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 médecine Pitié-Salpêtrière
91, bld de l'Hôpital - 3ème étage - Porte 305
75013 Paris - FRANCE
De : Marius van den Beek [mailto:m.vandenbeek@gmail.com]
Envoyé : vendredi 30 octobre 2015 10:07
À : Yvan Le Bras <yvan.le_bras(a)irisa.fr>
Cc : Olivier CLAUDE <o.claude(a)outlook.fr>; galaxy-dev <galaxy-dev(a)lists.galaxyproject.org>
Objet : Re: [galaxy-dev] new to galaxy
Hello Olivier,
Ivan is right. In addition, have a look here to a list of required packages that galaxy often assumes to be installed:
<https://wiki.galaxyproject.org/Admin/Config/ToolDependenciesList> https://wiki.galaxyproject.org/Admin/Config/ToolDependenciesList
If you have more trouble, we're at the UPMC, 7th floor, Batiment B.
Cheers,
Marius
On 30 October 2015 at 09:42, Yvan Le Bras < <mailto:yvan.le_bras@irisa.fr> yvan.le_bras(a)irisa.fr> wrote:
Hi Olivier,
The first error message seems to indicate that Galaxy can't install the samtools version 0.1.11 dependency because you don't have zlib1g installed on your server. Maybe something like executing this command line on the Galaxy server will fix this issue :
sudo apt-get install zlib1g-dev
Best Regards,
Yvan
_____
De: "Olivier CLAUDE" < <mailto:o.claude@outlook.fr> o.claude(a)outlook.fr>
À: <mailto:galaxy-dev@lists.galaxyproject.org> galaxy-dev(a)lists.galaxyproject.org
Envoyé: Vendredi 30 Octobre 2015 08:42:53
Objet: [galaxy-dev] new to galaxy
Hello,
My name is olivier, I am a PhD student in biology.
I have to run bioinformatical prediction on protein sequences and i chose galaxy to do it.
I have some basic skills with linux, and I may have missed some steps.
My galaxy server is running for more than one week now; the installation was ok, but I am facing some problems to install some dependencies:
- Samtools 0.1.18 returns errors everytime I try to install it:
“this tool dependency’s required tool dependency samtools version 0.1.18 has status error”
“In file included from bgzf.c:32:0: bgzf.h:33:18: fatal error: zlib.h: No such file or directory #include <zlib.h> ^ compilation terminated. make[2]: *** [bgzf.o] Error 1 make[1]: *** [lib-recur] Error 1 make: *** [all-recur] Error 1”
- Atlas 3.10.2 2 won’t install correctly neither : ” mkdir: cannot create directory ‘ATLAS/build’: No such file or 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 - 3ème étage - Porte 305
75013 Paris - FRANCE
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--
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Yvan Le Bras, PhD @Yvan2935 <°))))><
e-Biogenouest project http://www.e-biogenouest.org
CNRS UMR 6074 IRISA-INRIA, Campus de Beaulieu, 35042 Rennes Cedex
tél.: +33 (0) 2 99 84 71 79 <tel:%2B33%20%280%29%202%2099%2084%2071%2079> / +33 (0) 6.10.43.96.51 <tel:%2B33%20%280%29%206.10.43.96.51>
yvan.le_bras(a)irisa.fr <mailto:yvan.le_bras@irisa.fr>
___________________________________________________________
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