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 <[email protected]> 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 <[email protected]> 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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