Re: [galaxy-dev] atlas 3.10 IUC error

e...@phe.gov.uk] Envoyé : mercredi 1 juin 2016 11:50 À : Olivier CLAUDE ; 'Peter Cock' ; nsora...@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

Re: [galaxy-dev] wolfpsort

r you anymore Peter. Regards, Olivier. -Message d'origine- De : Peter Cock [mailto:p.j.a.c...@googlemail.com] Envoyé : vendredi 4 décembre 2015 15:17 À : Olivier CLAUDE Cc : galaxy-dev@lists.galaxyproject.org Objet : Re: [galaxy-dev] wolfpsort On Fri, Dec 4, 2015 at 12:59 PM, Oliv

Re: [galaxy-dev] wolfpsort

Ok i did not saw it. I runned it with ./ and it worked fine. It gave me the same answer you gave me earlier. Olivier -Message d'origine- De : Peter Cock [mailto:p.j.a.c...@googlemail.com] Envoyé : vendredi 4 décembre 2015 12:40 À : Olivier CLAUDE Cc : galax

Re: [galaxy-dev] wolfpsort

ivier -Message d'origine- De : Peter Cock [mailto:p.j.a.c...@googlemail.com] Envoyé : vendredi 4 décembre 2015 11:16 À : Olivier CLAUDE Cc : galaxy-dev@lists.galaxyproject.org Objet : Re: [galaxy-dev] wolfpsort Hi Olivier, First of all, let's double check what kind of machine you are

Re: [galaxy-dev] wolfpsort

omething somewhere. Any lead? thanks De : Peter Cock [mailto:p.j.a.c...@googlemail.com] Envoyé : mercredi 2 décembre 2015 18:59 À : Olivier CLAUDE Cc : galaxy-dev@lists.galaxyproject.org; Björn Grüning Objet : Re: [galaxy-dev] 3 questions On Wed, Dec 2, 2015 at 5:07 PM, Olivier

Re: [galaxy-dev] 3 questions

Hello Peter, Thanks again for all your explanations. Hello again, 1/ I managed to find WolfPsort on github. You mean https://github.com/fmaguire/WoLFPSort ? I can see why Finlay Maguire did that although I'm not 100% sure that is within the licence. In other news, it looks like som

[galaxy-dev] 3 questions

maximum 4 threads? Can I assume it will use 4 core in parallel? 3/I use blast + from the devteam is there any possibility to use more than 1 core? If yes where? Thanks ! M Olivier CLAUDE- PhD Student INSERM/UPMC UMRS ICAN 1166 – Equipe 2 Faculté de médecine Pitié-Salpêtrière

Re: [galaxy-dev] Tmhmm and signal P

amp; help! Olivier On Fri, Nov 13, 2015 at 10:40 AM, Olivier CLAUDE wrote: > Hello, > > This is working! For signlaP and promoter at least. > Good. > I still got this weird error with tmhmm ("no output from tmhmm") and I can't > figure what's wrong . > The

Re: [galaxy-dev] Tmhmm and signal P

a while now and I am not able to find it anywhere? Thanks again! Olivier . -Message d'origine- De : Peter Cock [mailto:p.j.a.c...@googlemail.com] Envoyé : jeudi 12 novembre 2015 17:35 À : Olivier CLAUDE Cc : Björn Grüning ; galaxy-dev Objet : Re: [galaxy-dev] Tmhmm and signal P

Re: [galaxy-dev] Tmhmm and signal P

üning Cc : Olivier CLAUDE ; galaxy-dev Objet : Re: [galaxy-dev] Tmhmm and signal P On Thu, Nov 12, 2015 at 2:56 PM, Björn Grüning wrote: > Hi, > > please make also sure the /bin directory inside of the signalp folder > is in your PATH. > > Things like combine-hmm-plp

Re: [galaxy-dev] Tmhmm and signal P

---Message d'origine- De : Björn Grüning [mailto:bjoern.gruen...@gmail.com] Envoyé : jeudi 12 novembre 2015 15:56 À : Olivier CLAUDE ; 'Peter Cock' Cc : 'Björn Grüning' ; 'galaxy-dev' Objet : Re: [galaxy-dev] Tmhmm and signal P Hi, please make also sure the /bin

Re: [galaxy-dev] Tmhmm and signal P

one this machine. Is Galaxy considered as another user? I installed it as a simple user, to avoid all the problems with the rights with the root. Thanks again, Olivier -Message d'origine- De : Peter Cock [mailto:p.j.a.c...@googlemail.com] Envoyé : jeudi 12 novembre 2015 14:22

Re: [galaxy-dev] Tmhmm and signal P

ovembre 2015 12:48 À : Olivier CLAUDE Cc : 'galaxy-dev' Objet : Re: [galaxy-dev] Tmhmm and signal P Hi Olivier, you need to have signalp in version 3. You have installed it already and it is now on your $PATH? > Signal P: with v3.0: it can’t localize it (signal not found) (I can’t

[galaxy-dev] Tmhmm and signal P

) With v4.1 it can’t be reached by galaxy (I am thinking about something with the name 3.0 vs 4.1 but I can’t figure where I have to change …) Do anybody have an idea? Regards, M Olivier CLAUDE- PhD Student INSERM/UPMC UMRS ICAN 1166 – Equipe 2 Faculté de médecine Pitié

Re: [galaxy-dev] OpenMS caused Error downloading from URL

Hello Mic, You should try to change the link in the tool_dependencies.xml of openMS with this link : http://sourceforge.net/projects/open-ms/files/OpenMS/OpenMS-1.10/OpenMS-1.10.0.tar.gz/ and t

Re: [galaxy-dev] atlas 3.10 IUC error

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.c...@googlemail.com] Envoyé : mardi 3 novembre 2015 19:24 À : o.cla...@outlook.fr Cc : Nicola So

[galaxy-dev] atlas 3.10 IUC error

t 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 __

Re: [galaxy-dev] netcdf 4.3 error

Hi Björn, Thanks a lot, it works now. Regards, Olivier. -Message d'origine- De : Björn Grüning [mailto:bjoern.gruen...@gmail.com] Envoyé : lundi 2 novembre 2015 16:32 À : Olivier CLAUDE ; 'galaxy-dev' Objet : Re: [galaxy-dev] netcdf 4.3 error Hi Olivier, can you chan

[galaxy-dev] netcdf 4.3 error

pub/netcdf/old/netcdf-4.3.1.1.tar.gz> old/netcdf-4.3.1.1.tar.gz What can I do to override this? Thank you, 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 Par

[galaxy-dev] new to galaxy

Hi Yvan and Marius, Thanks to both of you almost everything is ok now. I still experience some issues, but I’ll try some things on my own before asking questions. Thank you Marius for the invite! M Olivier CLAUDE- PhD Student INSERM/UPMC UMRS ICAN 1166 – Equipe 2 Faculté de

[galaxy-dev] new to galaxy

directory” - Same goes for Numpy 1.7.1, samtools 1.2, tophat 1.4.0, rsem 1.1.17 Do you have any idea? Or tips? Thank you and have a nice day, M Olivier CLAUDE- PhD Student INSERM/UPMC UMRS ICAN 1166 – Equipe 2 Faculté de médecine Pitié-Salpêtrière 91, bld de l'Hôpital -