Re: [galaxy-dev] HOWTO for making new toolshed package
Hello Pieter, Please send questions like this to the galaxy-dev@bx.psu.edu or galaxy-dev@lists.bx.psu.edu mailing list rather than individual email addresses to ensure optimal, timely responses. The Tool Shed wiki contains all of the information you need: http://wiki.galaxyproject.org/Tool%20Shed This page provides a nice overview of repository features: http://wiki.galaxyproject.org/ToolShedRepositoryFeatures See additional specific pages below for each item you've listed: On Sep 11, 2013, at 11:52 AM, "Lukasse, Pieter" <pieter.lukasse@wur.nl> wrote:
Hi Greg,
I want to make a toolshed package with the following contents:
The above "package" is actually a mercurial repository in the tool shed.
· A number of tools
The following pages will provide all of the information you'll need for building Galaxy tools for the Tool Shed. http://wiki.galaxyproject.org/ToolShedToolFeatures
· Some workflows
The following pages provide information for enabling workflow sharing via the Tool Shed. http://wiki.galaxyproject.org/ToolShedWorkflowSharing
· Datatypes
Datatype features in the Tool Shed are described in the following pages: http://wiki.galaxyproject.org/ToolShedDatatypesFeatures
· Installation configurations for installing external tools like R, Gnuplot and X!Tandem
The above information is document in the "ToolShedToolFeatures" section of the wiki, specifically in the following pages: http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-party_too...
· Dependencies configurations to other packages
If by "packages", you are referring to other tool shed repositories, then the documentation describing defining these relationships is located in the following pages: http://wiki.galaxyproject.org/DefiningRepositoryDependencies
Is there a HOWTO wiki page where I can find exactly which files I should add to the .zip file and how they should be named? Or maybe an example package which I could use?
Regards,
Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
+31-317480891; skype: pieter.lukasse.wur
Hi Greg, Fantastic, thanks for your detailed answer! I am trying out some things and I noticed that it is not possible to select a specific revision of a repository for installation (see screenshot). I thought I saw you present something like this at Oslo...is that possible ? [cid:image001.png@01CEAFB8.216DF2A0] Regards, Pieter. From: Greg Von Kuster [mailto:greg@bx.psu.edu] Sent: woensdag 11 september 2013 19:25 To: Lukasse, Pieter Cc: Galaxy Dev Subject: Re: HOWTO for making new toolshed package Hello Pieter, Please send questions like this to the galaxy-dev@bx.psu.edu<mailto:galaxy-dev@bx.psu.edu> or galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> mailing list rather than individual email addresses to ensure optimal, timely responses. The Tool Shed wiki contains all of the information you need: http://wiki.galaxyproject.org/Tool%20Shed This page provides a nice overview of repository features: http://wiki.galaxyproject.org/ToolShedRepositoryFeatures See additional specific pages below for each item you've listed: On Sep 11, 2013, at 11:52 AM, "Lukasse, Pieter" <pieter.lukasse@wur.nl<mailto:pieter.lukasse@wur.nl>> wrote: Hi Greg, I want to make a toolshed package with the following contents: The above "package" is actually a mercurial repository in the tool shed. * A number of tools The following pages will provide all of the information you'll need for building Galaxy tools for the Tool Shed. http://wiki.galaxyproject.org/ToolShedToolFeatures * Some workflows The following pages provide information for enabling workflow sharing via the Tool Shed. http://wiki.galaxyproject.org/ToolShedWorkflowSharing * Datatypes Datatype features in the Tool Shed are described in the following pages: http://wiki.galaxyproject.org/ToolShedDatatypesFeatures * Installation configurations for installing external tools like R, Gnuplot and X!Tandem The above information is document in the "ToolShedToolFeatures" section of the wiki, specifically in the following pages: http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-party_too... * Dependencies configurations to other packages If by "packages", you are referring to other tool shed repositories, then the documentation describing defining these relationships is located in the following pages: http://wiki.galaxyproject.org/DefiningRepositoryDependencies Is there a HOWTO wiki page where I can find exactly which files I should add to the .zip file and how they should be named? Or maybe an example package which I could use? Regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>
Hi Pieter, yes that is possible. Have a look at other repositories. You can only choose between different tool versions, it there are more than one 'installable version' of a tool. It is not the case in your example. Lets imagine I only fix some help text in the tool. I do not want to have separated version, I would prefer to just update the tool in place. But if I change a version number or increase the dependency version I would like a new 'installable version' of my tool. The toolshed can distinguish between such cases. Cheers, Bjoern
Hi Greg,
Fantastic, thanks for your detailed answer!
I am trying out some things and I noticed that it is not possible to select a specific revision of a repository for installation (see screenshot). I thought I saw you present something like this at Oslo...is that possible ?
Regards,
Pieter.
From: Greg Von Kuster [mailto:greg@bx.psu.edu] Sent: woensdag 11 september 2013 19:25 To: Lukasse, Pieter Cc: Galaxy Dev Subject: Re: HOWTO for making new toolshed package
Hello Pieter,
Please send questions like this to the galaxy-dev@bx.psu.edu or galaxy-dev@lists.bx.psu.edu mailing list rather than individual email addresses to ensure optimal, timely responses.
The Tool Shed wiki contains all of the information you need:
http://wiki.galaxyproject.org/Tool%20Shed
This page provides a nice overview of repository features:
http://wiki.galaxyproject.org/ToolShedRepositoryFeatures
See additional specific pages below for each item you've listed:
On Sep 11, 2013, at 11:52 AM, "Lukasse, Pieter" <pieter.lukasse@wur.nl> wrote:
Hi Greg,
I want to make a toolshed package with the following contents:
The above "package" is actually a mercurial repository in the tool shed.
· A number of tools
The following pages will provide all of the information you'll need for building Galaxy tools for the Tool Shed.
http://wiki.galaxyproject.org/ToolShedToolFeatures
· Some workflows
The following pages provide information for enabling workflow sharing via the Tool Shed.
http://wiki.galaxyproject.org/ToolShedWorkflowSharing
· Datatypes
Datatype features in the Tool Shed are described in the following pages:
http://wiki.galaxyproject.org/ToolShedDatatypesFeatures
· Installation configurations for installing external tools like R, Gnuplot and X!Tandem
The above information is document in the "ToolShedToolFeatures" section of the wiki, specifically in the following pages:
http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-party_too...
· Dependencies configurations to other packages
If by "packages", you are referring to other tool shed repositories, then the documentation describing defining these relationships is located in the following pages:
http://wiki.galaxyproject.org/DefiningRepositoryDependencies
Is there a HOWTO wiki page where I can find exactly which files I should add to the .zip file and how they should be named? Or maybe an example package which I could use?
Regards,
Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
+31-317480891; skype: pieter.lukasse.wur
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hello Pieter, Bjoern is correct here for tools, and the same behavior occurs for other Galaxy utilities that may be contained in tool shed repositories ( e.g., tool dependency definitions, repository dependency definitions, custom datatypes, etc ). Each type of Galaxy utility is associated with a set of rules that define whether changes to the utility result in a new installable changeset revision or not. Greg Von Kuster On Sep 12, 2013, at 7:14 AM, Bjoern Gruening <bjoern.gruening@gmail.com> wrote:
Hi Pieter,
yes that is possible. Have a look at other repositories. You can only choose between different tool versions, it there are more than one 'installable version' of a tool. It is not the case in your example. Lets imagine I only fix some help text in the tool. I do not want to have separated version, I would prefer to just update the tool in place. But if I change a version number or increase the dependency version I would like a new 'installable version' of my tool. The toolshed can distinguish between such cases.
Cheers, Bjoern
Hi Greg,
Fantastic, thanks for your detailed answer!
I am trying out some things and I noticed that it is not possible to select a specific revision of a repository for installation (see screenshot). I thought I saw you present something like this at Oslo...is that possible ?
Regards,
Pieter.
From: Greg Von Kuster [mailto:greg@bx.psu.edu] Sent: woensdag 11 september 2013 19:25 To: Lukasse, Pieter Cc: Galaxy Dev Subject: Re: HOWTO for making new toolshed package
Hello Pieter,
Please send questions like this to the galaxy-dev@bx.psu.edu or galaxy-dev@lists.bx.psu.edu mailing list rather than individual email addresses to ensure optimal, timely responses.
The Tool Shed wiki contains all of the information you need:
http://wiki.galaxyproject.org/Tool%20Shed
This page provides a nice overview of repository features:
http://wiki.galaxyproject.org/ToolShedRepositoryFeatures
See additional specific pages below for each item you've listed:
On Sep 11, 2013, at 11:52 AM, "Lukasse, Pieter" <pieter.lukasse@wur.nl> wrote:
Hi Greg,
I want to make a toolshed package with the following contents:
The above "package" is actually a mercurial repository in the tool shed.
· A number of tools
The following pages will provide all of the information you'll need for building Galaxy tools for the Tool Shed.
http://wiki.galaxyproject.org/ToolShedToolFeatures
· Some workflows
The following pages provide information for enabling workflow sharing via the Tool Shed.
http://wiki.galaxyproject.org/ToolShedWorkflowSharing
· Datatypes
Datatype features in the Tool Shed are described in the following pages:
http://wiki.galaxyproject.org/ToolShedDatatypesFeatures
· Installation configurations for installing external tools like R, Gnuplot and X!Tandem
The above information is document in the "ToolShedToolFeatures" section of the wiki, specifically in the following pages:
http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-party_too...
· Dependencies configurations to other packages
If by "packages", you are referring to other tool shed repositories, then the documentation describing defining these relationships is located in the following pages:
http://wiki.galaxyproject.org/DefiningRepositoryDependencies
Is there a HOWTO wiki page where I can find exactly which files I should add to the .zip file and how they should be named? Or maybe an example package which I could use?
Regards,
Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
+31-317480891; skype: pieter.lukasse.wur
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Ok, cool...I get the picture. One small downside is that then admin has to trust the developer has the discipline and sound judgment to correctly increase version numbers when applicable....I'm just thinking of scenarios where there is a "bad update" released and the admin would like to quickly revert back to the previous revision after noticing that this update has an unexpected bug.... Regards, Pieter. -----Original Message----- From: Bjoern Gruening [mailto:bjoern.gruening@gmail.com] Sent: donderdag 12 september 2013 13:15 To: Lukasse, Pieter Cc: 'Greg Von Kuster'; Galaxy Dev Subject: Re: [galaxy-dev] HOWTO for making new toolshed package Hi Pieter, yes that is possible. Have a look at other repositories. You can only choose between different tool versions, it there are more than one 'installable version' of a tool. It is not the case in your example. Lets imagine I only fix some help text in the tool. I do not want to have separated version, I would prefer to just update the tool in place. But if I change a version number or increase the dependency version I would like a new 'installable version' of my tool. The toolshed can distinguish between such cases. Cheers, Bjoern
Hi Greg,
Fantastic, thanks for your detailed answer!
I am trying out some things and I noticed that it is not possible to select a specific revision of a repository for installation (see screenshot). I thought I saw you present something like this at Oslo...is that possible ?
Regards,
Pieter.
From: Greg Von Kuster [mailto:greg@bx.psu.edu] Sent: woensdag 11 september 2013 19:25 To: Lukasse, Pieter Cc: Galaxy Dev Subject: Re: HOWTO for making new toolshed package
Hello Pieter,
Please send questions like this to the galaxy-dev@bx.psu.edu or galaxy-dev@lists.bx.psu.edu mailing list rather than individual email addresses to ensure optimal, timely responses.
The Tool Shed wiki contains all of the information you need:
http://wiki.galaxyproject.org/Tool%20Shed
This page provides a nice overview of repository features:
http://wiki.galaxyproject.org/ToolShedRepositoryFeatures
See additional specific pages below for each item you've listed:
On Sep 11, 2013, at 11:52 AM, "Lukasse, Pieter" <pieter.lukasse@wur.nl> wrote:
Hi Greg,
I want to make a toolshed package with the following contents:
The above "package" is actually a mercurial repository in the tool shed.
· A number of tools
The following pages will provide all of the information you'll need for building Galaxy tools for the Tool Shed.
http://wiki.galaxyproject.org/ToolShedToolFeatures
· Some workflows
The following pages provide information for enabling workflow sharing via the Tool Shed.
http://wiki.galaxyproject.org/ToolShedWorkflowSharing
· Datatypes
Datatype features in the Tool Shed are described in the following pages:
http://wiki.galaxyproject.org/ToolShedDatatypesFeatures
· Installation configurations for installing external tools like R, Gnuplot and X!Tandem
The above information is document in the "ToolShedToolFeatures" section of the wiki, specifically in the following pages:
http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-par ty_tool_dependency_installation_and_compilation_with_installed_reposit ories
· Dependencies configurations to other packages
If by "packages", you are referring to other tool shed repositories, then the documentation describing defining these relationships is located in the following pages:
http://wiki.galaxyproject.org/DefiningRepositoryDependencies
Is there a HOWTO wiki page where I can find exactly which files I should add to the .zip file and how they should be named? Or maybe an example package which I could use?
Regards,
Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
+31-317480891; skype: pieter.lukasse.wur
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
This scenario should be hopefully handled by the automated nightly tests that run on repositories in the test and main Galaxy tool sheds. This test framework does not yet provide full coverage, but it eventually will. Each repository that has been tested includes a "Tool test results" container when viewing or managing the repository. Greg Von Kuster On Sep 12, 2013, at 7:23 AM, "Lukasse, Pieter" <pieter.lukasse@wur.nl> wrote:
Ok, cool...I get the picture.
One small downside is that then admin has to trust the developer has the discipline and sound judgment to correctly increase version numbers when applicable....I'm just thinking of scenarios where there is a "bad update" released and the admin would like to quickly revert back to the previous revision after noticing that this update has an unexpected bug....
Regards,
Pieter.
-----Original Message----- From: Bjoern Gruening [mailto:bjoern.gruening@gmail.com] Sent: donderdag 12 september 2013 13:15 To: Lukasse, Pieter Cc: 'Greg Von Kuster'; Galaxy Dev Subject: Re: [galaxy-dev] HOWTO for making new toolshed package
Hi Pieter,
yes that is possible. Have a look at other repositories. You can only choose between different tool versions, it there are more than one 'installable version' of a tool. It is not the case in your example. Lets imagine I only fix some help text in the tool. I do not want to have separated version, I would prefer to just update the tool in place. But if I change a version number or increase the dependency version I would like a new 'installable version' of my tool. The toolshed can distinguish between such cases.
Cheers, Bjoern
Hi Greg,
Fantastic, thanks for your detailed answer!
I am trying out some things and I noticed that it is not possible to select a specific revision of a repository for installation (see screenshot). I thought I saw you present something like this at Oslo...is that possible ?
Regards,
Pieter.
From: Greg Von Kuster [mailto:greg@bx.psu.edu] Sent: woensdag 11 september 2013 19:25 To: Lukasse, Pieter Cc: Galaxy Dev Subject: Re: HOWTO for making new toolshed package
Hello Pieter,
Please send questions like this to the galaxy-dev@bx.psu.edu or galaxy-dev@lists.bx.psu.edu mailing list rather than individual email addresses to ensure optimal, timely responses.
The Tool Shed wiki contains all of the information you need:
http://wiki.galaxyproject.org/Tool%20Shed
This page provides a nice overview of repository features:
http://wiki.galaxyproject.org/ToolShedRepositoryFeatures
See additional specific pages below for each item you've listed:
On Sep 11, 2013, at 11:52 AM, "Lukasse, Pieter" <pieter.lukasse@wur.nl> wrote:
Hi Greg,
I want to make a toolshed package with the following contents:
The above "package" is actually a mercurial repository in the tool shed.
· A number of tools
The following pages will provide all of the information you'll need for building Galaxy tools for the Tool Shed.
http://wiki.galaxyproject.org/ToolShedToolFeatures
· Some workflows
The following pages provide information for enabling workflow sharing via the Tool Shed.
http://wiki.galaxyproject.org/ToolShedWorkflowSharing
· Datatypes
Datatype features in the Tool Shed are described in the following pages:
http://wiki.galaxyproject.org/ToolShedDatatypesFeatures
· Installation configurations for installing external tools like R, Gnuplot and X!Tandem
The above information is document in the "ToolShedToolFeatures" section of the wiki, specifically in the following pages:
http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-par ty_tool_dependency_installation_and_compilation_with_installed_reposit ories
· Dependencies configurations to other packages
If by "packages", you are referring to other tool shed repositories, then the documentation describing defining these relationships is located in the following pages:
http://wiki.galaxyproject.org/DefiningRepositoryDependencies
Is there a HOWTO wiki page where I can find exactly which files I should add to the .zip file and how they should be named? Or maybe an example package which I could use?
Regards,
Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
+31-317480891; skype: pieter.lukasse.wur
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
One extra detail I'm trying to find in the docs but haven't found yet: How can I ensure that the tools of my package are presented in a specific order in the menu panel item I selected during install? And is it possible to define some labels to appear between the tools (Something like the screenshot below)? Or is this something the admin should configure in shed_tool_conf.xml? And will this order configuration be kept also when new versions of the tools are installed? Example: [cid:image001.png@01CEAFC3.5DFF77B0] -----Original Message----- From: Greg Von Kuster [mailto:greg@bx.psu.edu] Sent: donderdag 12 september 2013 13:27 To: Lukasse, Pieter Cc: Galaxy Dev Subject: Re: [galaxy-dev] HOWTO for making new toolshed package This scenario should be hopefully handled by the automated nightly tests that run on repositories in the test and main Galaxy tool sheds. This test framework does not yet provide full coverage, but it eventually will. Each repository that has been tested includes a "Tool test results" container when viewing or managing the repository. Greg Von Kuster On Sep 12, 2013, at 7:23 AM, "Lukasse, Pieter" <pieter.lukasse@wur.nl<mailto:pieter.lukasse@wur.nl>> wrote:
Ok, cool...I get the picture.
One small downside is that then admin has to trust the developer has the discipline and sound judgment to correctly increase version numbers when applicable....I'm just thinking of scenarios where there is a "bad update" released and the admin would like to quickly revert back to the previous revision after noticing that this update has an unexpected bug....
Regards,
Pieter.
-----Original Message-----
From: Bjoern Gruening [mailto:bjoern.gruening@gmail.com]
Sent: donderdag 12 september 2013 13:15
To: Lukasse, Pieter
Cc: 'Greg Von Kuster'; Galaxy Dev
Subject: Re: [galaxy-dev] HOWTO for making new toolshed package
Hi Pieter,
yes that is possible. Have a look at other repositories. You can only choose between different tool versions, it there are more than one 'installable version' of a tool. It is not the case in your example.
Lets imagine I only fix some help text in the tool. I do not want to have separated version, I would prefer to just update the tool in place.
But if I change a version number or increase the dependency version I would like a new 'installable version' of my tool. The toolshed can distinguish between such cases.
Cheers,
Bjoern
Hi Greg,
Fantastic, thanks for your detailed answer!
I am trying out some things and I noticed that it is not possible to
select a specific revision of a repository for installation (see
screenshot). I thought I saw you present something like this at
Oslo...is that possible ?
Regards,
Pieter.
From: Greg Von Kuster [mailto:greg@bx.psu.edu]
Sent: woensdag 11 september 2013 19:25
To: Lukasse, Pieter
Cc: Galaxy Dev
Subject: Re: HOWTO for making new toolshed package
Hello Pieter,
Please send questions like this to the galaxy-dev@bx.psu.edu<mailto:galaxy-dev@bx.psu.edu> or
galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> mailing list rather than individual email
addresses to ensure optimal, timely responses.
The Tool Shed wiki contains all of the information you need:
This page provides a nice overview of repository features:
See additional specific pages below for each item you've listed:
On Sep 11, 2013, at 11:52 AM, "Lukasse, Pieter"
<pieter.lukasse@wur.nl<mailto:pieter.lukasse@wur.nl>> wrote:
Hi Greg,
I want to make a toolshed package with the following contents:
The above "package" is actually a mercurial repository in the tool
shed.
* A number of tools
The following pages will provide all of the information you'll need
for building Galaxy tools for the Tool Shed.
* Some workflows
The following pages provide information for enabling workflow sharing
via the Tool Shed.
* Datatypes
Datatype features in the Tool Shed are described in the following
pages:
* Installation configurations for installing external tools
like R, Gnuplot and X!Tandem
The above information is document in the "ToolShedToolFeatures"
section of the wiki, specifically in the following pages:
http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-pa
r
ty_tool_dependency_installation_and_compilation_with_installed_reposi
t
ories
* Dependencies configurations to other packages
If by "packages", you are referring to other tool shed repositories,
then the documentation describing defining these relationships is
located in the following pages:
http://wiki.galaxyproject.org/DefiningRepositoryDependencies
Is there a HOWTO wiki page where I can find exactly which files I
should add to the .zip file and how they should be named? Or maybe an
example package which I could use?
Regards,
Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
+31-317480891; skype: pieter.lukasse.wur
___________________________________________________________
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:
To search Galaxy mailing lists use the unified search 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:
To search Galaxy mailing lists use the unified search at:
Hi Pieter, to manipulate the ordering of tools is currently not trivial, as far as I know. You can add label into your shed_tool_conf.xml and tool_conf.xml file and they should appear and stay. The final ordering will be a merge of all your *_tool_conf.xml files into the integrated_tool_panel.xml. If you change that file you will see that the ordering will change, but that file can be overwritten. I would play with the shed_tool_conf.xml and tool_conf.xml, try to reorder your tools and delete the integrated_tool_panel.xml file. After restarting you will see the effects. In each case, the admin needs to do that. I have a pull request that enables dynamic filtering of tools by the user, maybe you are interested in testing: https://bitbucket.org/galaxy/galaxy-central/pull-request/179/implement-the-a... Cheers, Bjoern
One extra detail I'm trying to find in the docs but haven't found yet:
How can I ensure that the tools of my package are presented in a specific order in the menu panel item I selected during install? And is it possible to define some labels to appear between the tools (Something like the screenshot below)? Or is this something the admin should configure in shed_tool_conf.xml? And will this order configuration be kept also when new versions of the tools are installed?
Example:
-----Original Message----- From: Greg Von Kuster [mailto:greg@bx.psu.edu] Sent: donderdag 12 september 2013 13:27 To: Lukasse, Pieter Cc: Galaxy Dev Subject: Re: [galaxy-dev] HOWTO for making new toolshed package
This scenario should be hopefully handled by the automated nightly tests that run on repositories in the test and main Galaxy tool sheds. This test framework does not yet provide full coverage, but it eventually will. Each repository that has been tested includes a "Tool test results" container when viewing or managing the repository.
Greg Von Kuster
On Sep 12, 2013, at 7:23 AM, "Lukasse, Pieter" <pieter.lukasse@wur.nl> wrote:
Ok, cool...I get the picture.
One small downside is that then admin has to trust the developer has the discipline and sound judgment to correctly increase version numbers when applicable....I'm just thinking of scenarios where there is a "bad update" released and the admin would like to quickly revert back to the previous revision after noticing that this update has an unexpected bug....
Regards,
Pieter.
-----Original Message-----
From: Bjoern Gruening [mailto:bjoern.gruening@gmail.com]
Sent: donderdag 12 september 2013 13:15
To: Lukasse, Pieter
Cc: 'Greg Von Kuster'; Galaxy Dev
Subject: Re: [galaxy-dev] HOWTO for making new toolshed package
Hi Pieter,
yes that is possible. Have a look at other repositories. You can only choose between different tool versions, it there are more than one 'installable version' of a tool. It is not the case in your example.
Lets imagine I only fix some help text in the tool. I do not want to have separated version, I would prefer to just update the tool in place.
But if I change a version number or increase the dependency version I would like a new 'installable version' of my tool. The toolshed can distinguish between such cases.
Cheers,
Bjoern
Hi Greg,
Fantastic, thanks for your detailed answer!
I am trying out some things and I noticed that it is not possible to
select a specific revision of a repository for installation (see
screenshot). I thought I saw you present something like this at
Oslo...is that possible ?
Regards,
Pieter.
From: Greg Von Kuster [mailto:greg@bx.psu.edu]
Sent: woensdag 11 september 2013 19:25
To: Lukasse, Pieter
Cc: Galaxy Dev
Subject: Re: HOWTO for making new toolshed package
Hello Pieter,
Please send questions like this to the galaxy-dev@bx.psu.edu or
galaxy-dev@lists.bx.psu.edu mailing list rather than individual email
addresses to ensure optimal, timely responses.
The Tool Shed wiki contains all of the information you need:
This page provides a nice overview of repository features:
See additional specific pages below for each item you've listed:
On Sep 11, 2013, at 11:52 AM, "Lukasse, Pieter"
<pieter.lukasse@wur.nl> wrote:
Hi Greg,
I want to make a toolshed package with the following contents:
The above "package" is actually a mercurial repository in the tool
shed.
· A number of tools
The following pages will provide all of the information you'll need
for building Galaxy tools for the Tool Shed.
· Some workflows
The following pages provide information for enabling workflow sharing
via the Tool Shed.
· Datatypes
Datatype features in the Tool Shed are described in the following
pages:
· Installation configurations for installing external tools
like R, Gnuplot and X!Tandem
The above information is document in the "ToolShedToolFeatures"
section of the wiki, specifically in the following pages:
http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-pa
r
ty_tool_dependency_installation_and_compilation_with_installed_reposi
t
ories
· Dependencies configurations to other packages
If by "packages", you are referring to other tool shed repositories,
then the documentation describing defining these relationships is
located in the following pages:
http://wiki.galaxyproject.org/DefiningRepositoryDependencies
Is there a HOWTO wiki page where I can find exactly which files I
should add to the .zip file and how they should be named? Or maybe an
example package which I could use?
Regards,
Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
+31-317480891; skype: pieter.lukasse.wur
___________________________________________________________
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:
To search Galaxy mailing lists use the unified search 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:
To search Galaxy mailing lists use the unified search 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Bjoern, Thanks, that is helpful information. Updates to new revisions seem to work fine, i.e. the order as configured in shed_tool_conf.xml seems to be preserved. We are now facing what I think could be a small bug in the $PATH_TO_IMAGES part as documented in http://wiki.galaxyproject.org/ToolShedToolFeatures#Properly_defining_the_loc... We get the tool UI rendered but without the images in the documentation section. When looking at the URL in this section we find the following: http://10.73.10.111/galaxy_testing/$PATH_TO_IMAGES/napq_overview.png so the variable is not being replaced by the value of the path...is this a known issue? Regards, Pieter. -----Original Message----- From: Bjoern Gruening [mailto:bjoern.gruening@gmail.com] Sent: donderdag 12 september 2013 14:31 To: Lukasse, Pieter Cc: 'Greg Von Kuster'; Galaxy Dev Subject: Changing tool panel ordering [was:] HOWTO for making new toolshed package Hi Pieter, to manipulate the ordering of tools is currently not trivial, as far as I know. You can add label into your shed_tool_conf.xml and tool_conf.xml file and they should appear and stay. The final ordering will be a merge of all your *_tool_conf.xml files into the integrated_tool_panel.xml. If you change that file you will see that the ordering will change, but that file can be overwritten. I would play with the shed_tool_conf.xml and tool_conf.xml, try to reorder your tools and delete the integrated_tool_panel.xml file. After restarting you will see the effects. In each case, the admin needs to do that. I have a pull request that enables dynamic filtering of tools by the user, maybe you are interested in testing: https://bitbucket.org/galaxy/galaxy-central/pull-request/179/implement-the-a... Cheers, Bjoern
One extra detail I'm trying to find in the docs but haven't found yet:
How can I ensure that the tools of my package are presented in a specific order in the menu panel item I selected during install? And is it possible to define some labels to appear between the tools (Something like the screenshot below)? Or is this something the admin should configure in shed_tool_conf.xml? And will this order configuration be kept also when new versions of the tools are installed?
Example:
-----Original Message----- From: Greg Von Kuster [mailto:greg@bx.psu.edu] Sent: donderdag 12 september 2013 13:27 To: Lukasse, Pieter Cc: Galaxy Dev Subject: Re: [galaxy-dev] HOWTO for making new toolshed package
This scenario should be hopefully handled by the automated nightly tests that run on repositories in the test and main Galaxy tool sheds. This test framework does not yet provide full coverage, but it eventually will. Each repository that has been tested includes a "Tool test results" container when viewing or managing the repository.
Greg Von Kuster
On Sep 12, 2013, at 7:23 AM, "Lukasse, Pieter" <pieter.lukasse@wur.nl> wrote:
Ok, cool...I get the picture.
One small downside is that then admin has to trust the developer has the discipline and sound judgment to correctly increase version numbers when applicable....I'm just thinking of scenarios where there is a "bad update" released and the admin would like to quickly revert back to the previous revision after noticing that this update has an unexpected bug....
Regards,
Pieter.
-----Original Message-----
From: Bjoern Gruening [mailto:bjoern.gruening@gmail.com]
Sent: donderdag 12 september 2013 13:15
To: Lukasse, Pieter
Cc: 'Greg Von Kuster'; Galaxy Dev
Subject: Re: [galaxy-dev] HOWTO for making new toolshed package
Hi Pieter,
yes that is possible. Have a look at other repositories. You can only choose between different tool versions, it there are more than one 'installable version' of a tool. It is not the case in your example.
Lets imagine I only fix some help text in the tool. I do not want to have separated version, I would prefer to just update the tool in place.
But if I change a version number or increase the dependency version I would like a new 'installable version' of my tool. The toolshed can distinguish between such cases.
Cheers,
Bjoern
Hi Greg,
Fantastic, thanks for your detailed answer!
I am trying out some things and I noticed that it is not possible to
select a specific revision of a repository for installation (see
screenshot). I thought I saw you present something like this at
Oslo...is that possible ?
Regards,
Pieter.
From: Greg Von Kuster [mailto:greg@bx.psu.edu]
Sent: woensdag 11 september 2013 19:25
To: Lukasse, Pieter
Cc: Galaxy Dev
Subject: Re: HOWTO for making new toolshed package
Hello Pieter,
Please send questions like this to the galaxy-dev@bx.psu.edu or
galaxy-dev@lists.bx.psu.edu mailing list rather than individual email
addresses to ensure optimal, timely responses.
The Tool Shed wiki contains all of the information you need:
This page provides a nice overview of repository features:
See additional specific pages below for each item you've listed:
On Sep 11, 2013, at 11:52 AM, "Lukasse, Pieter"
<pieter.lukasse@wur.nl> wrote:
Hi Greg,
I want to make a toolshed package with the following contents:
The above "package" is actually a mercurial repository in the tool
shed.
· A number of tools
The following pages will provide all of the information you'll need
for building Galaxy tools for the Tool Shed.
· Some workflows
The following pages provide information for enabling workflow sharing
via the Tool Shed.
· Datatypes
Datatype features in the Tool Shed are described in the following
pages:
· Installation configurations for installing external tools
like R, Gnuplot and X!Tandem
The above information is document in the "ToolShedToolFeatures"
section of the wiki, specifically in the following pages:
http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-pa
r
ty_tool_dependency_installation_and_compilation_with_installed_reposi
t
ories
· Dependencies configurations to other packages
If by "packages", you are referring to other tool shed repositories,
then the documentation describing defining these relationships is
located in the following pages:
http://wiki.galaxyproject.org/DefiningRepositoryDependencies
Is there a HOWTO wiki page where I can find exactly which files I
should add to the .zip file and how they should be named? Or maybe an
example package which I could use?
Regards,
Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
+31-317480891; skype: pieter.lukasse.wur
___________________________________________________________
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:
To search Galaxy mailing lists use the unified search 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:
To search Galaxy mailing lists use the unified search 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi guys, We discovered that the problem is at our apache configuration side...working on it now... ;) Regards, Pieter. -----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter Sent: donderdag 12 september 2013 16:13 To: 'Bjoern Gruening' Cc: 'Greg Von Kuster'; Galaxy Dev Subject: Re: [galaxy-dev] Changing tool panel ordering [was:] HOWTO for making new toolshed package Hi Bjoern, Thanks, that is helpful information. Updates to new revisions seem to work fine, i.e. the order as configured in shed_tool_conf.xml seems to be preserved. We are now facing what I think could be a small bug in the $PATH_TO_IMAGES part as documented in http://wiki.galaxyproject.org/ToolShedToolFeatures#Properly_defining_the_loc... We get the tool UI rendered but without the images in the documentation section. When looking at the URL in this section we find the following: http://10.73.10.111/galaxy_testing/$PATH_TO_IMAGES/napq_overview.png so the variable is not being replaced by the value of the path...is this a known issue? Regards, Pieter. -----Original Message----- From: Bjoern Gruening [mailto:bjoern.gruening@gmail.com] Sent: donderdag 12 september 2013 14:31 To: Lukasse, Pieter Cc: 'Greg Von Kuster'; Galaxy Dev Subject: Changing tool panel ordering [was:] HOWTO for making new toolshed package Hi Pieter, to manipulate the ordering of tools is currently not trivial, as far as I know. You can add label into your shed_tool_conf.xml and tool_conf.xml file and they should appear and stay. The final ordering will be a merge of all your *_tool_conf.xml files into the integrated_tool_panel.xml. If you change that file you will see that the ordering will change, but that file can be overwritten. I would play with the shed_tool_conf.xml and tool_conf.xml, try to reorder your tools and delete the integrated_tool_panel.xml file. After restarting you will see the effects. In each case, the admin needs to do that. I have a pull request that enables dynamic filtering of tools by the user, maybe you are interested in testing: https://bitbucket.org/galaxy/galaxy-central/pull-request/179/implement-the-a... Cheers, Bjoern
One extra detail I'm trying to find in the docs but haven't found yet:
How can I ensure that the tools of my package are presented in a specific order in the menu panel item I selected during install? And is it possible to define some labels to appear between the tools (Something like the screenshot below)? Or is this something the admin should configure in shed_tool_conf.xml? And will this order configuration be kept also when new versions of the tools are installed?
Example:
-----Original Message----- From: Greg Von Kuster [mailto:greg@bx.psu.edu] Sent: donderdag 12 september 2013 13:27 To: Lukasse, Pieter Cc: Galaxy Dev Subject: Re: [galaxy-dev] HOWTO for making new toolshed package
This scenario should be hopefully handled by the automated nightly tests that run on repositories in the test and main Galaxy tool sheds. This test framework does not yet provide full coverage, but it eventually will. Each repository that has been tested includes a "Tool test results" container when viewing or managing the repository.
Greg Von Kuster
On Sep 12, 2013, at 7:23 AM, "Lukasse, Pieter" <pieter.lukasse@wur.nl> wrote:
Ok, cool...I get the picture.
One small downside is that then admin has to trust the developer has the discipline and sound judgment to correctly increase version numbers when applicable....I'm just thinking of scenarios where there is a "bad update" released and the admin would like to quickly revert back to the previous revision after noticing that this update has an unexpected bug....
Regards,
Pieter.
-----Original Message-----
From: Bjoern Gruening [mailto:bjoern.gruening@gmail.com]
Sent: donderdag 12 september 2013 13:15
To: Lukasse, Pieter
Cc: 'Greg Von Kuster'; Galaxy Dev
Subject: Re: [galaxy-dev] HOWTO for making new toolshed package
Hi Pieter,
yes that is possible. Have a look at other repositories. You can only choose between different tool versions, it there are more than one 'installable version' of a tool. It is not the case in your example.
Lets imagine I only fix some help text in the tool. I do not want to have separated version, I would prefer to just update the tool in place.
But if I change a version number or increase the dependency version I would like a new 'installable version' of my tool. The toolshed can distinguish between such cases.
Cheers,
Bjoern
Hi Greg,
Fantastic, thanks for your detailed answer!
I am trying out some things and I noticed that it is not possible to
select a specific revision of a repository for installation (see
screenshot). I thought I saw you present something like this at
Oslo...is that possible ?
Regards,
Pieter.
From: Greg Von Kuster [mailto:greg@bx.psu.edu]
Sent: woensdag 11 september 2013 19:25
To: Lukasse, Pieter
Cc: Galaxy Dev
Subject: Re: HOWTO for making new toolshed package
Hello Pieter,
Please send questions like this to the galaxy-dev@bx.psu.edu or
galaxy-dev@lists.bx.psu.edu mailing list rather than individual email
addresses to ensure optimal, timely responses.
The Tool Shed wiki contains all of the information you need:
This page provides a nice overview of repository features:
See additional specific pages below for each item you've listed:
On Sep 11, 2013, at 11:52 AM, "Lukasse, Pieter"
<pieter.lukasse@wur.nl> wrote:
Hi Greg,
I want to make a toolshed package with the following contents:
The above "package" is actually a mercurial repository in the tool
shed.
· A number of tools
The following pages will provide all of the information you'll need
for building Galaxy tools for the Tool Shed.
· Some workflows
The following pages provide information for enabling workflow sharing
via the Tool Shed.
· Datatypes
Datatype features in the Tool Shed are described in the following
pages:
· Installation configurations for installing external tools
like R, Gnuplot and X!Tandem
The above information is document in the "ToolShedToolFeatures"
section of the wiki, specifically in the following pages:
http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-pa
r
ty_tool_dependency_installation_and_compilation_with_installed_reposi
t
ories
· Dependencies configurations to other packages
If by "packages", you are referring to other tool shed repositories,
then the documentation describing defining these relationships is
located in the following pages:
http://wiki.galaxyproject.org/DefiningRepositoryDependencies
Is there a HOWTO wiki page where I can find exactly which files I
should add to the .zip file and how they should be named? Or maybe an
example package which I could use?
Regards,
Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
+31-317480891; skype: pieter.lukasse.wur
___________________________________________________________
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:
To search Galaxy mailing lists use the unified search 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:
To search Galaxy mailing lists use the unified search 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (3)
-
Bjoern Gruening -
Greg Von Kuster -
Lukasse, Pieter