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:///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 0x7fd60463c740 (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 0x7fb0d2eb6740 (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 0x7fc80d5df740 (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@ bin]# ./anaconda search -t conda gnuplot
Using Anaconda API: https://api.anaconda.org
Run 'anaconda show ' 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
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