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.vandenb...@gmail.com] 
Envoyé : vendredi 30 octobre 2015 10:07
À : Yvan Le Bras <yvan.le_b...@irisa.fr>
Cc : Olivier CLAUDE <o.cla...@outlook.fr>; galaxy-dev 
<galaxy-dev@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_b...@irisa.fr> 
yvan.le_b...@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.cla...@outlook.fr> o.cla...@outlook.fr>
À:  <mailto:galaxy-dev@lists.galaxyproject.org> 
galaxy-dev@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_b...@irisa.fr <mailto:yvan.le_b...@irisa.fr> 

 


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