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(a)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(a)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_u...
>
> 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
>
>