On Fri, Sep 20, 2013 at 1:48 PM, Bjoern Gruening <bjoern.gruening@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