Re: [galaxy-dev] Updating Bioblend on existing Galaxy installation
Sorry all, moving this Q over to biostars. -- "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 On 22 February 2018 at 16:21, Lachlan Musicman wrote: > Hola, > > I've just noticed that our Galaxy 17.09 installation has Bioblend 0.9 > installed, and that one of the changes in Bioblend 0.10 was "support for > galaxy 17.09". > > Can someone hip me to the easiest way to update bioblend? > > Is it just to activate the venv and pip install -U bioblend? > > 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/
[galaxy-dev] Updating Bioblend on existing Galaxy installation
Hola, I've just noticed that our Galaxy 17.09 installation has Bioblend 0.9 installed, and that one of the changes in Bioblend 0.10 was "support for galaxy 17.09". Can someone hip me to the easiest way to update bioblend? Is it just to activate the venv and pip install -U bioblend? 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/
[galaxy-dev] Pause queued jobs
Hi, I'm new to Galaxy and have been tasked with learning how to admin it. We are running commit 407da92f88ac859d3f9b259be83640516159fe15 I notice there is a screen called "Manage Jobs". How to I re-order, re-prioritise or pause jobs in that list? It seems to only have the options to stop (which I presume cannot be restarted because it's called stop not pause), and Job Lock, which I presume controls if users can or cannot submit jobs, rather than locking individual jobs. Are my assumptions incorrect - is one of these options a "pause" option? 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/
Re: [galaxy-dev] Installing Galaxy, Conda and Python
On 11 August 2017 at 14:33, Lachlan Musicman 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: > FWIW, we eventually found the problem and solution - http://dev.list.galaxyproject.org/Problem-with-installing-tools-using-Conda-td4670590.html 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/
[galaxy-dev] Installing Galaxy, Conda and Python
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
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy list
