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:
And current wrapper/binary versions in galaxy-dist/central are
With help for managing those dependencies here:
Hopefully this helps,
On 9/24/13 9:41 AM, Reiter, Larry T
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