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-Jackson
http://galaxyproject.org
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