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

----- Mail original -----

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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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

---

Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/