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 <leiyan2...@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 <j...@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_uninstalling_tool_shed_repositories_within_a_Galaxy_instance
>>
>> 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
>>
>>
>
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