Installing Galaxy, Conda and Python

classic Classic list List threaded Threaded
2 messages Options
| Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Installing Galaxy, Conda and Python

Lachlan Musicman
Hola,

We are attempting to install Galaxy, from git, version 17.05

We largely have it installed, but seem to be falling over at the installation of dependencies.

In particular, conda via Galaxy can't find Gnuplot 4.6, and the conda libraries don't show a gnuplot < 5.x

The error:

10.126.160.84 - - [11/Aug/2017:13:49:08 +1100] "GET /galaxy/admin/manage_tool_dependencies HTTP/1.1" 200 - "http://<server>/galaxy/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_12_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/60.0.3112.90 Safari/537.36"
[pid: 24515|app: 0|req: 3/4] 10.126.160.84 () {66 vars in 1432 bytes} [Fri Aug 11 13:49:08 2017] GET /galaxy/admin/manage_tool_dependencies => generated 13534 bytes in 220 msecs (HTTP/1.1 200) 2 headers in 73 bytes (1 switches on core 0)
galaxy.tools.deps.conda_util DEBUG 2017-08-11 13:49:12,042 Executing command: /galaxy/production_database/dependencies/_conda/bin/conda create -y --name __gnuplot@4.6 gnuplot=4.6
Fatal Python error: Py_Initialize: Unable to get the locale encoding
ImportError: No module named 'encodings'

Current thread 0x00007fd60463c740 (most recent call first):
galaxy.tools.deps.resolvers.conda DEBUG 2017-08-11 13:49:12,070 Removing failed conda install of [CondaTarget[gnuplot,version=4.6]]
galaxy.tools.deps.conda_util DEBUG 2017-08-11 13:49:12,072 Executing command: /galaxy/production_database/dependencies/_conda/bin/conda create -y --name __gnuplot@4.6 gnuplot=4.6
Fatal Python error: Py_Initialize: Unable to get the locale encoding
ImportError: No module named 'encodings'

Current thread 0x00007fb0d2eb6740 (most recent call first):
galaxy.tools.deps.resolvers.conda DEBUG 2017-08-11 13:49:12,102 Removing failed conda install of gnuplot, version '4.6'
galaxy.tools.deps.conda_util DEBUG 2017-08-11 13:49:12,106 Executing command: /galaxy/production_database/dependencies/_conda/bin/conda create -y --name __gnuplot@_uv_ gnuplot
Fatal Python error: Py_Initialize: Unable to get the locale encoding
ImportError: No module named 'encodings'

Current thread 0x00007fc80d5df740 (most recent call first):
galaxy.tools.deps.resolvers.conda DEBUG 2017-08-11 13:49:12,139 Removing failed conda install of [CondaTarget[gnuplot,unversioned]]
galaxy.tools.deps.conda_util DEBUG 2017-08-11 13:49:12,142 Executing command: /galaxy/production_database/dependencies/_conda/bin/conda create -y --name __gnuplot@_uv_ gnuplot
Fatal Python error: Py_Initialize: Unable to get the locale encoding
ImportError: No module named 'encodings'


https://anaconda.org/bioconda/gnuplot/files shows that there is a 4.6.0-1 in there, but for whatever reason it's not being found by the search function?

When I try the recommended


[root@<server> bin]# ./anaconda search -t conda gnuplot
Using Anaconda API: https://api.anaconda.org
Run 'anaconda show <USER/PACKAGE>' to get more details:
Packages:
     Name                      |  Version | Package Types   | Platforms     
     ------------------------- |   ------ | --------------- | ---------------
     BioBuilds/gnuplot         |    5.0.5 | conda           | linux-ppc64le, linux-64, osx-64
                                          : Portable command-line driven graphing utility
     OpenAlea/gnuplot          |    5.0.4 | conda           | linux-64, osx-64
     alexbw/lua-gnuplot        |    1.0.1 | conda           | linux-64, osx-64
                                          : Torch interface to Gnuplot
     bioconda/gnuplot          |    5.0.4 | conda           | linux-64, osx-64
                                          : Gnuplot, plotting from command line
     bioconda/gnuplot-py       |      1.8 | conda           | linux-64, osx-64
     conda-forge/gnuplot       |    5.0.6 | conda           | linux-64, osx-64
                                          : Gnuplot, plotting from command line
     gbaty/gnuplot             |    5.0.1 | conda           | linux-64      
                                          : Gnuplot is a portable command-line driven graphing utility for many platforms.
     johannr/py-gnuplot        |      1.8 | conda           | linux-64, osx-64
                                          : A Python interface to the gnuplot plotting program.
Found 8 packages


There's no 4.6 there, hence the fail I guess.

Does anyone have a work around for this?

cheers
L.


------
"The antidote to apocalypticism is apocalyptic civics. Apocalyptic civics is the insistence that we cannot ignore the truth, nor should we panic about it. It is a shared consciousness that our institutions have failed and our ecosystem is collapsing, yet we are still here — and we are creative agents who can shape our destinies. Apocalyptic civics is the conviction that the only way out is through, and the only way through is together. "

Greg Bloom @greggish https://twitter.com/greggish/status/873177525903609857

___________________________________________________________
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/
| Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Installing Galaxy, Conda and Python

Lachlan Musicman

On 11 August 2017 at 14:33, Lachlan Musicman <[hidden email]> wrote:
Hola,

We are attempting to install Galaxy, from git, version 17.05

We largely have it installed, but seem to be falling over at the installation of dependencies.

In particular, conda via Galaxy can't find Gnuplot 4.6, and the conda libraries don't show a gnuplot < 5.x

The error:


It was identical. Looks like there is a rogue supervisord online tutorial out there that people are want to follow.

cheers
L.


------
"The antidote to apocalypticism is apocalyptic civics. Apocalyptic civics is the insistence that we cannot ignore the truth, nor should we panic about it. It is a shared consciousness that our institutions have failed and our ecosystem is collapsing, yet we are still here — and we are creative agents who can shape our destinies. Apocalyptic civics is the conviction that the only way out is through, and the only way through is together. "

Greg Bloom @greggish https://twitter.com/greggish/status/873177525903609857
 


___________________________________________________________
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/
Loading...