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 If you have more trouble, we're at the UPMC, 7th floor, Batiment B. Cheers, Marius On 30 October 2015 at 08:42, Olivier CLAUDE <o.claude@outlook.fr> wrote:
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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-- Marius van den Beek, PhD Drosophila Genetics and Epigenetics Institut de Biologie Paris Seine <http://www.ibps.upmc.fr/fr/Recherche/umr-biologie-developpement/genetique-et-epigenetique-de-la-drosophile> 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 01 44 27 34 01 marius.van_den_beek@upmc.fr