Are you executing `sudo` as the galaxy user, or as the ubuntu user?  The
galaxy user is not a sudoer, and you shouldn't need to use sudo for
anything you want to do as the galaxy user.  The only use in this
particular case for using `sudo` as root is to switch *to* the galaxy user.

-Dannon

On Wed, Feb 27, 2013 at 6:34 PM, Sun, Wenping [USA] <sun_wenp...@bah.com>wrote:

> Hello,
> When I sudo galaxy user at ssh terminal, the password prompted for galaxy.
> What is it?
> Thanks,
> Kathryn
>
> -----Original Message-----
> From: Dannon Baker [mailto:dannonba...@me.com]
> Sent: Friday, January 11, 2013 12:12 PM
> To: Jennifer Jackson
> Cc: Galaxy Dev; Sun, Wenping [USA]
> Subject: [External] Re: macs error for chipseq data
>
> There's an issue with the MACS installation on the current cloud tools
> volume (which will be fixed with the next volume update coming soon).
>
> For existing instances, you can get MACS working correctly by executing
> the following two commands (which change the default version of macs used)
> after ssh'ing in to your instance:
>
> sudo su galaxy
> ln -sfn /mnt/galaxyTools/tools/macs/1.3.7.1/mnt/galaxyTools/tools/macs/default
>
> And that's it, no need to restart galaxy or anything.
>
> -Dannon
>
> On Jan 11, 2013, at 10:59 AM, Jennifer Jackson <j...@bx.psu.edu> wrote:
>
> > Hi Kathryn,
> >
> > I am going to post this back to the galaxy-dev list and cc Dannon so
> that he or or one of the developers more experienced with troubleshooting
> cloud issues can help. My guess is that there is a path problem (covered in
> the first wiki link) but by no means is that the only possibility.
> >
> > Thanks!
> > Jen
> > Galaxy team
> >
> > On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote:
> >> Hi Jen,
> >>
> >> Sorry that I missed some part of your email. It is not for local galaxy
> install. I am using the cloudman from aws and it seemed to have everything
> for having the input files and reference genome chose. The job was shown on
> the right panel and then the error message coming out.
> >>
> >> It seems to me that MACS was installed.... What is the issue?
> >>
> >> Thank you very much,
> >> Kathryn
> > On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote:
> >> Hi Jennifer,
> >>
> >> Thanks for the information on MACS tools.
> >>
> >> Yes, I forgot to mention that I used bowtie mapped files as the input.
> >>
> >> Thank you very much,
> >> Kathryn
> >>
> >>
> >> From: Jennifer Jackson [mailto:j...@bx.psu.edu]
> >> Sent: Friday, January 11, 2013 3:48 AM
> >> To: Sun, Wenping [USA]
> >> Cc: galaxy-u...@bx.psu.edu
> >> Subject: [External] Re: [galaxy-user] macs error for chipseq data
> >>
> >> Hello Kathryn,
> >>
> >> This is occurring on your local Galaxy install? Have you installed the
> actual MACS tool and set up the proper configuration paths? Details for how
> to do this are in these wikis:
> >> http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
> >> http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
> >>
> >> Apart from that, I should let you know that prior to running MACS,
> groomed fastq datasets first need to be mapped. An example can be found in
> our Using Galaxy paper, protocol #3. Links to the paper and supplemental
> materials (including a screencast walk-through) are available here:
> >> https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012
> >>
> >> If you need more help with your local install, directing questions to
> >> the galaxy-...@bx.psu.edu mailing list would be best,
> >>
> >> Thanks!
> >>
> >> Jen
> >> Galaxy team
> >>
> >> On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote:
> >> Dear galaxy users,
> >>
> >> I've encountered the error while running macs on galaxy for chipseq
> >> data. I used fastq groomed files as input and had the following error
> >>
> >> An error occurred running this job: /bin/sh: macs: not found
> >>
> >> Anybody can kindly provide some hints?
> >>
> >> Thanks,
> >> Kathryn
> >>
> >>
> >>
> >> ___________________________________________________________
> >> The Galaxy User list should be used for the discussion of Galaxy
> >> analysis and other features on the public server at usegalaxy.org.
> >> Please keep all replies on the list by using "reply all" in your mail
> >> client.  For discussion of local Galaxy instances and the Galaxy
> >> source code, please use the Galaxy Development list:
> >>
> >>   http://lists.bx.psu.edu/listinfo/galaxy-dev
> >>
> >> To manage your subscriptions to this and other Galaxy lists, please
> >> use the interface at:
> >>
> >>   http://lists.bx.psu.edu/
> >>
> >>
> >> --
> >> Jennifer Hillman-Jackson
> >> Galaxy Support and Training
> >> http://galaxyproject.org
> >
> > --
> > Jennifer Hillman-Jackson
> > Galaxy Support and Training
> >
> > http://galaxyproject.org
>
>
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