!

Kunio

[jgoecks]

Kunio,

Here are instructions for setting up indices for NGS tools:

http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup

Good luck,
J.