Re: [galaxy-dev] [galaxy-user] Installing new tools from the tool shed
On Feb 13, 2013, at 6:16 PM, David Joly <idjoly@gmail.com> wrote:
Hi!
Ok, I know many people had the same issue, but I just can't figure what's going on. I'm quite new about using a local instance of Galaxy and I'm trying to figure how to install a tool from the tool shed. Reading the tutorial (Installing Galaxy tool shed repository tools into a local Galaxy instance) looked pretty simple, but maybe I missed something.
First, I modified the universe_wsgi.ini file by removing the "#" before the tool_config_file and tool_path lines.
This one step should really be all you need to do (any other files get created automatically with reasonable defaults if missing) as far as configuration goes. Did you restart your galaxy instance after editing universe_wsgi.ini? -Dannon
Ok, one more step closer (I thought closing the browser would be enough to restart galaxy, but obviously, I had to reboot the computer). But now it says: ValueError: too many values to unpack 2013/2/13 Dannon Baker <dannon.baker@gmail.com>
On Feb 13, 2013, at 6:16 PM, David Joly <idjoly@gmail.com> wrote:
Hi!
Ok, I know many people had the same issue, but I just can't figure what's going on. I'm quite new about using a local instance of Galaxy and I'm trying to figure how to install a tool from the tool shed. Reading the tutorial (Installing Galaxy tool shed repository tools into a local Galaxy instance) looked pretty simple, but maybe I missed something.
First, I modified the universe_wsgi.ini file by removing the "#" before the tool_config_file and tool_path lines.
This one step should really be all you need to do (any other files get created automatically with reasonable defaults if missing) as far as configuration goes. Did you restart your galaxy instance after editing universe_wsgi.ini?
-Dannon
How old is the galaxy you're running? To use the main toolshed you'll need to use a galaxy-dist release from December or later. After this point in time the interface was standardized and is backwards compatible. To update, you should be able to simply navigate to your galaxy-dist directory, 'hg pull -u', and you'll be off and running. Also, since this deals with a local install, please do keep replies on the 'galaxy-dev' list that I transitioned this thread to instead of galaxy-user. Thanks! -Dannon On Feb 13, 2013, at 6:43 PM, David Joly <idjoly@gmail.com> wrote:
Ok, one more step closer (I thought closing the browser would be enough to restart galaxy, but obviously, I had to reboot the computer).
But now it says: ValueError: too many values to unpack
2013/2/13 Dannon Baker <dannon.baker@gmail.com> On Feb 13, 2013, at 6:16 PM, David Joly <idjoly@gmail.com> wrote:
Hi!
Ok, I know many people had the same issue, but I just can't figure what's going on. I'm quite new about using a local instance of Galaxy and I'm trying to figure how to install a tool from the tool shed. Reading the tutorial (Installing Galaxy tool shed repository tools into a local Galaxy instance) looked pretty simple, but maybe I missed something.
First, I modified the universe_wsgi.ini file by removing the "#" before the tool_config_file and tool_path lines.
This one step should really be all you need to do (any other files get created automatically with reasonable defaults if missing) as far as configuration goes. Did you restart your galaxy instance after editing universe_wsgi.ini?
-Dannon
This could be the problem, I just installed BioLinux 7 on my computer with Galaxy running out-of-the-box... However, it looks like they changed a few things, there is no .hg file and no galaxy-dist folder. Can I update outside of mercurial? 2013/2/13 Dannon Baker <dannon.baker@gmail.com>
How old is the galaxy you're running? To use the main toolshed you'll need to use a galaxy-dist release from December or later. After this point in time the interface was standardized and is backwards compatible.
To update, you should be able to simply navigate to your galaxy-dist directory, 'hg pull -u', and you'll be off and running.
Also, since this deals with a local install, please do keep replies on the 'galaxy-dev' list that I transitioned this thread to instead of galaxy-user.
Thanks!
-Dannon
On Feb 13, 2013, at 6:43 PM, David Joly <idjoly@gmail.com> wrote:
Ok, one more step closer (I thought closing the browser would be enough to restart galaxy, but obviously, I had to reboot the computer).
But now it says: ValueError: too many values to unpack
2013/2/13 Dannon Baker <dannon.baker@gmail.com> On Feb 13, 2013, at 6:16 PM, David Joly <idjoly@gmail.com> wrote:
Hi!
Ok, I know many people had the same issue, but I just can't figure what's going on. I'm quite new about using a local instance of Galaxy and I'm trying to figure how to install a tool from the tool shed. Reading the tutorial (Installing Galaxy tool shed repository tools into a local Galaxy instance) looked pretty simple, but maybe I missed something.
First, I modified the universe_wsgi.ini file by removing the "#" before the tool_config_file and tool_path lines.
This one step should really be all you need to do (any other files get created automatically with reasonable defaults if missing) as far as configuration goes. Did you restart your galaxy instance after editing universe_wsgi.ini?
-Dannon
I still haven't heard back from the Bio-Linux guys regarding how to update Galaxy within Bio-Linux... In the meantime, I tried to play with the "Manage data libraries", in order to import large datasets. I modified the "library_import_dir" line in the universe_wsgi.ini. The first thing I can say is that when you make a mistake in the path (e.g. "../../directory" instead of "../../../directory"), Galaxy won't start at all! Anyway, even now that I figured that out, "This dataset is uploading" stays forever. As a test, I tried to upload small dataset using the usual way ("Get Data"), and here too "Dataset is uploading" stays forever. If I revert the "library_import_dir" to normal, I can upload via "Get Data". Is this also an issue related to the Galaxy version I'm using? Or is the Galaxy in Bio-Linux screwed up? Many thanks, DJ 2013/2/13 David Joly <idjoly@gmail.com>
This could be the problem, I just installed BioLinux 7 on my computer with Galaxy running out-of-the-box...
However, it looks like they changed a few things, there is no .hg file and no galaxy-dist folder. Can I update outside of mercurial?
2013/2/13 Dannon Baker <dannon.baker@gmail.com>
How old is the galaxy you're running? To use the main toolshed you'll need to use a galaxy-dist release from December or later. After this point in time the interface was standardized and is backwards compatible.
To update, you should be able to simply navigate to your galaxy-dist directory, 'hg pull -u', and you'll be off and running.
Also, since this deals with a local install, please do keep replies on the 'galaxy-dev' list that I transitioned this thread to instead of galaxy-user.
Thanks!
-Dannon
On Feb 13, 2013, at 6:43 PM, David Joly <idjoly@gmail.com> wrote:
Ok, one more step closer (I thought closing the browser would be enough to restart galaxy, but obviously, I had to reboot the computer).
But now it says: ValueError: too many values to unpack
2013/2/13 Dannon Baker <dannon.baker@gmail.com> On Feb 13, 2013, at 6:16 PM, David Joly <idjoly@gmail.com> wrote:
Hi!
Ok, I know many people had the same issue, but I just can't figure what's going on. I'm quite new about using a local instance of Galaxy and I'm trying to figure how to install a tool from the tool shed. Reading the tutorial (Installing Galaxy tool shed repository tools into a local Galaxy instance) looked pretty simple, but maybe I missed something.
First, I modified the universe_wsgi.ini file by removing the "#" before the tool_config_file and tool_path lines.
This one step should really be all you need to do (any other files get created automatically with reasonable defaults if missing) as far as configuration goes. Did you restart your galaxy instance after editing universe_wsgi.ini?
-Dannon
It's really hard to say what's going on with those issues without more information about the particular version of galaxy (which unfortunately we'd get from `hg tip`, which won't work on your bio linux install) or proxy configuration, if any. I'm also not sure what the appropriate bio linux update procedure is or how much customization they've done to galaxy to make all the tools work in that environment, but what I'd personally try would be to just clone a fresh galaxy (http://wiki.galaxyproject.org/Admin/Get%20Galaxy) and migrate your configuration files, etc. if you find that it works. Once you have an actual mercurial repository updates are trivial (just the `hg pull -u` that you already tried). -Dannon On Thu, Feb 14, 2013 at 2:08 PM, David Joly <idjoly@gmail.com> wrote:
I still haven't heard back from the Bio-Linux guys regarding how to update Galaxy within Bio-Linux...
In the meantime, I tried to play with the "Manage data libraries", in order to import large datasets. I modified the "library_import_dir" line in the universe_wsgi.ini. The first thing I can say is that when you make a mistake in the path (e.g. "../../directory" instead of "../../../directory"), Galaxy won't start at all! Anyway, even now that I figured that out, "This dataset is uploading" stays forever. As a test, I tried to upload small dataset using the usual way ("Get Data"), and here too "Dataset is uploading" stays forever. If I revert the "library_import_dir" to normal, I can upload via "Get Data".
Is this also an issue related to the Galaxy version I'm using? Or is the Galaxy in Bio-Linux screwed up?
Many thanks,
DJ
2013/2/13 David Joly <idjoly@gmail.com>
This could be the problem, I just installed BioLinux 7 on my computer with Galaxy running out-of-the-box...
However, it looks like they changed a few things, there is no .hg file and no galaxy-dist folder. Can I update outside of mercurial?
2013/2/13 Dannon Baker <dannon.baker@gmail.com>
How old is the galaxy you're running? To use the main toolshed you'll need to use a galaxy-dist release from December or later. After this point in time the interface was standardized and is backwards compatible.
To update, you should be able to simply navigate to your galaxy-dist directory, 'hg pull -u', and you'll be off and running.
Also, since this deals with a local install, please do keep replies on the 'galaxy-dev' list that I transitioned this thread to instead of galaxy-user.
Thanks!
-Dannon
On Feb 13, 2013, at 6:43 PM, David Joly <idjoly@gmail.com> wrote:
Ok, one more step closer (I thought closing the browser would be enough to restart galaxy, but obviously, I had to reboot the computer).
But now it says: ValueError: too many values to unpack
2013/2/13 Dannon Baker <dannon.baker@gmail.com> On Feb 13, 2013, at 6:16 PM, David Joly <idjoly@gmail.com> wrote:
Hi!
Ok, I know many people had the same issue, but I just can't figure what's going on. I'm quite new about using a local instance of Galaxy and I'm trying to figure how to install a tool from the tool shed. Reading the tutorial (Installing Galaxy tool shed repository tools into a local Galaxy instance) looked pretty simple, but maybe I missed something.
First, I modified the universe_wsgi.ini file by removing the "#" before the tool_config_file and tool_path lines.
This one step should really be all you need to do (any other files get created automatically with reasonable defaults if missing) as far as configuration goes. Did you restart your galaxy instance after editing universe_wsgi.ini?
-Dannon
It's really hard to say what's going on with those issues without more information about the particular version of galaxy (which unfortunately we'd get from `hg tip`, which won't work on your bio linux install) or proxy configuration, if any. I'm also not sure what the appropriate bio linux update procedure is or how much customization they've done to galaxy to make all the tools work in that environment, but what I'd personally try would be to just clone a fresh galaxy (http://wiki.galaxyproject.org/Admin/Get%20Galaxy) and migrate your configuration files, etc. if you find that it works. Once you have an actual mercurial repository updates are trivial (just the `hg pull -u` that you already tried). Let me know how this goes! -Dannon On Thu, Feb 14, 2013 at 2:08 PM, David Joly <idjoly@gmail.com> wrote:
I still haven't heard back from the Bio-Linux guys regarding how to update Galaxy within Bio-Linux...
In the meantime, I tried to play with the "Manage data libraries", in order to import large datasets. I modified the "library_import_dir" line in the universe_wsgi.ini. The first thing I can say is that when you make a mistake in the path (e.g. "../../directory" instead of "../../../directory"), Galaxy won't start at all! Anyway, even now that I figured that out, "This dataset is uploading" stays forever. As a test, I tried to upload small dataset using the usual way ("Get Data"), and here too "Dataset is uploading" stays forever. If I revert the "library_import_dir" to normal, I can upload via "Get Data".
Is this also an issue related to the Galaxy version I'm using? Or is the Galaxy in Bio-Linux screwed up?
Many thanks,
DJ
2013/2/13 David Joly <idjoly@gmail.com>
This could be the problem, I just installed BioLinux 7 on my computer with Galaxy running out-of-the-box...
However, it looks like they changed a few things, there is no .hg file and no galaxy-dist folder. Can I update outside of mercurial?
2013/2/13 Dannon Baker <dannon.baker@gmail.com>
How old is the galaxy you're running? To use the main toolshed you'll need to use a galaxy-dist release from December or later. After this point in time the interface was standardized and is backwards compatible.
To update, you should be able to simply navigate to your galaxy-dist directory, 'hg pull -u', and you'll be off and running.
Also, since this deals with a local install, please do keep replies on the 'galaxy-dev' list that I transitioned this thread to instead of galaxy-user.
Thanks!
-Dannon
On Feb 13, 2013, at 6:43 PM, David Joly <idjoly@gmail.com> wrote:
Ok, one more step closer (I thought closing the browser would be enough to restart galaxy, but obviously, I had to reboot the computer).
But now it says: ValueError: too many values to unpack
2013/2/13 Dannon Baker <dannon.baker@gmail.com> On Feb 13, 2013, at 6:16 PM, David Joly <idjoly@gmail.com> wrote:
Hi!
Ok, I know many people had the same issue, but I just can't figure what's going on. I'm quite new about using a local instance of Galaxy and I'm trying to figure how to install a tool from the tool shed. Reading the tutorial (Installing Galaxy tool shed repository tools into a local Galaxy instance) looked pretty simple, but maybe I missed something.
First, I modified the universe_wsgi.ini file by removing the "#" before the tool_config_file and tool_path lines.
This one step should really be all you need to do (any other files get created automatically with reasonable defaults if missing) as far as configuration goes. Did you restart your galaxy instance after editing universe_wsgi.ini?
-Dannon
participants (2)
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Dannon Baker -
David Joly