On Thu, Sep 19, 2013 at 5:15 PM, Björn Grüning <bjoern.gruening@pharmazie.uni-freiburg.de> wrote:
Hi Peter and Carlos,
On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto <carlos.borroto@gmail.com> wrote:
I did an extra test. Started with a clean 'galaxy-dist'. This time both repositories fail with the same error. I guess before something was cached for the repository with version 0.1.4.
I used biopython repository as a guide to write my tool dependency definition: http://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61
I can confirm biopython repository is failing to install for me with exactly the same error. I wonder if a recently addition in the test toolshed broke the treatment of "prior_installation_required".
Thanks, Carlos
Could be - note that currently Biopython isn't currently installing properly on the Test Tool Shed due to ALTAS failing (a requirement of NumPy which is a requirement of Biopython). Dave and Bjoern are I think looking at this already...
I can't do much I tested it again and for me its working fine on my computers I have at hand ... sorry.
In case it helps, this is how the INSTALLATION.log file ends on OS X 10.8.4: $ tail -n 3 ~/src/shed_tools_dependencies.central/atlas/3.10.1/iuc/package_atlas_3_10/3508de0ebae1/INSTALLATION.log x ATLAS/tune/lapack/lanbsrch.c tar: Error exit delayed from previous errors. ############################################# This is the relevant part I can find in Galaxy's log: [localhost] local: tar xfvj atlas3.10.1.tar.bz2 Warning: local() encountered an error (return code 1) while executing 'tar xfvj atlas3.10.1.tar.bz2' After noticing this I got what I'm guessing is the original file from sourceforge: http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.1/atlas3.10.... I can confirm that trying to untar this file fails with the exact same error. However, on Ubuntu 13.04 untaring this file works just fine. On Ubuntu 13.04 the error I see is: 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 ############################################# Björn, you said cpu throttling can be easily disable on Ubuntu. Can you comment how? Do I need to disable it completely, or should the install script do it when installing? Thanks, Carlos