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

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De: "Olivier CLAUDE" <o.claude@outlook.fr>
À: 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                                                                                                                                              <°))))><

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                                                                  yvan.le_bras@irisa.fr

___________________________________________________________
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