Hi all It turns out that when the gfortran package is installed, it happily uses the pre-compiled binaries. If it cannot be found it tries to compile it unsuccessfully. Thanks Ulf On 01/06/16 13:49, Olivier CLAUDE wrote:
Hi Ulf,
I did not notified natefoo, since I make it work.
I do not remember clearly how I managed to solve this problem. But I think that I installed it manually through two ways : I installed in linux via synaptic, and then retried in galaxy. Now it is working fine but I can't remember if this was sufficient to make it work or not. At the beginning I was on a 32bit machine and I switched to a 64 bits since some tools weren't able to run with 32bits. Everything then is based on x86_64.
Good luck,
Olivier
-----Message d'origine----- De : Ulf Schaefer [mailto:Ulf.Schaefer@phe.gov.uk] Envoyé : mercredi 1 juin 2016 11:50 À : Olivier CLAUDE <o.claude@outlook.fr>; 'Peter Cock' <p.j.a.cock@googlemail.com>; nsoranzo@tiscali.it Cc : galaxy-dev@lists.galaxyproject.org Objet : Re: [galaxy-dev] atlas 3.10 IUC error
Hi all
Sorry to be resuscitating this old thread, but has anyone looked at it, or has an issue been created on Github, notifying @natefoo?
I am running into the same issue, only the machine that the compile from source fails on actually is x86_64. So I am not sure why it is not using the pre-compiled binaries.
On another x86_64 machine the install works fine with the pre-compiled binaries.
Thanks very much Ulf
On 04/11/15 08:26, Olivier CLAUDE wrote:
Thanks Peter, Nicola,
Ok, I'll try to switch on an 64bits computer then, maybe there's some other errors due to this. Thanks a lot.
Olivier
-----Message d'origine----- De : Peter Cock [mailto:p.j.a.cock@googlemail.com] Envoyé : mardi 3 novembre 2015 19:24 À : o.claude@outlook.fr Cc : Nicola Soranzo <nsoranzo@tiscali.it>; galaxy-dev@lists.galaxyproject.org Objet : Re: [galaxy-dev] atlas 3.10 IUC error
On Tue, Nov 3, 2015 at 6:16 PM, <o.claude@outlook.fr> wrote:
Hi Nicola
It is an i686. Is it a problem ?
Cheers, Olivier
Currently only for 64bit Linux are pre-compiled binaries used:
https://github.com/galaxyproject/tools-iuc/blob/master/packages/packag e_atlas_3_10/tool_dependencies.xml
There's a special case for Mac, but otherwise the current Atlas recipe would attempt to compile from source for 32bit Linux. And that is failing for some reason...
The easiest fix would be if pre-compiled binaries for 32bit Linux were available, we would need <actions os="linux" architecture="i386"> and/or <actions os="linux" architecture="i686"> actions, e.g.
https://github.com/peterjc/galaxy_blast/blob/master/packages/package_b last_plus_2_2_30/tool_dependencies.xml
However, the compile from source recipe will need looking at...
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