Hello again, I am truly sorry to bother everyone again but i still experience problems: This time with atlas 3.10 owned by iuc At the beginning without modifying anything, the error log was saying " mkdir : cannot create directory ATLAS/build : No such file or directory" After that I tried to modify the tool_dependencies.xml : L48 : "mkdir ATLAS/build &&" changed to "mkdir build &&" The error is "/bin/sh: 4 : cannot open /host/static_full_blas_lapack.diff: No such file" I can see it, if I go with a web browser, but I cannot download it manually nor click on it without crashing the web browser. Any idea? Thanks again, M Olivier CLAUDE- PhD Student INSERM/UPMC UMRS ICAN 1166 – Equipe 2 Faculté de médecine Pitié-Salpêtrière 91, bld de l'Hôpital - 3ème étage - Porte 305 75013 Paris - FRANCE
Hi Olivier, what are your operating system and architecture (x86_64 or i386)? Cheers, Nicola On 03/11/15 17:25, Olivier CLAUDE wrote:
Hello again,
I am truly sorry to bother everyone again but i still experience problems:
This time with atlas 3.10 owned by iuc
At the beginning without modifying anything, the error log was saying " mkdir : cannot create directory ATLAS/build : No such file or directory"
After that I tried to modify the tool_dependencies.xml :
L48 : "mkdir ATLAS/build &&" changed to "mkdir build &&" The error is "/bin/sh: 4 : cannot open /host/static_full_blas_lapack.diff: No such file"
I can see it, if I go with a web browser, but I cannot download it manually nor click on it without crashing the web browser.
Any idea?
Thanks again,
M Olivier CLAUDE- PhD Student INSERM/UPMC UMRS ICAN 1166 – Equipe 2 Faculté de médecine Pitié-Salpêtrière 91, bld de l'Hôpital - 3ème étage - Porte 305 75013 Paris - FRANCE ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Nicola It is an i686. Is it a problem ? Cheers, Olivier De : Nicola Soranzo Envoyé : mardi 3 novembre 19:08 Objet : Re: [galaxy-dev] atlas 3.10 IUC error À : Olivier CLAUDE, 'galaxy-dev' Hi Olivier, what are your operating system and architecture (x86_64 or i386)? Cheers, Nicola On 03/11/15 17:25, Olivier CLAUDE wrote:
Hello again,
I am truly sorry to bother everyone again but i still experience problems:
This time with atlas 3.10 owned by iuc
At the beginning without modifying anything, the error log was saying " mkdir : cannot create directory ATLAS/build : No such file or directory"
After that I tried to modify the tool_dependencies.xml :
L48 : "mkdir ATLAS/build &&" changed to "mkdir build &&"
The error is "/bin/sh: 4 : cannot open /host/static_full_blas_lapack.diff: No such file"
I can see it, if I go with a web browser, but I cannot download it manually nor click on it without crashing the web browser.
Any idea?
Thanks again,
M Olivier CLAUDE- PhD Student
INSERM/UPMC UMRS ICAN 1166 – Equipe 2
Faculté de médecine Pitié-Salpêtrière
91, bld de l'Hôpital - 3ème étage - Porte 305
75013 Paris - FRANCE
___________________________________________________________
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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/package_atla... 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_blast_p... However, the compile from source recipe will need looking at... Peter
Peter is correct, can you open an issue at https://github.com/galaxyproject/tools-iuc/issues/new and ping @natefoo ? Thanks, Nicola On 03/11/15 18:23, Peter Cock wrote:
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/package_atla...
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_blast_p...
However, the compile from source recipe will need looking at...
Peter
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/package_atla... 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_blast_p... However, the compile from source recipe will need looking at... Peter
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/package_atla...
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_blast_p...
However, the compile from source recipe will need looking at...
Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************
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...
Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************
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...
Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************
************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************
participants (5)
-
Nicola Soranzo -
o.claude＠outlook.fr -
Olivier CLAUDE
-
Peter Cock -
Ulf Schaefer