enable emboss tools
Hi, I'm trying to enable all the emboss tools on a local galaxy install. I found this tidbit (below) which I thought might help, but when I look at the tool_conf.xml, I don't see a list of emboss tools to uncomment. What should I try next? Kelly Vincent kpvincent at bx.psu.edu Fri Jan 14 11:26:37 EST 2011 Previous message: [galaxy-dev] Restricted user builds Next message: [galaxy-dev] API connection error Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Rob, When you start the Galaxy server, it looks in tool_conf.xml for which tools to load. Note that functional tests use tool_conf.xml.sample, and we leave the EMBOSS tools commented out in that file, so your tool_conf.xml file will still have them commented out if you haven't changed that. Uncomment the relevant lines and the EMBOSS tools should show up. After making changes to tool_conf.xml, you'll have to restart the server.
Hi Paul, It seems that you probably did not use the Emboss tools in your local Galaxy instance before (maybe you have a new instance). If this is the case, you can install the emboss_datatypes repository and the emboss_5 repository from the main Galaxy tool shed using the Admin UI features on your local galaxy instance. See the following sections of the tool shed wiki for details. http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_... http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_... Greg Von Kuster On Sep 13, 2012, at 4:46 PM, Paul Tanger wrote:
Hi,
I'm trying to enable all the emboss tools on a local galaxy install. I found this tidbit (below) which I thought might help, but when I look at the tool_conf.xml, I don't see a list of emboss tools to uncomment. What should I try next?
Kelly Vincent kpvincent at bx.psu.edu Fri Jan 14 11:26:37 EST 2011 Previous message: [galaxy-dev] Restricted user builds Next message: [galaxy-dev] API connection error Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Rob,
When you start the Galaxy server, it looks in tool_conf.xml for which tools to load. Note that functional tests use tool_conf.xml.sample, and we leave the EMBOSS tools commented out in that file, so your tool_conf.xml file will still have them commented out if you haven't changed that. Uncomment the relevant lines and the EMBOSS tools should show up. After making changes to tool_conf.xml, you'll have to restart the server. ___________________________________________________________ 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:
Hmm, ok this tool shed is all new to me. I followed the instructions until when I click on the "preview and install", I get this error: Not Found The resource could not be found. No action for /admin_toolshed/prepare_for_install On Thu, Sep 13, 2012 at 2:51 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Paul,
It seems that you probably did not use the Emboss tools in your local Galaxy instance before (maybe you have a new instance). If this is the case, you can install the emboss_datatypes repository and the emboss_5 repository from the main Galaxy tool shed using the Admin UI features on your local galaxy instance. See the following sections of the tool shed wiki for details.
http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_...
http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_...
Greg Von Kuster
On Sep 13, 2012, at 4:46 PM, Paul Tanger wrote:
Hi,
I'm trying to enable all the emboss tools on a local galaxy install. I found this tidbit (below) which I thought might help, but when I look at the tool_conf.xml, I don't see a list of emboss tools to uncomment. What should I try next?
Kelly Vincent kpvincent at bx.psu.edu Fri Jan 14 11:26:37 EST 2011 Previous message: [galaxy-dev] Restricted user builds Next message: [galaxy-dev] API connection error Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Rob,
When you start the Galaxy server, it looks in tool_conf.xml for which tools to load. Note that functional tests use tool_conf.xml.sample, and we leave the EMBOSS tools commented out in that file, so your tool_conf.xml file will still have them commented out if you haven't changed that. Uncomment the relevant lines and the EMBOSS tools should show up. After making changes to tool_conf.xml, you'll have to restart the server. ___________________________________________________________ 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:
Hi Paul, You have to be running the latest Galaxy dist release from https://bitbucket.org/galaxy/galaxy-dist in your local Galaxy instance. Your repository tip should be e6444e7a1685. Greg Von Kuster On Sep 13, 2012, at 5:24 PM, Paul Tanger wrote:
Hmm, ok this tool shed is all new to me. I followed the instructions until when I click on the "preview and install", I get this error:
Not Found
The resource could not be found. No action for /admin_toolshed/prepare_for_install
On Thu, Sep 13, 2012 at 2:51 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Paul,
It seems that you probably did not use the Emboss tools in your local Galaxy instance before (maybe you have a new instance). If this is the case, you can install the emboss_datatypes repository and the emboss_5 repository from the main Galaxy tool shed using the Admin UI features on your local galaxy instance. See the following sections of the tool shed wiki for details.
http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_...
http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_...
Greg Von Kuster
On Sep 13, 2012, at 4:46 PM, Paul Tanger wrote:
Hi,
I'm trying to enable all the emboss tools on a local galaxy install. I found this tidbit (below) which I thought might help, but when I look at the tool_conf.xml, I don't see a list of emboss tools to uncomment. What should I try next?
Kelly Vincent kpvincent at bx.psu.edu Fri Jan 14 11:26:37 EST 2011 Previous message: [galaxy-dev] Restricted user builds Next message: [galaxy-dev] API connection error Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Rob,
When you start the Galaxy server, it looks in tool_conf.xml for which tools to load. Note that functional tests use tool_conf.xml.sample, and we leave the EMBOSS tools commented out in that file, so your tool_conf.xml file will still have them commented out if you haven't changed that. Uncomment the relevant lines and the EMBOSS tools should show up. After making changes to tool_conf.xml, you'll have to restart the server. ___________________________________________________________ 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:
Thanks for your help with this. So I updated to the latest version, but didn't read the instructions about creating a tools directory and so I have repositories stuck in limbo, like described here: ------------------------------------------------------------------------------------------------------------- Re: [galaxy-dev] Can't get automatic toolshed installation to work.... Greg Von Kuster Fri, 03 Aug 2012 17:58:58 -0700 To get the repositories out of the limbo state, you'll have to get into your database and run the following sql command. Doing this will allow you to install those repositories that were in limbo. After they are installed, you can uninstall them if you want to. The case on the Strings is necessary. update tool_shed_repository set status = 'New' where status = 'Cloning'; It was great to talk with you at the conference as well! Greg http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg06437.html ------------------------------------------------------------------------------------------------------------- I'm just using the sqlite that came with the galaxy-dist, so I don't know how to enter that sql command? On Thu, Sep 13, 2012 at 3:58 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Paul,
You have to be running the latest Galaxy dist release from https://bitbucket.org/galaxy/galaxy-dist in your local Galaxy instance. Your repository tip should be e6444e7a1685.
Greg Von Kuster
On Sep 13, 2012, at 5:24 PM, Paul Tanger wrote:
Hmm, ok this tool shed is all new to me. I followed the instructions until when I click on the "preview and install", I get this error:
Not Found
The resource could not be found. No action for /admin_toolshed/prepare_for_install
On Thu, Sep 13, 2012 at 2:51 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Paul,
It seems that you probably did not use the Emboss tools in your local Galaxy instance before (maybe you have a new instance). If this is the case, you can install the emboss_datatypes repository and the emboss_5 repository from the main Galaxy tool shed using the Admin UI features on your local galaxy instance. See the following sections of the tool shed wiki for details.
http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_...
http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_...
Greg Von Kuster
On Sep 13, 2012, at 4:46 PM, Paul Tanger wrote:
Hi,
I'm trying to enable all the emboss tools on a local galaxy install.
I found this tidbit (below) which I thought might help, but when I
look at the tool_conf.xml, I don't see a list of emboss tools to
uncomment.
What should I try next?
Kelly Vincent kpvincent at bx.psu.edu
Fri Jan 14 11:26:37 EST 2011
Previous message: [galaxy-dev] Restricted user builds
Next message: [galaxy-dev] API connection error
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
Rob,
When you start the Galaxy server, it looks in tool_conf.xml for which
tools to load. Note that functional tests use tool_conf.xml.sample,
and we leave the EMBOSS tools commented out in that file, so your
tool_conf.xml file will still have them commented out if you haven't
changed that. Uncomment the relevant lines and the EMBOSS tools should
show up. After making changes to tool_conf.xml, you'll have to restart
the server.
___________________________________________________________
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:
Hi Paul, You should be able to get things working using the same sql command in the email below. This process will be a new UI feature in the next Galaxy release. Greg Von Kuster On Sep 13, 2012, at 6:15 PM, Paul Tanger wrote:
Thanks for your help with this. So I updated to the latest version, but didn't read the instructions about creating a tools directory and so I have repositories stuck in limbo, like described here: ------------------------------------------------------------------------------------------------------------- Re: [galaxy-dev] Can't get automatic toolshed installation to work.... Greg Von Kuster Fri, 03 Aug 2012 17:58:58 -0700
To get the repositories out of the limbo state, you'll have to get into your database and run the following sql command. Doing this will allow you to install those repositories that were in limbo. After they are installed, you can uninstall them if you want to. The case on the Strings is necessary.
update tool_shed_repository set status = 'New' where status = 'Cloning';
It was great to talk with you at the conference as well!
Greg http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg06437.html -------------------------------------------------------------------------------------------------------------
I'm just using the sqlite that came with the galaxy-dist, so I don't know how to enter that sql command?
On Thu, Sep 13, 2012 at 3:58 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Paul,
You have to be running the latest Galaxy dist release from https://bitbucket.org/galaxy/galaxy-dist in your local Galaxy instance. Your repository tip should be e6444e7a1685.
Greg Von Kuster
On Sep 13, 2012, at 5:24 PM, Paul Tanger wrote:
Hmm, ok this tool shed is all new to me. I followed the instructions until when I click on the "preview and install", I get this error:
Not Found
The resource could not be found. No action for /admin_toolshed/prepare_for_install
On Thu, Sep 13, 2012 at 2:51 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Paul,
It seems that you probably did not use the Emboss tools in your local Galaxy instance before (maybe you have a new instance). If this is the case, you can install the emboss_datatypes repository and the emboss_5 repository from the main Galaxy tool shed using the Admin UI features on your local galaxy instance. See the following sections of the tool shed wiki for details.
http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_...
http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_...
Greg Von Kuster
On Sep 13, 2012, at 4:46 PM, Paul Tanger wrote:
Hi,
I'm trying to enable all the emboss tools on a local galaxy install.
I found this tidbit (below) which I thought might help, but when I
look at the tool_conf.xml, I don't see a list of emboss tools to
uncomment.
What should I try next?
Kelly Vincent kpvincent at bx.psu.edu
Fri Jan 14 11:26:37 EST 2011
Previous message: [galaxy-dev] Restricted user builds
Next message: [galaxy-dev] API connection error
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
Rob,
When you start the Galaxy server, it looks in tool_conf.xml for which
tools to load. Note that functional tests use tool_conf.xml.sample,
and we leave the EMBOSS tools commented out in that file, so your
tool_conf.xml file will still have them commented out if you haven't
changed that. Uncomment the relevant lines and the EMBOSS tools should
show up. After making changes to tool_conf.xml, you'll have to restart
the server.
___________________________________________________________
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:
___________________________________________________________ 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:
Ok I just gave up and did a fresh install and it seems to work. Thanks for your help. On Thu, Sep 13, 2012 at 7:17 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Paul,
You should be able to get things working using the same sql command in the email below. This process will be a new UI feature in the next Galaxy release.
Greg Von Kuster
On Sep 13, 2012, at 6:15 PM, Paul Tanger wrote:
Thanks for your help with this. So I updated to the latest version, but didn't read the instructions about creating a tools directory and so I have repositories stuck in limbo, like described here:
-------------------------------------------------------------------------------------------------------------
Re: [galaxy-dev] Can't get automatic toolshed installation to work.... Greg Von Kuster Fri, 03 Aug 2012 17:58:58 -0700
To get the repositories out of the limbo state, you'll have to get into your database and run the following sql command. Doing this will allow you to install those repositories that were in limbo. After they are installed, you can uninstall them if you want to. The case on the Strings is necessary.
update tool_shed_repository set status = 'New' where status = 'Cloning';
It was great to talk with you at the conference as well!
Greg http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg06437.html
-------------------------------------------------------------------------------------------------------------
I'm just using the sqlite that came with the galaxy-dist, so I don't know how to enter that sql command?
On Thu, Sep 13, 2012 at 3:58 PM, Greg Von Kuster <greg@bx.psu.edu>
wrote:
Hi Paul,
You have to be running the latest Galaxy dist release from https://bitbucket.org/galaxy/galaxy-dist in your local Galaxy instance. Your repository tip should be e6444e7a1685.
Greg Von Kuster
On Sep 13, 2012, at 5:24 PM, Paul Tanger wrote:
Hmm, ok this tool shed is all new to me. I followed the instructions until when I click on the "preview and install", I get this error:
Not Found
The resource could not be found. No action for /admin_toolshed/prepare_for_install
On Thu, Sep 13, 2012 at 2:51 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Paul,
It seems that you probably did not use the Emboss tools in your local Galaxy instance before (maybe you have a new instance). If this is the case, you can install the emboss_datatypes repository and the emboss_5 repository from the main Galaxy tool shed using the Admin UI features on your local galaxy instance. See the following sections of the tool shed wiki for details.
http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_...
http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_...
Greg Von Kuster
On Sep 13, 2012, at 4:46 PM, Paul Tanger wrote:
Hi,
I'm trying to enable all the emboss tools on a local galaxy install.
I found this tidbit (below) which I thought might help, but when I
look at the tool_conf.xml, I don't see a list of emboss tools to
uncomment.
What should I try next?
Kelly Vincent kpvincent at bx.psu.edu
Fri Jan 14 11:26:37 EST 2011
Previous message: [galaxy-dev] Restricted user builds
Next message: [galaxy-dev] API connection error
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
Rob,
When you start the Galaxy server, it looks in tool_conf.xml for which
tools to load. Note that functional tests use tool_conf.xml.sample,
and we leave the EMBOSS tools commented out in that file, so your
tool_conf.xml file will still have them commented out if you haven't
changed that. Uncomment the relevant lines and the EMBOSS tools should
show up. After making changes to tool_conf.xml, you'll have to restart
the server.
___________________________________________________________
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:
___________________________________________________________ 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:
Hi Paul, the EMBOSS Tools are located in the http://toolshed.g2.bx.psu.edu/. You need to install them from there. http://wiki.g2.bx.psu.edu/Tool% 20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance Hope that helps! Bjoern
Hi,
I'm trying to enable all the emboss tools on a local galaxy install. I found this tidbit (below) which I thought might help, but when I look at the tool_conf.xml, I don't see a list of emboss tools to uncomment. What should I try next?
Kelly Vincent kpvincent at bx.psu.edu Fri Jan 14 11:26:37 EST 2011 Previous message: [galaxy-dev] Restricted user builds Next message: [galaxy-dev] API connection error Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Rob,
When you start the Galaxy server, it looks in tool_conf.xml for which tools to load. Note that functional tests use tool_conf.xml.sample, and we leave the EMBOSS tools commented out in that file, so your tool_conf.xml file will still have them commented out if you haven't changed that. Uncomment the relevant lines and the EMBOSS tools should show up. After making changes to tool_conf.xml, you'll have to restart the server. ___________________________________________________________ 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:
participants (3)
-
Björn Grüning -
Greg Von Kuster -
Paul Tanger