> 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?

Yes. My hope was to use tarfile from python and not 'tar', because
bsdtar seems to crash with that package.

> > 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 :(

For whatever reason I get the following in my log. Galaxy tries to
continue with the installation, that fine. But in your case Galaxy
aborts. Nevertheless, failing silently means, that biopython and numpy
will not be affected (hopefully).
I can also remove the manuell deactivation of cpu throttling, it was
just an idea to support more systems out of the box without admin
invention.


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

                # 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
Error calling SetGovernor: Caller is not authorized
#############################################

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

                    mkdir build &&
                    cd build &&

mkdir 
/home/gruening/projects/code/galaxy-central/tool_deps/atlas/3.11.11/iuc/package_atlas_3_11/3e1635c33e26/atlas/
 &&
                    ../configure -Fa alg -fPIC
--prefix=/home/gruening/projects/code/galaxy-central/tool_deps/atlas/3.11.11/iuc/package_atlas_3_11/3e1635c33e26/atlas/
 --with-netlib-lapack-tarfile=../lapack-3.4.2.tgz
                
STDOUT
gcc
-I/home/gruening/projects/code/galaxy-central/database/tmp/tmp-toolshed-mtdfjNMLM/ATLAS/build/..//CONFIG/include
  -g -w -c 
/home/gruening/projects/code/galaxy-central/database/tmp/tmp-toolshed-mtdfjNMLM/ATLAS/build/..//CONFIG/src/atlconf_misc.c
gcc
-I/home/gruening/projects/code/galaxy-central/database/tmp/tmp-toolshed-mtdfjNMLM/ATLAS/build/..//CONFIG/include
  -g -w -o xconfig 
/home/gruening/projects/code/galaxy-central/database/tmp/tmp-toolshed-mtdfjNMLM/ATLAS/build/..//CONFIG/src/config.c
 atlconf_misc.o 
./xconfig -d
s 
/home/gruening/projects/code/galaxy-central/database/tmp/tmp-toolshed-mtdfjNMLM/ATLAS/build/../
 -d b 
/home/gruening/projects/code/galaxy-central/database/tmp/tmp-toolshed-mtdfjNMLM/ATLAS/build
  -Fa alg -fPIC -Si lapackref 1

OS configured as Linux (1)

Assembly configured as GAS_x8664 (2)

Vector ISA Extension configured as  AVX (5,480)

Architecture configured as  Corei2 (27)

Clock rate configured as 1600Mhz

Maximum number of threads configured as  4
Parallel make command configured as '$(MAKE) -j 4'
CPU Throttling apparently enabled!
xconfig exited with 1
#############################################

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

                    mkdir build &&
                    cd build &&

mkdir 
/home/gruening/projects/code/galaxy-central/tool_deps/atlas/3.11.11/iuc/package_atlas_3_11/3e1635c33e26/atlas/
 &&
                    ../configure -Fa alg -fPIC
--prefix=/home/gruening/projects/code/galaxy-central/tool_deps/atlas/3.11.11/iuc/package_atlas_3_11/3e1635c33e26/atlas/
 --with-netlib-lapack-tarfile=../lapack-3.4.2.tgz
                
STDERR
It appears you have cpu throttling enabled, which makes timings
unreliable and an ATLAS install nonsensical.  Aborting.
See ATLAS/INSTALL.txt for further information
#############################################

> Peter



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