Re: [galaxy-user] Need your helps about Galaxy

PATH=/mnt/galaxyTools/tools/macs/1.3.7.1/bin:$PATH PYTHONPATH=/mnt/galaxyTools/tools/macs/

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&gt; 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 > >