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 dependencys 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 wont 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
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
___________________________________________________________ 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/ --
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 / +33 (0) 6.10.43.96.51 yvan.le_bras@irisa.fr
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 09:42, Yvan Le Bras <yvan.le_bras@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" <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
___________________________________________________________ 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/
--
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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 / +33 (0) 6.10.43.96.51
yvan.le_bras@irisa.fr
___________________________________________________________ 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/
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/
-- 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
participants (4)
-
Marius van den Beek -
Marius van den Beek -
Olivier CLAUDE -
Yvan Le Bras