Re: [galaxy-user] Egg build failed for numpy 1.6.0
Hi, I am trying to install a local version of galaxy on my mac book (x86_64, OSx 10.8.4). I seem to be having a lot of trouble with fetching and installing specific egg dependencies. Initially pysam was giving me
Hi, I am preferentially using the main server. But recently I have also tried to build a local Galaxy server. I also have a mac (Mac Pro OSx 10.6.8). Since I am not a specialist at all, I asked some kind of "expert" people from my institute. They told me that installing Galaxy on Mac can really be nightmare because there are some conflicts in the versions of python... This could explain the problem you are encountering with the egg dependencies. So they advised me to install an Ubuntu (12.04) operating system in a virtual machine using Virtual box. This is supposed to be much easier to install Galaxy and indeed, the installation of my local galaxy server ran fast and well. However, I don't know whether the tip is good or not, because I am now facing big problems with the virtual machine: the Ubuntu virtual machine is very unstable and often crashes while running big datas on Galaxy... The problem does not come from Galaxy, but from either Ubuntu guest system, the virtual machine or the communication with the mac host system and I haven't found out how to fix it yet. But since your version of Mac is different, you can try this solution, it might work better in your configuration. Hope that helps, Fabrice But at the moment, I have lots of problem with the trouble, but once I ran scramble.py -e pysam, the problem was fixed. Now I have trouble with the numpy egg dependency. Does anyone have any idea
why a egg would fail to build. I am assuming it is because I have a more recent numpy version (1.7.1) installed already. What should I do, short of uninstalling the newer version of numpy ? Any help on the matter would be greatly appreciated. Thank you. L -- ===================================
Dr. Lahcen Campbell < Contact: lahcencampbell@gmail.com < http://bioinf.may.ie/index.html < ===================================
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Fabrice Besnard Institute of Biology of the Ecole Normale Supérieure (IBENS) 46 rue d'Ulm, 75230 Paris cedex 05, France 8th floor. Office: Room 802. Lab: Room 817. mail: fbesnard@biologie.ens.fr Tel: +33-1-44-32-39-44
Hi, Almost all of the Galaxy development team uses Macs, so it should certainly work. The problems with eggs, as you have both found, typically come with using non-standard versions of Python. Your best bet is to use the version that shipped with your version of OS X, which can be found in /System/Library/Frameworks/Python.framework. You can ensure that this version is always used by putting it first on $PATH or setting up a virtualenv with it, e.g.: % virtualenv --python=/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python genv --nate On Aug 5, 2013, at 8:12 AM, Fabrice BESNARD wrote:
Hi,
I am preferentially using the main server. But recently I have also tried to build a local Galaxy server. I also have a mac (Mac Pro OSx 10.6.8).
Since I am not a specialist at all, I asked some kind of "expert" people from my institute. They told me that installing Galaxy on Mac can really be nightmare because there are some conflicts in the versions of python... This could explain the problem you are encountering with the egg dependencies.
So they advised me to install an Ubuntu (12.04) operating system in a virtual machine using Virtual box. This is supposed to be much easier to install Galaxy and indeed, the installation of my local galaxy server ran fast and well.
However, I don't know whether the tip is good or not, because I am now facing big problems with the virtual machine: the Ubuntu virtual machine is very unstable and often crashes while running big datas on Galaxy... The problem does not come from Galaxy, but from either Ubuntu guest system, the virtual machine or the communication with the mac host system and I haven't found out how to fix it yet. But since your version of Mac is different, you can try this solution, it might work better in your configuration.
Hope that helps,
Fabrice
Hi, I am trying to install a local version of galaxy on my mac book (x86_64, OSx 10.8.4). I seem to be having a lot of trouble with fetching and installing specific egg dependencies. Initially pysam was giving me
But at the moment, I have lots of problem with the trouble, but once I ran scramble.py -e pysam, the problem was fixed. Now I have trouble with the numpy egg dependency. Does anyone have any idea
why a egg would fail to build. I am assuming it is because I have a more recent numpy version (1.7.1) installed already. What should I do, short of uninstalling the newer version of numpy ? Any help on the matter would be greatly appreciated. Thank you. L -- ===================================
Dr. Lahcen Campbell < Contact: lahcencampbell@gmail.com < http://bioinf.may.ie/index.html < ===================================
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Fabrice Besnard Institute of Biology of the Ecole Normale Supérieure (IBENS) 46 rue d'Ulm, 75230 Paris cedex 05, France 8th floor. Office: Room 802. Lab: Room 817. mail: fbesnard@biologie.ens.fr Tel: +33-1-44-32-39-44
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
participants (2)
-
Fabrice BESNARD -
Nate Coraor