Hi all,
I think I have fixed this bug, and Galaxy GUI can execute MACS successfully on my cloud Galaxy. I did the following changes to fix it:
- It looks like the latest version of cloud Galaxy uses MACS 1.3, so I changed the default:
default -> /mnt/galaxy/tools/macs/1.3.7.1/
- There are two path mistakes in the MACS environment variable file (/mnt/galaxy/tools/macs/1.3.7.1/env.sh), and "galaxyTools" should be "galaxy":
< PATH=/mnt/galaxy/tools/macs/1.3.7.1/bin:$PATH < PYTHONPATH=/mnt/galaxy/tools/macs/ 1.3.7.1/lib/python2.6/site-packages:$PYTHONPATH
PATH=/mnt/galaxyTools/tools/macs/1.3.7.1/bin:$PATH PYTHONPATH=/mnt/galaxyTools/tools/macs/
1.3.7.1/lib/python2.6/site-packages:$PYTHONPATH
Maybe this can help somebody.
Lei Yan Center for Integrative and Translational Genomics UTHSC
On Tue, Sep 24, 2013 at 2:55 PM, Lei Yan leiyan2000@gmail.com wrote:
Hi all,
http://galaxyclass.genenetwork.org/ This cloud Galaxy was built by Cloud Galaxy Launch ( https://main.g2.bx.psu.edu/cloudlaunch) yesterday. I found two problems about MACS on it:
- When I execute MACS on Galaxy GUI, I got a “not found” error. Please
see attachment (error1.png).
- If I login the Galaxy server by ssh, I found it looks like MACS was
already installed on it, please see attachment (error2.png). But if I run MACS in a terminal, I got another error. Please see attachment (error3.png).
Anybody has any idea for this? Thanks a lot.
Lei Yan Center for Integrative and Translational Genomics UTHSC
On Tue, Sep 24, 2013 at 2:24 PM, Jennifer Jackson jen@bx.psu.edu wrote:
Hi Lawrence,
What version of MACS are you running? The Galaxy wrapper in galaxy-dist supports v1.3. I am 99% certain that the latest Cloudman image is the same, but Dannon can correct me. The two Tool Shed repos for MACS support v1.4 and v2.0.10. Making sure that the wrapper & binary are a match might be the first place to check - these can get easily confused, especially when binaries install with un-versioned symbolic links by default.
If you are re-running a workflow/job that came from the public Main server, and running galaxy-dist/central, then you want to use the v1.3 binary, unless purposefully upgrading both wrapper & binary. The workflow reproducibility tracking will alert you about a change in tool versions and permit you to select updated tools upon execution (once tool is configured) if from the *same exact wrapper/tool*, but not if a *different wrapper/tool/repo* - so will likely take a workflow edit to change out the tool in this case if upgrading to newer MACS version.
I noticed that the tool form README link for the MACS v2.0.10 wrapper is incorrect, copy link & add an ".rst" to find doc. Fairly certain these are expected to be ".txt" - I'll ask our team if this is a Tool Shed or repo input issue if extension different.
Full help for installing tools from the Tool Shed is here:
http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_unin...
And current wrapper/binary versions in galaxy-dist/central are listed here: http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies With help for managing those dependencies here: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
Hopefully this helps,
Jen Galaxy team
On 9/24/13 9:41 AM, Reiter, Larry T wrote:
Thanks, James. I worked it out by downloading my data files and workflow. For some reason MACS still doesn't work. Any ideas?
Lawrence T Reiter, PhD UTHSC, Memphis, TN
-- Jennifer Hillman-Jacksonhttp://galaxyproject.org