On Fri, Sep 20, 2013 at 8:48 AM, Bjoern Gruening <bjoern.gruening@gmail.com> wrote:
Hi,
I tried to things to solve it.
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
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.
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'.
I don't have access to my OS X box until later tonight. On Ubuntu with an up-to-date instance of galaxy-central is failing now for me with a different error: STDOUT ./xconfig -d s /home/cborroto/src/galaxy-central/database/tmp/tmp-toolshed-mtdyWTv64/ATLAS/build/../ -d b /home/cborroto/src/galaxy-central/database/tmp/tmp-toolshed-mtdyWTv64/ATLAS/build -Fa alg -fPIC -Si lapa ckref 1 xconfig exited with 127 ############################################# ############################################# mkdir build && cd build && mkdir /home/cborroto/src/shed_tools_dependencies.central/atlas/3.10.1/iuc/package_atlas_3_10/d32504e1aea8/atlas/ && ../configure -Fa alg -fPIC --prefix=/home/cborroto/src/shed_tools_dependencies.central/atlas/3.10.1/iuc/package_atlas_3_10/d32504e1aea8/atlas/ --with-netlib-lapack-tarfile=../lapack-3.4.2.tgz STDERR cat: ..//CONFIG/src/Makefile: No such file or directory cp: cannot stat ‘..//CONFIG/src/atlcomp.txt’: No such file or directory make: *** No rule to make target `xconfig'. Stop. /bin/sh: 1: ./xconfig: not found Full INSTALLATION.log: http://pastebin.com/raw.php?i=hvqFWvgJ Somehow this is also a silent failing and numpy, biopython and ngs-tools(my tool package depending on biopython) get "Installed"(Green) while lapack, atlas and split_by_barcode(my actual tool wrapper depending on ngs-tools package) get "Installed, missing tool dependencies"(Grey). This means if I try to use my wrapper in this state I get this error: /bin/sh: 1: ngs-tools: not found However, if I do a "Repair repository" on split_by_barcode it goes into "Installed"(Green) and everything seems to work from then on. Thanks for working on this, Carlos