Adding categories to Main
Dear Galaxy Team, A colleague would like to upload some NLP (Natural Language Processing) tools to the Galaxy Test/Main tools sheds, but we are unclear what "categories" to use for the tools. I see that the Main/Test tools sheds have a category for "Text Manipulation", but that does not seem appropriate for NLP tools. Is it possible to have new categories added to the tool shed(s)? If so, what is the process? I am just starting to investigate setting up our own local tool shed and I am coming across mentions of repository capsules and exporting tool sheds. Would it be preferable to install the NLP tools to a local tool shed and then export a repository/capsule to be imported to the Test/Main tools sheds? What happens if our tool shed uses a disjoint set of categories than Test/Main? Cheers, Keith ------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
Hi Keith, the Galaxy team can add new categories to the Tool Shed very easily and such a mail is exactly the way to go. As soon as the Galaxy teams has added the category you can use tools like planemo to upload all your tools at once. https://github.com/galaxyproject/planemo Looking forward to see NLP tools in Galaxy and the Main TS! Awesome! Bjoern
Dear Galaxy Team,
A colleague would like to upload some NLP (Natural Language Processing) tools to the Galaxy Test/Main tools sheds, but we are unclear what "categories" to use for the tools. I see that the Main/Test tools sheds have a category for "Text Manipulation", but that does not seem appropriate for NLP tools. Is it possible to have new categories added to the tool shed(s)? If so, what is the process?
I am just starting to investigate setting up our own local tool shed and I am coming across mentions of repository capsules and exporting tool sheds. Would it be preferable to install the NLP tools to a local tool shed and then export a repository/capsule to be imported to the Test/Main tools sheds? What happens if our tool shed uses a disjoint set of categories than Test/Main?
Cheers, Keith
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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Dear Keith, I have created 'NLP' category at https://testtoolshed.g2.bx.psu.edu for you to test out the Tool Shed environment. Unless your tools are proprietary I strongly recommend using the Main Tool Shed at https://toolshed.g2.bx.psu.edu for their publishing and distribution. Let me know when you are ready with the tools and I will create the category for you in there. We happily welcome every tool contribution to Galaxy! Thank you for it. Martin, Galaxy Team On Fri, Aug 7, 2015 at 12:56 PM Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Keith,
the Galaxy team can add new categories to the Tool Shed very easily and such a mail is exactly the way to go. As soon as the Galaxy teams has added the category you can use tools like planemo to upload all your tools at once.
https://github.com/galaxyproject/planemo
Looking forward to see NLP tools in Galaxy and the Main TS! Awesome! Bjoern
Dear Galaxy Team,
A colleague would like to upload some NLP (Natural Language Processing) tools to the Galaxy Test/Main tools sheds, but we are unclear what "categories" to use for the tools. I see that the Main/Test tools sheds have a category for "Text Manipulation", but that does not seem appropriate for NLP tools. Is it possible to have new categories added to the tool shed(s)? If so, what is the process?
I am just starting to investigate setting up our own local tool shed and I am coming across mentions of repository capsules and exporting tool sheds. Would it be preferable to install the NLP tools to a local tool shed and then export a repository/capsule to be imported to the Test/Main tools sheds? What happens if our tool shed uses a disjoint set of categories than Test/Main?
Cheers, Keith
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Awesome! One concern we have is lumping all NLP tools into a single category; are sub-categories (and sub-sub-categories) possible? However, we can start with this and see what we need later. Cheers, Keith On Aug 7, 2015, at 12:25 PM, Martin Čech <marten@bx.psu.edu> wrote:
Dear Keith,
I have created 'NLP' category at https://testtoolshed.g2.bx.psu.edu for you to test out the Tool Shed environment.
Unless your tools are proprietary I strongly recommend using the Main Tool Shed at https://toolshed.g2.bx.psu.edu for their publishing and distribution. Let me know when you are ready with the tools and I will create the category for you in there.
We happily welcome every tool contribution to Galaxy! Thank you for it.
Martin, Galaxy Team
On Fri, Aug 7, 2015 at 12:56 PM Björn Grüning <bjoern.gruening@gmail.com> wrote: Hi Keith,
the Galaxy team can add new categories to the Tool Shed very easily and such a mail is exactly the way to go. As soon as the Galaxy teams has added the category you can use tools like planemo to upload all your tools at once.
https://github.com/galaxyproject/planemo
Looking forward to see NLP tools in Galaxy and the Main TS! Awesome! Bjoern
Dear Galaxy Team,
A colleague would like to upload some NLP (Natural Language Processing) tools to the Galaxy Test/Main tools sheds, but we are unclear what "categories" to use for the tools. I see that the Main/Test tools sheds have a category for "Text Manipulation", but that does not seem appropriate for NLP tools. Is it possible to have new categories added to the tool shed(s)? If so, what is the process?
I am just starting to investigate setting up our own local tool shed and I am coming across mentions of repository capsules and exporting tool sheds. Would it be preferable to install the NLP tools to a local tool shed and then export a repository/capsule to be imported to the Test/Main tools sheds? What happens if our tool shed uses a disjoint set of categories than Test/Main?
Cheers, Keith
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
No sub-categories yet; we plan on tackling the browsing issue by having good search. :) M. On Fri, Aug 7, 2015 at 2:43 PM Keith Suderman <suderman@cs.vassar.edu> wrote:
Awesome!
One concern we have is lumping all NLP tools into a single category; are sub-categories (and sub-sub-categories) possible? However, we can start with this and see what we need later.
Cheers, Keith
On Aug 7, 2015, at 12:25 PM, Martin Čech <marten@bx.psu.edu> wrote:
Dear Keith,
I have created 'NLP' category at https://testtoolshed.g2.bx.psu.edu for you to test out the Tool Shed environment.
Unless your tools are proprietary I strongly recommend using the Main Tool Shed at https://toolshed.g2.bx.psu.edu for their publishing and distribution. Let me know when you are ready with the tools and I will create the category for you in there.
We happily welcome every tool contribution to Galaxy! Thank you for it.
Martin, Galaxy Team
On Fri, Aug 7, 2015 at 12:56 PM Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Keith,
the Galaxy team can add new categories to the Tool Shed very easily and such a mail is exactly the way to go. As soon as the Galaxy teams has added the category you can use tools like planemo to upload all your tools at once.
https://github.com/galaxyproject/planemo
Looking forward to see NLP tools in Galaxy and the Main TS! Awesome! Bjoern
Dear Galaxy Team,
A colleague would like to upload some NLP (Natural Language Processing) tools to the Galaxy Test/Main tools sheds, but we are unclear what "categories" to use for the tools. I see that the Main/Test tools sheds have a category for "Text Manipulation", but that does not seem appropriate for NLP tools. Is it possible to have new categories added to the tool shed(s)? If so, what is the process?
I am just starting to investigate setting up our own local tool shed and I am coming across mentions of repository capsules and exporting tool sheds. Would it be preferable to install the NLP tools to a local tool shed and then export a repository/capsule to be imported to the Test/Main tools sheds? What happens if our tool shed uses a disjoint set of categories than Test/Main?
Cheers, Keith
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
Hi Keith, how is the NLP category working for you? Do you want it on Main Tool Shed? Also I have noticed you are putting the version of your tools in the repository names. I would like to discourage that as it will create confusion once you update your tool (as you will be unable to update the repo name). The XML wrappers have they own version tracking tag for these purposes. You can learn about this and more in the Tooldev Best Practices document: http://galaxy-iuc-standards.readthedocs.org/en/latest/ Thank you for using Galaxy. Martin On Fri, Aug 7, 2015 at 2:57 PM Martin Čech <marten@bx.psu.edu> wrote:
No sub-categories yet; we plan on tackling the browsing issue by having good search. :)
M.
On Fri, Aug 7, 2015 at 2:43 PM Keith Suderman <suderman@cs.vassar.edu> wrote:
Awesome!
One concern we have is lumping all NLP tools into a single category; are sub-categories (and sub-sub-categories) possible? However, we can start with this and see what we need later.
Cheers, Keith
On Aug 7, 2015, at 12:25 PM, Martin Čech <marten@bx.psu.edu> wrote:
Dear Keith,
I have created 'NLP' category at https://testtoolshed.g2.bx.psu.edu for you to test out the Tool Shed environment.
Unless your tools are proprietary I strongly recommend using the Main Tool Shed at https://toolshed.g2.bx.psu.edu for their publishing and distribution. Let me know when you are ready with the tools and I will create the category for you in there.
We happily welcome every tool contribution to Galaxy! Thank you for it.
Martin, Galaxy Team
On Fri, Aug 7, 2015 at 12:56 PM Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Keith,
the Galaxy team can add new categories to the Tool Shed very easily and such a mail is exactly the way to go. As soon as the Galaxy teams has added the category you can use tools like planemo to upload all your tools at once.
https://github.com/galaxyproject/planemo
Looking forward to see NLP tools in Galaxy and the Main TS! Awesome! Bjoern
Dear Galaxy Team,
A colleague would like to upload some NLP (Natural Language Processing) tools to the Galaxy Test/Main tools sheds, but we are unclear what "categories" to use for the tools. I see that the Main/Test tools sheds have a category for "Text Manipulation", but that does not seem appropriate for NLP tools. Is it possible to have new categories added to the tool shed(s)? If so, what is the process?
I am just starting to investigate setting up our own local tool shed and I am coming across mentions of repository capsules and exporting tool sheds. Would it be preferable to install the NLP tools to a local tool shed and then export a repository/capsule to be imported to the Test/Main tools sheds? What happens if our tool shed uses a disjoint set of categories than Test/Main?
Cheers, Keith
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
Hi Martin, On Sep 11, 2015, at 12:44 PM, Martin Čech <marten@bx.psu.edu> wrote:
Hi Keith,
how is the NLP category working for you? Do you want it on Main Tool Shed?
The NLP category is working great. I am still in the early testing phase and likely won't need anything in Main for some time yet, but Steve Cassidy might have a different opinion.
Also I have noticed you are putting the version of your tools in the repository names. I would like to discourage that as it will create confusion once you update your tool (as you will be unable to update the repo name). The XML wrappers have they own version tracking tag for these purposes. You can learn about this and more in the Tooldev Best Practices document: http://galaxy-iuc-standards.readthedocs.org/en/latest/
I was under the impression (http://gregvonkuster.org/galaxy-tool-shed-revisiting-best-practices-populati...) that the best practice for package names was package_<name>_<version> and for tools it was <name>_<version>. There is also some friction (for lack of a better term) between versioning our web services and versioning the Galaxy wrappers that call our web services. For example, I might have multiple versions of the Galaxy wrappers for our stanford_2.0.0 services and multiple versions of the Galaxy wrappers for our stanford_2.1.0 services. The 2.0.0 services are not going away just because the 2.1.0 services are available, so I think the stanford_2.0.0 and stanford_2.1.0 Galaxy wrappers have to be separate repositories. Having said that, I am planning to remove all my current repositories and repopulate as I try to automate things on my end so suggestions for naming strategies are always welcome. "There are only two hard problems in computer science, cache invalidation and naming things" - author unknown
Thank you for using Galaxy.
Thank you (all) for making Galaxy! ;-) Cheers, Keith
Martin
On Fri, Aug 7, 2015 at 2:57 PM Martin Čech <marten@bx.psu.edu> wrote: No sub-categories yet; we plan on tackling the browsing issue by having good search. :)
M.
On Fri, Aug 7, 2015 at 2:43 PM Keith Suderman <suderman@cs.vassar.edu> wrote: Awesome!
One concern we have is lumping all NLP tools into a single category; are sub-categories (and sub-sub-categories) possible? However, we can start with this and see what we need later.
Cheers, Keith
On Aug 7, 2015, at 12:25 PM, Martin Čech <marten@bx.psu.edu> wrote:
Dear Keith,
I have created 'NLP' category at https://testtoolshed.g2.bx.psu.edu for you to test out the Tool Shed environment.
Unless your tools are proprietary I strongly recommend using the Main Tool Shed at https://toolshed.g2.bx.psu.edu for their publishing and distribution. Let me know when you are ready with the tools and I will create the category for you in there.
We happily welcome every tool contribution to Galaxy! Thank you for it.
Martin, Galaxy Team
On Fri, Aug 7, 2015 at 12:56 PM Björn Grüning <bjoern.gruening@gmail.com> wrote: Hi Keith,
the Galaxy team can add new categories to the Tool Shed very easily and such a mail is exactly the way to go. As soon as the Galaxy teams has added the category you can use tools like planemo to upload all your tools at once.
https://github.com/galaxyproject/planemo
Looking forward to see NLP tools in Galaxy and the Main TS! Awesome! Bjoern
Dear Galaxy Team,
A colleague would like to upload some NLP (Natural Language Processing) tools to the Galaxy Test/Main tools sheds, but we are unclear what "categories" to use for the tools. I see that the Main/Test tools sheds have a category for "Text Manipulation", but that does not seem appropriate for NLP tools. Is it possible to have new categories added to the tool shed(s)? If so, what is the process?
I am just starting to investigate setting up our own local tool shed and I am coming across mentions of repository capsules and exporting tool sheds. Would it be preferable to install the NLP tools to a local tool shed and then export a repository/capsule to be imported to the Test/Main tools sheds? What happens if our tool shed uses a disjoint set of categories than Test/Main?
Cheers, Keith
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
Keith, please see the comments inline. thanks M. On Fri, Sep 11, 2015 at 4:54 PM Suderman Keith <suderman@cs.vassar.edu> wrote:
Hi Martin,
On Sep 11, 2015, at 12:44 PM, Martin Čech <marten@bx.psu.edu> wrote:
Hi Keith,
how is the NLP category working for you? Do you want it on Main Tool Shed?
The NLP category is working great. I am still in the early testing phase and likely won't need anything in Main for some time yet, but Steve Cassidy might have a different opinion.
Also I have noticed you are putting the version of your tools in the repository names. I would like to discourage that as it will create confusion once you update your tool (as you will be unable to update the repo name). The XML wrappers have they own version tracking tag for these purposes. You can learn about this and more in the Tooldev Best Practices document: http://galaxy-iuc-standards.readthedocs.org/en/latest/
I was under the impression ( http://gregvonkuster.org/galaxy-tool-shed-revisiting-best-practices-populati...) that the best practice for package names was package_<name>_<version> and for tools it was <name>_<version>.
That is correct for packages and suites but incorrect for tools. Sorry for the confusion.
There is also some friction (for lack of a better term) between versioning our web services and versioning the Galaxy wrappers that call our web services. For example, I might have multiple versions of the Galaxy wrappers for our stanford_2.0.0 services and multiple versions of the Galaxy wrappers for our stanford_2.1.0 services. The 2.0.0 services are not going away just because the 2.1.0 services are available, so I think the stanford_2.0.0 and stanford_2.1.0 Galaxy wrappers have to be separate repositories.
In this case the naming kinda makes sense to me (lapps_stanford_2_0_0 and lapps_stanford_2_1_0 that is). However could the remote Standford API version be a parameter of the tool instead? i.e. you would have only 'lapps_stanford' and select the version you want to use from a dropdown and the tool form would adjust (this is technically possible and used) and after execution called the right underlying script?
Having said that, I am planning to remove all my current repositories and repopulate as I try to automate things on my end so suggestions for naming strategies are always welcome.
"There are only two hard problems in computer science, cache invalidation and naming things" - author unknown
Thank you for using Galaxy.
Thank you (all) for making Galaxy! ;-)
Cheers, Keith
Martin
On Fri, Aug 7, 2015 at 2:57 PM Martin Čech <marten@bx.psu.edu> wrote:
No sub-categories yet; we plan on tackling the browsing issue by having good search. :)
M.
On Fri, Aug 7, 2015 at 2:43 PM Keith Suderman <suderman@cs.vassar.edu> wrote:
Awesome!
One concern we have is lumping all NLP tools into a single category; are sub-categories (and sub-sub-categories) possible? However, we can start with this and see what we need later.
Cheers, Keith
On Aug 7, 2015, at 12:25 PM, Martin Čech <marten@bx.psu.edu> wrote:
Dear Keith,
I have created 'NLP' category at https://testtoolshed.g2.bx.psu.edu for you to test out the Tool Shed environment.
Unless your tools are proprietary I strongly recommend using the Main Tool Shed at https://toolshed.g2.bx.psu.edu for their publishing and distribution. Let me know when you are ready with the tools and I will create the category for you in there.
We happily welcome every tool contribution to Galaxy! Thank you for it.
Martin, Galaxy Team
On Fri, Aug 7, 2015 at 12:56 PM Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Keith,
the Galaxy team can add new categories to the Tool Shed very easily and such a mail is exactly the way to go. As soon as the Galaxy teams has added the category you can use tools like planemo to upload all your tools at once.
https://github.com/galaxyproject/planemo
Looking forward to see NLP tools in Galaxy and the Main TS! Awesome! Bjoern
Dear Galaxy Team,
A colleague would like to upload some NLP (Natural Language Processing) tools to the Galaxy Test/Main tools sheds, but we are unclear what "categories" to use for the tools. I see that the Main/Test tools sheds have a category for "Text Manipulation", but that does not seem appropriate for NLP tools. Is it possible to have new categories added to the tool shed(s)? If so, what is the process?
I am just starting to investigate setting up our own local tool shed and I am coming across mentions of repository capsules and exporting tool sheds. Would it be preferable to install the NLP tools to a local tool shed and then export a repository/capsule to be imported to the Test/Main tools sheds? What happens if our tool shed uses a disjoint set of categories than Test/Main?
Cheers, Keith
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
Am 12.09.2015 um 00:09 schrieb Martin Čech:
Keith, please see the comments inline. thanks M.
On Fri, Sep 11, 2015 at 4:54 PM Suderman Keith <suderman@cs.vassar.edu> wrote:
Hi Martin,
On Sep 11, 2015, at 12:44 PM, Martin Čech <marten@bx.psu.edu> wrote:
Hi Keith,
how is the NLP category working for you? Do you want it on Main Tool Shed?
The NLP category is working great. I am still in the early testing phase and likely won't need anything in Main for some time yet, but Steve Cassidy might have a different opinion.
Also I have noticed you are putting the version of your tools in the repository names. I would like to discourage that as it will create confusion once you update your tool (as you will be unable to update the repo name). The XML wrappers have they own version tracking tag for these purposes. You can learn about this and more in the Tooldev Best Practices document: http://galaxy-iuc-standards.readthedocs.org/en/latest/
I was under the impression ( http://gregvonkuster.org/galaxy-tool-shed-revisiting-best-practices-populati...) that the best practice for package names was package_<name>_<version> and for tools it was <name>_<version>.
That is correct for packages and suites but incorrect for tools. Sorry for the confusion.
There is also some friction (for lack of a better term) between versioning our web services and versioning the Galaxy wrappers that call our web services. For example, I might have multiple versions of the Galaxy wrappers for our stanford_2.0.0 services and multiple versions of the Galaxy wrappers for our stanford_2.1.0 services. The 2.0.0 services are not going away just because the 2.1.0 services are available, so I think the stanford_2.0.0 and stanford_2.1.0 Galaxy wrappers have to be separate repositories.
In this case the naming kinda makes sense to me (lapps_stanford_2_0_0 and lapps_stanford_2_1_0 that is). However could the remote Standford API version be a parameter of the tool instead? i.e. you would have only 'lapps_stanford' and select the version you want to use from a dropdown and the tool form would adjust (this is technically possible and used) and after execution called the right underlying script?
+1 for putting this all in one tool. I (as admin) should not decide which API version to use :)
Having said that, I am planning to remove all my current repositories and repopulate as I try to automate things on my end so suggestions for naming strategies are always welcome.
"There are only two hard problems in computer science, cache invalidation and naming things" - author unknown
Thank you for using Galaxy.
Thank you (all) for making Galaxy! ;-)
Cheers, Keith
Martin
On Fri, Aug 7, 2015 at 2:57 PM Martin Čech <marten@bx.psu.edu> wrote:
No sub-categories yet; we plan on tackling the browsing issue by having good search. :)
M.
On Fri, Aug 7, 2015 at 2:43 PM Keith Suderman <suderman@cs.vassar.edu> wrote:
Awesome!
One concern we have is lumping all NLP tools into a single category; are sub-categories (and sub-sub-categories) possible? However, we can start with this and see what we need later.
Cheers, Keith
On Aug 7, 2015, at 12:25 PM, Martin Čech <marten@bx.psu.edu> wrote:
Dear Keith,
I have created 'NLP' category at https://testtoolshed.g2.bx.psu.edu for you to test out the Tool Shed environment.
Unless your tools are proprietary I strongly recommend using the Main Tool Shed at https://toolshed.g2.bx.psu.edu for their publishing and distribution. Let me know when you are ready with the tools and I will create the category for you in there.
We happily welcome every tool contribution to Galaxy! Thank you for it.
Martin, Galaxy Team
On Fri, Aug 7, 2015 at 12:56 PM Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Keith,
the Galaxy team can add new categories to the Tool Shed very easily and such a mail is exactly the way to go. As soon as the Galaxy teams has added the category you can use tools like planemo to upload all your tools at once.
https://github.com/galaxyproject/planemo
Looking forward to see NLP tools in Galaxy and the Main TS! Awesome! Bjoern
Dear Galaxy Team,
A colleague would like to upload some NLP (Natural Language Processing) tools to the Galaxy Test/Main tools sheds, but we are unclear what "categories" to use for the tools. I see that the Main/Test tools sheds have a category for "Text Manipulation", but that does not seem appropriate for NLP tools. Is it possible to have new categories added to the tool shed(s)? If so, what is the process?
I am just starting to investigate setting up our own local tool shed and I am coming across mentions of repository capsules and exporting tool sheds. Would it be preferable to install the NLP tools to a local tool shed and then export a repository/capsule to be imported to the Test/Main tools sheds? What happens if our tool shed uses a disjoint set of categories than Test/Main?
Cheers, Keith
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
I'm going to trim the replies a bit so my comments are easier to find.
Am 12.09.2015 um 00:09 schrieb Martin Čech:
In this case the naming kinda makes sense to me (lapps_stanford_2_0_0 and lapps_stanford_2_1_0 that is). However could the remote Standford API version be a parameter of the tool instead? i.e. you would have only 'lapps_stanford' and select the version you want to use from a dropdown and the tool form would adjust (this is technically possible and used) and after execution called the right underlying script?
Yes, this wouldn't be very difficult, but I think I prefer keeping everything as distinct as possible. That way changes to the v1.1 wrapper for the lapps_stanford_2.1.0 tools are guaranteed to have no effect on the v1.0 wrapper for the lapps_stanford_2.0.0 tools. Also, all my wrapper XML files and test data are machine generated and keeping everything separate makes that process a little easier. On Sep 12, 2015, at 4:09 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
+1 for putting this all in one tool. I (as admin) should not decide which API version to use :)
The user would still be able to select which API version to use simply by selecting a different tool. However, keeping in mind TS best practices I will likely go with whatever is the easiest to implement and maintain. Cheers, Keith
participants (4)
-
Björn Grüning -
Keith Suderman -
Martin Čech -
Suderman Keith