On Fri, Sep 20, 2013 at 1:48 PM, Bjoern Gruening
<bjoern.gruen...@gmail.com> wrote:
> Hi,
>
> I tried to things to solve it.

Was this specifically to solve ATLAS under Mac OS X,
or more generally include the problem shown on the
Galaxy (Test) Tool Shed?

> 1: I uploaded a new version to:
>  http://testtoolshed.g2.bx.psu.edu/view/iuc/package_atlas_3_10 this time
> with target_filename="ATLAS.tar.bz2". That is a rather new feature, so
> you will need a recent Galaxy version. The prosite is that we do not
> need to call 'tar', we are using the python tarfile module. Hopefully
> that will work, also on OS-X

Not tried.

> 2: I have created:
> http://testtoolshed.g2.bx.psu.edu/view/iuc/package_atlas_3_11
> Peter was able to install it on OS-X, at least on commandline, so I have
> hope that this one is working, well. The downside is, that it is a
> unstable version and will disappear from the server.

Tried on a CentOS machine (running galaxy-central), it appeared
to work but on closer inspection:

Missing tool dependencies - click the name to install the missing dependency
Name Version Type Installation status
atlas 3.11.11 package Error

$ cat 
/opt/galaxy-dist-shed-tools/atlas/3.11.11/iuc/package_atlas_3_11/3e1635c33e26/INSTALLATION.log

#############################################

                # try to disable cpu throttling
                if hash cpufreq-selector 2>/dev/null; then
                    cpufreq-selector -g performance
                elif hash cpupower 2>/dev/null; then
                    cpupower frequency-set -g performance
                else
                    echo 'Please deactivate CPU throttling by your
own, or install cpufreq-selector'
                    exit
                fi

STDOUT

#############################################

#############################################

                # try to disable cpu throttling
                if hash cpufreq-selector 2>/dev/null; then
                    cpufreq-selector -g performance
                elif hash cpupower 2>/dev/null; then
                    cpupower frequency-set -g performance
                else
                    echo 'Please deactivate CPU throttling by your
own, or install cpufreq-selector'
                    exit
                fi

STDERR
You must be root
#############################################


> Would be great if you can give both a try. For me its working. That
> means on ubuntu its installed and on Fedora its failing silently with
> 'It appears you have cpu throttling enabled, which makes timings
> unreliable and an ATLAS install nonsensical. Aborting. See
> ATLAS/INSTALL.txt for further information'.

Like Fedora, on CentOS I am getting a silent failure :(

Peter
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