Hi,
We've been running into an issue when attempting to create a new toolshed tool. We have the toolshed and the main galaxy web app setup and running, but updating our tool to the latest version always fails.
When clicking "Get updates" on our installed tool we find that the initial request is sent fine to the community application, but the reply is missing a slash after the galaxy url. This causes the request to fail.
Our solution to this problem was to modify lib/galaxy/webapps/community/controllers/repository.py on line 795 to include a slash after the galaxy url.
After we did this though we encountered another problem .. this time in lib/galaxy/web/controllers/admin_toolshed.py . In this case there is a named parameter to a method but the name of the parameter does not match the method definition. The problem was on 688 where "name = name" should read "repository_name=name".
After making these changes the get updates function seems to work fine.
Hope this helps. Ira
Hello Ira,
Thanks for reporting this - there are several similar issues that I've corrected in my next change set, which will be available today. This change set will introduce tool versioning for Galaxy tools, whether they are installed from a tool shed, or are available with the distribution. This will affect the tool shed as well as repositories installed from tool sheds that contain tools. This versioning feature will provide a chain of ancestor tool versions and descendant tool versions for any tool instance.
It would be great if you and others that have set up local Galaxy tool sheds can test this out. I will get fixes for issues (if any exist) as fast as possible. My hope is that this will be the last major feature introduced until we get everything stabilized a bit more between the tool shed and Galaxy.
Thanks!
Greg Von Kuster
On Feb 2, 2012, at 8:40 PM, Ira Cooke wrote:
Hi,
We've been running into an issue when attempting to create a new toolshed tool. We have the toolshed and the main galaxy web app setup and running, but updating our tool to the latest version always fails.
When clicking "Get updates" on our installed tool we find that the initial request is sent fine to the community application, but the reply is missing a slash after the galaxy url. This causes the request to fail.
Our solution to this problem was to modify lib/galaxy/webapps/community/controllers/repository.py on line 795 to include a slash after the galaxy url.
After we did this though we encountered another problem .. this time in lib/galaxy/web/controllers/admin_toolshed.py . In this case there is a named parameter to a method but the name of the parameter does not match the method definition. The problem was on 688 where "name = name" should read "repository_name=name".
After making these changes the get updates function seems to work fine.
Hope this helps. Ira
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Things should be working in change set 6667:86d9c5ddbafc, which is now available from the Galaxy central repository. Please let me know if you bump into any problems.
To use the latest features related to tool versioning, update your local tool shed as well as your local Galaxy instance ( both require updating the database schema ). In your local tool shed, reset all metadata for each repository using the Repository Actions pop-up for each repository. Since you already have repositories in your tool shed, you'll need to do this once for each existing repository. Any updates to the repository will automatically do this. New repositories created from here on will handle this automatically as well.
Then, in your local Galaxy instance, set tool versions for each installed tool shed repository using the repository's pop-up.
On Feb 3, 2012, at 11:07 AM, Greg Von Kuster wrote:
Hello Ira,
Thanks for reporting this - there are several similar issues that I've corrected in my next change set, which will be available today. This change set will introduce tool versioning for Galaxy tools, whether they are installed from a tool shed, or are available with the distribution. This will affect the tool shed as well as repositories installed from tool sheds that contain tools. This versioning feature will provide a chain of ancestor tool versions and descendant tool versions for any tool instance.
It would be great if you and others that have set up local Galaxy tool sheds can test this out. I will get fixes for issues (if any exist) as fast as possible. My hope is that this will be the last major feature introduced until we get everything stabilized a bit more between the tool shed and Galaxy.
Thanks!
Greg Von Kuster
On Feb 2, 2012, at 8:40 PM, Ira Cooke wrote:
Hi,
We've been running into an issue when attempting to create a new toolshed tool. We have the toolshed and the main galaxy web app setup and running, but updating our tool to the latest version always fails.
When clicking "Get updates" on our installed tool we find that the initial request is sent fine to the community application, but the reply is missing a slash after the galaxy url. This causes the request to fail.
Our solution to this problem was to modify lib/galaxy/webapps/community/controllers/repository.py on line 795 to include a slash after the galaxy url.
After we did this though we encountered another problem .. this time in lib/galaxy/web/controllers/admin_toolshed.py . In this case there is a named parameter to a method but the name of the parameter does not match the method definition. The problem was on 688 where "name = name" should read "repository_name=name".
After making these changes the get updates function seems to work fine.
Hope this helps. Ira
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Hi Greg,
Ok I pulled the latest changeset and updated the database. No probs. Now I am able to get tools from the galaxy main toolshed. Tested the table2html tool to be sure about no additional dependencies. It came up nicely with the section list I can install a tool to; but... I created an EMPTY section in the tool_conf.xml menu where I want the toolshed tools to go to at the moment. To keep it maintainable for now at testing. But It does not show up in the bullet list of sections to install to (as these sections also do not show up in the menu itself until they cotain a valid tool xml). Other custom sections are there. Part of the tool_conf.xml </section> <label text="External tools" id="externaltools" /> <section name="ToolShed auto tools" id="toolshedtools"> </section>
I added an empty <tool file="" /> line in the section and still not there. Adding a valid tool lets it show up in the bullit list as it now also shows up in the left panel.. (as expected). Another test on the EMPTY section when I tried adding the tool providing THE SAME section name as custom in the field as a new tool panel section... it just adds it to the end of the section lists in the left. But it does work. It also remains working when I enable my own section menu again by adding another tool to the xml first. The section with the same name shows up on two places in the section list when adding tools from toolshed (as expected). Probably due to the different section id. There might be a possible problem when the id turns out the same as an already used one?
I manually altered the shed_tool_conf.xml to match my section name and id and everything is ok.
Maybe something to look into? Just a minor issue I think.
Keep up the good work! Alex
Van: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Greg Von Kuster Verzonden: vrijdag 3 februari 2012 22:16 Aan: Ira Cooke CC: galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool
Things should be working in change set 6667:86d9c5ddbafc, which is now available from the Galaxy central repository. Please let me know if you bump into any problems.
To use the latest features related to tool versioning, update your local tool shed as well as your local Galaxy instance ( both require updating the database schema ). In your local tool shed, reset all metadata for each repository using the Repository Actions pop-up for each repository. Since you already have repositories in your tool shed, you'll need to do this once for each existing repository. Any updates to the repository will automatically do this. New repositories created from here on will handle this automatically as well.
Then, in your local Galaxy instance, set tool versions for each installed tool shed repository using the repository's pop-up.
On Feb 3, 2012, at 11:07 AM, Greg Von Kuster wrote:
Hello Ira,
Thanks for reporting this - there are several similar issues that I've corrected in my next change set, which will be available today. This change set will introduce tool versioning for Galaxy tools, whether they are installed from a tool shed, or are available with the distribution. This will affect the tool shed as well as repositories installed from tool sheds that contain tools. This versioning feature will provide a chain of ancestor tool versions and descendant tool versions for any tool instance.
It would be great if you and others that have set up local Galaxy tool sheds can test this out. I will get fixes for issues (if any exist) as fast as possible. My hope is that this will be the last major feature introduced until we get everything stabilized a bit more between the tool shed and Galaxy.
Thanks!
Greg Von Kuster
On Feb 2, 2012, at 8:40 PM, Ira Cooke wrote:
Hi,
We've been running into an issue when attempting to create a new toolshed tool. We have the toolshed and the main galaxy web app setup and running, but updating our tool to the latest version always fails.
When clicking "Get updates" on our installed tool we find that the initial request is sent fine to the community application, but the reply is missing a slash after the galaxy url. This causes the request to fail.
Our solution to this problem was to modify lib/galaxy/webapps/community/controllers/repository.py on line 795 to include a slash after the galaxy url.
After we did this though we encountered another problem .. this time in lib/galaxy/web/controllers/admin_toolshed.py . In this case there is a named parameter to a method but the name of the parameter does not match the method definition. The problem was on 688 where "name = name" should read "repository_name=name".
After making these changes the get updates function seems to work fine.
Hope this helps. Ira
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edumailto:greg@bx.psu.edu
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edumailto:greg@bx.psu.edu
___________________________________________________________ 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:
PS: when I make the section empty again in the original tool_conf.xml it doesn't show up anymore in that section. :-( Actually the complete section is again invisible.
Van: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Bossers, Alex Verzonden: maandag 6 februari 2012 8:45 Aan: 'Greg Von Kuster'; Ira Cooke CC: galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool
Hi Greg,
Ok I pulled the latest changeset and updated the database. No probs. Now I am able to get tools from the galaxy main toolshed. Tested the table2html tool to be sure about no additional dependencies. It came up nicely with the section list I can install a tool to; but... I created an EMPTY section in the tool_conf.xml menu where I want the toolshed tools to go to at the moment. To keep it maintainable for now at testing. But It does not show up in the bullet list of sections to install to (as these sections also do not show up in the menu itself until they cotain a valid tool xml). Other custom sections are there. Part of the tool_conf.xml </section> <label text="External tools" id="externaltools" /> <section name="ToolShed auto tools" id="toolshedtools"> </section>
I added an empty <tool file="" /> line in the section and still not there. Adding a valid tool lets it show up in the bullit list as it now also shows up in the left panel.. (as expected). Another test on the EMPTY section when I tried adding the tool providing THE SAME section name as custom in the field as a new tool panel section... it just adds it to the end of the section lists in the left. But it does work. It also remains working when I enable my own section menu again by adding another tool to the xml first. The section with the same name shows up on two places in the section list when adding tools from toolshed (as expected). Probably due to the different section id. There might be a possible problem when the id turns out the same as an already used one?
I manually altered the shed_tool_conf.xml to match my section name and id and everything is ok.
Maybe something to look into? Just a minor issue I think.
Keep up the good work! Alex
Van: galaxy-dev-bounces@lists.bx.psu.edumailto:galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu]mailto:[mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Greg Von Kuster Verzonden: vrijdag 3 februari 2012 22:16 Aan: Ira Cooke CC: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool
Things should be working in change set 6667:86d9c5ddbafc, which is now available from the Galaxy central repository. Please let me know if you bump into any problems.
To use the latest features related to tool versioning, update your local tool shed as well as your local Galaxy instance ( both require updating the database schema ). In your local tool shed, reset all metadata for each repository using the Repository Actions pop-up for each repository. Since you already have repositories in your tool shed, you'll need to do this once for each existing repository. Any updates to the repository will automatically do this. New repositories created from here on will handle this automatically as well.
Then, in your local Galaxy instance, set tool versions for each installed tool shed repository using the repository's pop-up.
On Feb 3, 2012, at 11:07 AM, Greg Von Kuster wrote:
Hello Ira,
Thanks for reporting this - there are several similar issues that I've corrected in my next change set, which will be available today. This change set will introduce tool versioning for Galaxy tools, whether they are installed from a tool shed, or are available with the distribution. This will affect the tool shed as well as repositories installed from tool sheds that contain tools. This versioning feature will provide a chain of ancestor tool versions and descendant tool versions for any tool instance.
It would be great if you and others that have set up local Galaxy tool sheds can test this out. I will get fixes for issues (if any exist) as fast as possible. My hope is that this will be the last major feature introduced until we get everything stabilized a bit more between the tool shed and Galaxy.
Thanks!
Greg Von Kuster
On Feb 2, 2012, at 8:40 PM, Ira Cooke wrote:
Hi,
We've been running into an issue when attempting to create a new toolshed tool. We have the toolshed and the main galaxy web app setup and running, but updating our tool to the latest version always fails.
When clicking "Get updates" on our installed tool we find that the initial request is sent fine to the community application, but the reply is missing a slash after the galaxy url. This causes the request to fail.
Our solution to this problem was to modify lib/galaxy/webapps/community/controllers/repository.py on line 795 to include a slash after the galaxy url.
After we did this though we encountered another problem .. this time in lib/galaxy/web/controllers/admin_toolshed.py . In this case there is a named parameter to a method but the name of the parameter does not match the method definition. The problem was on 688 where "name = name" should read "repository_name=name".
After making these changes the get updates function seems to work fine.
Hope this helps. Ira
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edumailto:greg@bx.psu.edu
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edumailto:greg@bx.psu.edu
___________________________________________________________ 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:
Hello Alex,
Empty sections are not displayed in the Galaxy tool panel by design. However, can you clarify the behavior when installing a tool shed repository? Are you saying that empty sections cannot be selected for containing the tool shed repository tools because they are not displayed in the radio button selection list during installation time? If this is the case, then I'll take a look at this.
Thanks!
Greg
On Feb 6, 2012, at 3:29 AM, Bossers, Alex wrote:
PS: when I make the section empty again in the original tool_conf.xml it doesn’t show up anymore in that section. :-( Actually the complete section is again invisible.
Van: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Bossers, Alex Verzonden: maandag 6 februari 2012 8:45 Aan: 'Greg Von Kuster'; Ira Cooke CC: galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool
Hi Greg,
Ok I pulled the latest changeset and updated the database. No probs. Now I am able to get tools from the galaxy main toolshed. Tested the table2html tool to be sure about no additional dependencies. It came up nicely with the section list I can install a tool to; but... I created an EMPTY section in the tool_conf.xml menu where I want the toolshed tools to go to at the moment. To keep it maintainable for now at testing. But It does not show up in the bullet list of sections to install to (as these sections also do not show up in the menu itself until they cotain a valid tool xml). Other custom sections are there. Part of the tool_conf.xml
</section> <label text="External tools" id="externaltools" /> <section name="ToolShed auto tools" id="toolshedtools"> </section>
I added an empty <tool file=”” /> line in the section and still not there. Adding a valid tool lets it show up in the bullit list as it now also shows up in the left panel.. (as expected). Another test on the EMPTY section when I tried adding the tool providing THE SAME section name as custom in the field as a new tool panel section... it just adds it to the end of the section lists in the left. But it does work. It also remains working when I enable my own section menu again by adding another tool to the xml first. The section with the same name shows up on two places in the section list when adding tools from toolshed (as expected). Probably due to the different section id. There might be a possible problem when the id turns out the same as an already used one?
I manually altered the shed_tool_conf.xml to match my section name and id and everything is ok.
Maybe something to look into? Just a minor issue I think.
Keep up the good work! Alex
Van: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Greg Von Kuster Verzonden: vrijdag 3 februari 2012 22:16 Aan: Ira Cooke CC: galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool
Things should be working in change set 6667:86d9c5ddbafc, which is now available from the Galaxy central repository. Please let me know if you bump into any problems.
To use the latest features related to tool versioning, update your local tool shed as well as your local Galaxy instance ( both require updating the database schema ). In your local tool shed, reset all metadata for each repository using the Repository Actions pop-up for each repository. Since you already have repositories in your tool shed, you'll need to do this once for each existing repository. Any updates to the repository will automatically do this. New repositories created from here on will handle this automatically as well.
Then, in your local Galaxy instance, set tool versions for each installed tool shed repository using the repository's pop-up.
On Feb 3, 2012, at 11:07 AM, Greg Von Kuster wrote:
Hello Ira,
Thanks for reporting this - there are several similar issues that I've corrected in my next change set, which will be available today. This change set will introduce tool versioning for Galaxy tools, whether they are installed from a tool shed, or are available with the distribution. This will affect the tool shed as well as repositories installed from tool sheds that contain tools. This versioning feature will provide a chain of ancestor tool versions and descendant tool versions for any tool instance.
It would be great if you and others that have set up local Galaxy tool sheds can test this out. I will get fixes for issues (if any exist) as fast as possible. My hope is that this will be the last major feature introduced until we get everything stabilized a bit more between the tool shed and Galaxy.
Thanks!
Greg Von Kuster
On Feb 2, 2012, at 8:40 PM, Ira Cooke wrote:
Hi,
We've been running into an issue when attempting to create a new toolshed tool. We have the toolshed and the main galaxy web app setup and running, but updating our tool to the latest version always fails.
When clicking "Get updates" on our installed tool we find that the initial request is sent fine to the community application, but the reply is missing a slash after the galaxy url. This causes the request to fail.
Our solution to this problem was to modify lib/galaxy/webapps/community/controllers/repository.py on line 795 to include a slash after the galaxy url.
After we did this though we encountered another problem .. this time in lib/galaxy/web/controllers/admin_toolshed.py . In this case there is a named parameter to a method but the name of the parameter does not match the method definition. The problem was on 688 where "name = name" should read "repository_name=name".
After making these changes the get updates function seems to work fine.
Hope this helps. Ira
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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:
Greg, Exactly as you say. You cannot insert the repository tool when it's an empty section. Sorry for being unclear. Alex
Van: Greg Von Kuster [mailto:greg@bx.psu.edu] Verzonden: maandag 6 februari 2012 12:57 Aan: Bossers, Alex CC: Ira Cooke; galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool
Hello Alex,
Empty sections are not displayed in the Galaxy tool panel by design. However, can you clarify the behavior when installing a tool shed repository? Are you saying that empty sections cannot be selected for containing the tool shed repository tools because they are not displayed in the radio button selection list during installation time? If this is the case, then I'll take a look at this.
Thanks!
Greg
On Feb 6, 2012, at 3:29 AM, Bossers, Alex wrote:
PS: when I make the section empty again in the original tool_conf.xml it doesn't show up anymore in that section. :-( Actually the complete section is again invisible.
Van: galaxy-dev-bounces@lists.bx.psu.edumailto:galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu]mailto:[mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Bossers, Alex Verzonden: maandag 6 februari 2012 8:45 Aan: 'Greg Von Kuster'; Ira Cooke CC: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool
Hi Greg,
Ok I pulled the latest changeset and updated the database. No probs. Now I am able to get tools from the galaxy main toolshed. Tested the table2html tool to be sure about no additional dependencies. It came up nicely with the section list I can install a tool to; but... I created an EMPTY section in the tool_conf.xml menu where I want the toolshed tools to go to at the moment. To keep it maintainable for now at testing. But It does not show up in the bullet list of sections to install to (as these sections also do not show up in the menu itself until they cotain a valid tool xml). Other custom sections are there. Part of the tool_conf.xml </section> <label text="External tools" id="externaltools" /> <section name="ToolShed auto tools" id="toolshedtools"> </section>
I added an empty <tool file="" /> line in the section and still not there. Adding a valid tool lets it show up in the bullit list as it now also shows up in the left panel.. (as expected). Another test on the EMPTY section when I tried adding the tool providing THE SAME section name as custom in the field as a new tool panel section... it just adds it to the end of the section lists in the left. But it does work. It also remains working when I enable my own section menu again by adding another tool to the xml first. The section with the same name shows up on two places in the section list when adding tools from toolshed (as expected). Probably due to the different section id. There might be a possible problem when the id turns out the same as an already used one?
I manually altered the shed_tool_conf.xml to match my section name and id and everything is ok.
Maybe something to look into? Just a minor issue I think.
Keep up the good work! Alex
Van: galaxy-dev-bounces@lists.bx.psu.edumailto:galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu]mailto:[mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Greg Von Kuster Verzonden: vrijdag 3 februari 2012 22:16 Aan: Ira Cooke CC: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool
Things should be working in change set 6667:86d9c5ddbafc, which is now available from the Galaxy central repository. Please let me know if you bump into any problems.
To use the latest features related to tool versioning, update your local tool shed as well as your local Galaxy instance ( both require updating the database schema ). In your local tool shed, reset all metadata for each repository using the Repository Actions pop-up for each repository. Since you already have repositories in your tool shed, you'll need to do this once for each existing repository. Any updates to the repository will automatically do this. New repositories created from here on will handle this automatically as well.
Then, in your local Galaxy instance, set tool versions for each installed tool shed repository using the repository's pop-up.
On Feb 3, 2012, at 11:07 AM, Greg Von Kuster wrote:
Hello Ira,
Thanks for reporting this - there are several similar issues that I've corrected in my next change set, which will be available today. This change set will introduce tool versioning for Galaxy tools, whether they are installed from a tool shed, or are available with the distribution. This will affect the tool shed as well as repositories installed from tool sheds that contain tools. This versioning feature will provide a chain of ancestor tool versions and descendant tool versions for any tool instance.
It would be great if you and others that have set up local Galaxy tool sheds can test this out. I will get fixes for issues (if any exist) as fast as possible. My hope is that this will be the last major feature introduced until we get everything stabilized a bit more between the tool shed and Galaxy.
Thanks!
Greg Von Kuster
On Feb 2, 2012, at 8:40 PM, Ira Cooke wrote:
Hi,
We've been running into an issue when attempting to create a new toolshed tool. We have the toolshed and the main galaxy web app setup and running, but updating our tool to the latest version always fails.
When clicking "Get updates" on our installed tool we find that the initial request is sent fine to the community application, but the reply is missing a slash after the galaxy url. This causes the request to fail.
Our solution to this problem was to modify lib/galaxy/webapps/community/controllers/repository.py on line 795 to include a slash after the galaxy url.
After we did this though we encountered another problem .. this time in lib/galaxy/web/controllers/admin_toolshed.py . In this case there is a named parameter to a method but the name of the parameter does not match the method definition. The problem was on 688 where "name = name" should read "repository_name=name".
After making these changes the get updates function seems to work fine.
Hope this helps. Ira
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edumailto:greg@bx.psu.edu
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edumailto:greg@bx.psu.edu
___________________________________________________________ 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:
This problem should be fixed in change set 6672:e38a9eb21336, which is now available in our central repo. Thanks for reporting this, and let me know if you discover other issues.
Greg
On Feb 6, 2012, at 7:54 AM, Bossers, Alex wrote:
Greg, Exactly as you say. You cannot insert the repository tool when it’s an empty section. Sorry for being unclear. Alex
Van: Greg Von Kuster [mailto:greg@bx.psu.edu] Verzonden: maandag 6 februari 2012 12:57 Aan: Bossers, Alex CC: Ira Cooke; galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool
Hello Alex,
Empty sections are not displayed in the Galaxy tool panel by design. However, can you clarify the behavior when installing a tool shed repository? Are you saying that empty sections cannot be selected for containing the tool shed repository tools because they are not displayed in the radio button selection list during installation time? If this is the case, then I'll take a look at this.
Thanks!
Greg
On Feb 6, 2012, at 3:29 AM, Bossers, Alex wrote:
PS: when I make the section empty again in the original tool_conf.xml it doesn’t show up anymore in that section. :-( Actually the complete section is again invisible.
Van: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Bossers, Alex Verzonden: maandag 6 februari 2012 8:45 Aan: 'Greg Von Kuster'; Ira Cooke CC: galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool
Hi Greg,
Ok I pulled the latest changeset and updated the database. No probs. Now I am able to get tools from the galaxy main toolshed. Tested the table2html tool to be sure about no additional dependencies. It came up nicely with the section list I can install a tool to; but... I created an EMPTY section in the tool_conf.xml menu where I want the toolshed tools to go to at the moment. To keep it maintainable for now at testing. But It does not show up in the bullet list of sections to install to (as these sections also do not show up in the menu itself until they cotain a valid tool xml). Other custom sections are there. Part of the tool_conf.xml
</section> <label text="External tools" id="externaltools" /> <section name="ToolShed auto tools" id="toolshedtools"> </section>
I added an empty <tool file=”” /> line in the section and still not there. Adding a valid tool lets it show up in the bullit list as it now also shows up in the left panel.. (as expected). Another test on the EMPTY section when I tried adding the tool providing THE SAME section name as custom in the field as a new tool panel section... it just adds it to the end of the section lists in the left. But it does work. It also remains working when I enable my own section menu again by adding another tool to the xml first. The section with the same name shows up on two places in the section list when adding tools from toolshed (as expected). Probably due to the different section id. There might be a possible problem when the id turns out the same as an already used one?
I manually altered the shed_tool_conf.xml to match my section name and id and everything is ok.
Maybe something to look into? Just a minor issue I think.
Keep up the good work! Alex
Van: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Greg Von Kuster Verzonden: vrijdag 3 februari 2012 22:16 Aan: Ira Cooke CC: galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool
Things should be working in change set 6667:86d9c5ddbafc, which is now available from the Galaxy central repository. Please let me know if you bump into any problems.
To use the latest features related to tool versioning, update your local tool shed as well as your local Galaxy instance ( both require updating the database schema ). In your local tool shed, reset all metadata for each repository using the Repository Actions pop-up for each repository. Since you already have repositories in your tool shed, you'll need to do this once for each existing repository. Any updates to the repository will automatically do this. New repositories created from here on will handle this automatically as well.
Then, in your local Galaxy instance, set tool versions for each installed tool shed repository using the repository's pop-up.
On Feb 3, 2012, at 11:07 AM, Greg Von Kuster wrote:
Hello Ira,
Thanks for reporting this - there are several similar issues that I've corrected in my next change set, which will be available today. This change set will introduce tool versioning for Galaxy tools, whether they are installed from a tool shed, or are available with the distribution. This will affect the tool shed as well as repositories installed from tool sheds that contain tools. This versioning feature will provide a chain of ancestor tool versions and descendant tool versions for any tool instance.
It would be great if you and others that have set up local Galaxy tool sheds can test this out. I will get fixes for issues (if any exist) as fast as possible. My hope is that this will be the last major feature introduced until we get everything stabilized a bit more between the tool shed and Galaxy.
Thanks!
Greg Von Kuster
On Feb 2, 2012, at 8:40 PM, Ira Cooke wrote:
Hi,
We've been running into an issue when attempting to create a new toolshed tool. We have the toolshed and the main galaxy web app setup and running, but updating our tool to the latest version always fails.
When clicking "Get updates" on our installed tool we find that the initial request is sent fine to the community application, but the reply is missing a slash after the galaxy url. This causes the request to fail.
Our solution to this problem was to modify lib/galaxy/webapps/community/controllers/repository.py on line 795 to include a slash after the galaxy url.
After we did this though we encountered another problem .. this time in lib/galaxy/web/controllers/admin_toolshed.py . In this case there is a named parameter to a method but the name of the parameter does not match the method definition. The problem was on 688 where "name = name" should read "repository_name=name".
After making these changes the get updates function seems to work fine.
Hope this helps. Ira
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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:
Greg, I just removed the dummy entry from our normal tool_conf.xml and the previously installed tool from the tool shed now nicely shows up in the menu. Also when installing new tools from the toolshed the radio list nicely shows the empty section in the panel to install too section. Haven't tested it with an empty section AND an empty shed_tool_conf though....will try to later...when I figured out how to completely remove a tool from the system. Thanks for the quick fix! Alex
Van: Greg Von Kuster [mailto:greg@bx.psu.edu] Verzonden: maandag 6 februari 2012 16:21 Aan: Bossers, Alex CC: Ira Cooke; galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool
This problem should be fixed in change set 6672:e38a9eb21336, which is now available in our central repo. Thanks for reporting this, and let me know if you discover other issues.
Greg
On Feb 6, 2012, at 7:54 AM, Bossers, Alex wrote:
Greg, Exactly as you say. You cannot insert the repository tool when it's an empty section. Sorry for being unclear. Alex
Van: Greg Von Kuster [mailto:greg@bx.psu.edu]mailto:[mailto:greg@bx.psu.edu] Verzonden: maandag 6 februari 2012 12:57 Aan: Bossers, Alex CC: Ira Cooke; galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool
Hello Alex,
Empty sections are not displayed in the Galaxy tool panel by design. However, can you clarify the behavior when installing a tool shed repository? Are you saying that empty sections cannot be selected for containing the tool shed repository tools because they are not displayed in the radio button selection list during installation time? If this is the case, then I'll take a look at this.
Thanks!
Greg
On Feb 6, 2012, at 3:29 AM, Bossers, Alex wrote:
PS: when I make the section empty again in the original tool_conf.xml it doesn't show up anymore in that section. :-( Actually the complete section is again invisible.
Van: galaxy-dev-bounces@lists.bx.psu.edumailto:galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu]mailto:[mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Bossers, Alex Verzonden: maandag 6 februari 2012 8:45 Aan: 'Greg Von Kuster'; Ira Cooke CC: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool
Hi Greg,
Ok I pulled the latest changeset and updated the database. No probs. Now I am able to get tools from the galaxy main toolshed. Tested the table2html tool to be sure about no additional dependencies. It came up nicely with the section list I can install a tool to; but... I created an EMPTY section in the tool_conf.xml menu where I want the toolshed tools to go to at the moment. To keep it maintainable for now at testing. But It does not show up in the bullet list of sections to install to (as these sections also do not show up in the menu itself until they cotain a valid tool xml). Other custom sections are there. Part of the tool_conf.xml </section> <label text="External tools" id="externaltools" /> <section name="ToolShed auto tools" id="toolshedtools"> </section>
I added an empty <tool file="" /> line in the section and still not there. Adding a valid tool lets it show up in the bullit list as it now also shows up in the left panel.. (as expected). Another test on the EMPTY section when I tried adding the tool providing THE SAME section name as custom in the field as a new tool panel section... it just adds it to the end of the section lists in the left. But it does work. It also remains working when I enable my own section menu again by adding another tool to the xml first. The section with the same name shows up on two places in the section list when adding tools from toolshed (as expected). Probably due to the different section id. There might be a possible problem when the id turns out the same as an already used one?
I manually altered the shed_tool_conf.xml to match my section name and id and everything is ok.
Maybe something to look into? Just a minor issue I think.
Keep up the good work! Alex
Van: galaxy-dev-bounces@lists.bx.psu.edumailto:galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu]mailto:[mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Greg Von Kuster Verzonden: vrijdag 3 februari 2012 22:16 Aan: Ira Cooke CC: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool
Things should be working in change set 6667:86d9c5ddbafc, which is now available from the Galaxy central repository. Please let me know if you bump into any problems.
To use the latest features related to tool versioning, update your local tool shed as well as your local Galaxy instance ( both require updating the database schema ). In your local tool shed, reset all metadata for each repository using the Repository Actions pop-up for each repository. Since you already have repositories in your tool shed, you'll need to do this once for each existing repository. Any updates to the repository will automatically do this. New repositories created from here on will handle this automatically as well.
Then, in your local Galaxy instance, set tool versions for each installed tool shed repository using the repository's pop-up.
On Feb 3, 2012, at 11:07 AM, Greg Von Kuster wrote:
Hello Ira,
Thanks for reporting this - there are several similar issues that I've corrected in my next change set, which will be available today. This change set will introduce tool versioning for Galaxy tools, whether they are installed from a tool shed, or are available with the distribution. This will affect the tool shed as well as repositories installed from tool sheds that contain tools. This versioning feature will provide a chain of ancestor tool versions and descendant tool versions for any tool instance.
It would be great if you and others that have set up local Galaxy tool sheds can test this out. I will get fixes for issues (if any exist) as fast as possible. My hope is that this will be the last major feature introduced until we get everything stabilized a bit more between the tool shed and Galaxy.
Thanks!
Greg Von Kuster
On Feb 2, 2012, at 8:40 PM, Ira Cooke wrote:
Hi,
We've been running into an issue when attempting to create a new toolshed tool. We have the toolshed and the main galaxy web app setup and running, but updating our tool to the latest version always fails.
When clicking "Get updates" on our installed tool we find that the initial request is sent fine to the community application, but the reply is missing a slash after the galaxy url. This causes the request to fail.
Our solution to this problem was to modify lib/galaxy/webapps/community/controllers/repository.py on line 795 to include a slash after the galaxy url.
After we did this though we encountered another problem .. this time in lib/galaxy/web/controllers/admin_toolshed.py . In this case there is a named parameter to a method but the name of the parameter does not match the method definition. The problem was on 688 where "name = name" should read "repository_name=name".
After making these changes the get updates function seems to work fine.
Hope this helps. Ira
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edumailto:greg@bx.psu.edu
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edumailto:greg@bx.psu.edu
___________________________________________________________ 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:
Alex,
To completely remove an installed repository (and all contained tools) from you Galaxy instance, you should be using the Uninstall option from the pop-up menu for the installed tool shed repository. Make sure to check the checkbox.
For all of the details see the following section in the tool shed wiki.
http://wiki.g2.bx.psu.edu/Tool%20Shed#Deactivating_and_uninstalling_tool_she...
On Feb 7, 2012, at 2:08 AM, Bossers, Alex wrote:
Greg, I just removed the dummy entry from our normal tool_conf.xml and the previously installed tool from the tool shed now nicely shows up in the menu. Also when installing new tools from the toolshed the radio list nicely shows the empty section in the panel to install too section. Haven’t tested it with an empty section AND an empty shed_tool_conf though....will try to later...when I figured out how to completely remove a tool from the system. Thanks for the quick fix! Alex
Van: Greg Von Kuster [mailto:greg@bx.psu.edu] Verzonden: maandag 6 februari 2012 16:21 Aan: Bossers, Alex CC: Ira Cooke; galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool
This problem should be fixed in change set 6672:e38a9eb21336, which is now available in our central repo. Thanks for reporting this, and let me know if you discover other issues.
Greg
On Feb 6, 2012, at 7:54 AM, Bossers, Alex wrote:
Greg, Exactly as you say. You cannot insert the repository tool when it’s an empty section. Sorry for being unclear. Alex
Van: Greg Von Kuster [mailto:greg@bx.psu.edu] Verzonden: maandag 6 februari 2012 12:57 Aan: Bossers, Alex CC: Ira Cooke; galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool
Hello Alex,
Empty sections are not displayed in the Galaxy tool panel by design. However, can you clarify the behavior when installing a tool shed repository? Are you saying that empty sections cannot be selected for containing the tool shed repository tools because they are not displayed in the radio button selection list during installation time? If this is the case, then I'll take a look at this.
Thanks!
Greg
On Feb 6, 2012, at 3:29 AM, Bossers, Alex wrote:
PS: when I make the section empty again in the original tool_conf.xml it doesn’t show up anymore in that section. :-( Actually the complete section is again invisible.
Van: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Bossers, Alex Verzonden: maandag 6 februari 2012 8:45 Aan: 'Greg Von Kuster'; Ira Cooke CC: galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool
Hi Greg,
Ok I pulled the latest changeset and updated the database. No probs. Now I am able to get tools from the galaxy main toolshed. Tested the table2html tool to be sure about no additional dependencies. It came up nicely with the section list I can install a tool to; but... I created an EMPTY section in the tool_conf.xml menu where I want the toolshed tools to go to at the moment. To keep it maintainable for now at testing. But It does not show up in the bullet list of sections to install to (as these sections also do not show up in the menu itself until they cotain a valid tool xml). Other custom sections are there. Part of the tool_conf.xml
</section> <label text="External tools" id="externaltools" /> <section name="ToolShed auto tools" id="toolshedtools"> </section>
I added an empty <tool file=”” /> line in the section and still not there. Adding a valid tool lets it show up in the bullit list as it now also shows up in the left panel.. (as expected). Another test on the EMPTY section when I tried adding the tool providing THE SAME section name as custom in the field as a new tool panel section... it just adds it to the end of the section lists in the left. But it does work. It also remains working when I enable my own section menu again by adding another tool to the xml first. The section with the same name shows up on two places in the section list when adding tools from toolshed (as expected). Probably due to the different section id. There might be a possible problem when the id turns out the same as an already used one?
I manually altered the shed_tool_conf.xml to match my section name and id and everything is ok.
Maybe something to look into? Just a minor issue I think.
Keep up the good work! Alex
Van: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Greg Von Kuster Verzonden: vrijdag 3 februari 2012 22:16 Aan: Ira Cooke CC: galaxy-dev@lists.bx.psu.edu Dev Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool
Things should be working in change set 6667:86d9c5ddbafc, which is now available from the Galaxy central repository. Please let me know if you bump into any problems.
To use the latest features related to tool versioning, update your local tool shed as well as your local Galaxy instance ( both require updating the database schema ). In your local tool shed, reset all metadata for each repository using the Repository Actions pop-up for each repository. Since you already have repositories in your tool shed, you'll need to do this once for each existing repository. Any updates to the repository will automatically do this. New repositories created from here on will handle this automatically as well.
Then, in your local Galaxy instance, set tool versions for each installed tool shed repository using the repository's pop-up.
On Feb 3, 2012, at 11:07 AM, Greg Von Kuster wrote:
Hello Ira,
Thanks for reporting this - there are several similar issues that I've corrected in my next change set, which will be available today. This change set will introduce tool versioning for Galaxy tools, whether they are installed from a tool shed, or are available with the distribution. This will affect the tool shed as well as repositories installed from tool sheds that contain tools. This versioning feature will provide a chain of ancestor tool versions and descendant tool versions for any tool instance.
It would be great if you and others that have set up local Galaxy tool sheds can test this out. I will get fixes for issues (if any exist) as fast as possible. My hope is that this will be the last major feature introduced until we get everything stabilized a bit more between the tool shed and Galaxy.
Thanks!
Greg Von Kuster
On Feb 2, 2012, at 8:40 PM, Ira Cooke wrote:
Hi,
We've been running into an issue when attempting to create a new toolshed tool. We have the toolshed and the main galaxy web app setup and running, but updating our tool to the latest version always fails.
When clicking "Get updates" on our installed tool we find that the initial request is sent fine to the community application, but the reply is missing a slash after the galaxy url. This causes the request to fail.
Our solution to this problem was to modify lib/galaxy/webapps/community/controllers/repository.py on line 795 to include a slash after the galaxy url.
After we did this though we encountered another problem .. this time in lib/galaxy/web/controllers/admin_toolshed.py . In this case there is a named parameter to a method but the name of the parameter does not match the method definition. The problem was on 688 where "name = name" should read "repository_name=name".
After making these changes the get updates function seems to work fine.
Hope this helps. Ira
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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:
galaxy-dev@lists.galaxyproject.org
-
Bossers, Alex -
Greg Von Kuster -
Ira Cooke