Re: [galaxy-dev] removing wrapper version info from tools?
Hi Nik,
Hi Bjorn,
Thanks for your response. It seems to me that the wrapper version is not really that useful... the thing that is important is the version of the underlying tool.
Sure, I agree. But on the other side the user should not care about the version, and is on most cases not interested as long as it works :) But as pointed out I would also like to shift to a more useful numbering, that the arbitrary one we are using now. I can certainly update the versions to be the versions of
the tool, if need be.
That will break many thing, if you combining your tools with the toolshed and updates would be more complicated. Don't do that, at least not for tools from the ToolShed. Try to convince the Tool Maintainers. However, I wasn't aware that you could have multiple
versions of the same tool to choose from. How do I get that to work?
You can simply install multiple versions (revisions) from the same tool from the Tool Shed. For example multimple Blast version.
I tried creating two different XML files with the same tool id, but that didn't work. And how would I make sure the wrapper scripts pointed to the correct version... it seems like I would have to tailor each script with an absolute path to the specific version....?
No you need to have the Tool Shed managing that for you. Each version is a separate tool with the same tool-id. Galaxy keeps track of every dependency of a certain tool. So the same tool with different versions with different dependencies will be working over time. Please read more about all of that in the galaxy wiki, especially about Tools and the Tool Shed: https://wiki.galaxyproject.org/ToolShed Cheers, Bjoern
- Nik.
On Mon, Jul 7, 2014 at 11:56 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Nik,
you can hack to tool rendering and omit the version string, but I would not recommend that. The version will be a selectbox as soon as you have multiple versions from the same tools installed. This is important for reproducibility. The best approach would be to fix the version string. Do you have any suggestions? For my wrappers I try to go with that version scheme: {Tool-Version}.{wrapper-version}.
Cheers, Bjoern
Am 08.07.2014 08:51, schrieb Nikhil Joshi:
Hi all,
So I am trying to remove the version info (at the top of a tool page) entirely for all the tools. As I understand, those versions are the versions of the wrappers and not the tools themselves. Although I could change that, I would rather just not have the versions on the tool pages at all. We currently show all the versions of our tools on our landing page. Is there any way to remove the version part of the tool title entirely? I.e., if it originally says "Map with BWA for Illumina (version 1.0.0)", I just want it to say "Map with BWA for Illumina".
- Nik.
___________________________________________________________ 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 Bjorn, So I actually don't use the toolshed at all, we have a galaxy AMI that I update and maintain. We have many of the canonical tools, but we also have many custom tool interfaces on there, some of which I wrote. We also use the latest version of the tool if possible. All of the XML files are local to the instance and are not from the toolshed. I am referring to the version that is used in the "<tool>" tag. That version number seems arbitrary and the students that use our Galaxy are constantly confused as to why the tool page has a different version than the tool itself. However, it seems like there is no easy way to remove that part, so I think I will just have to update the version numbers myself. What would be the best way to have multiple versions of a tool *without* using the toolshed? Any help is highly appreciated. Thanks! - Nik. On Tue, Jul 8, 2014 at 1:12 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Nik,
Hi Bjorn,
Thanks for your response. It seems to me that the wrapper version is not really that useful... the thing that is important is the version of the underlying tool.
Sure, I agree. But on the other side the user should not care about the version, and is on most cases not interested as long as it works :) But as pointed out I would also like to shift to a more useful numbering, that the arbitrary one we are using now.
I can certainly update the versions to be the versions of
the tool, if need be.
That will break many thing, if you combining your tools with the toolshed and updates would be more complicated. Don't do that, at least not for tools from the ToolShed. Try to convince the Tool Maintainers.
However, I wasn't aware that you could have multiple
versions of the same tool to choose from. How do I get that to work?
You can simply install multiple versions (revisions) from the same tool from the Tool Shed. For example multimple Blast version.
I tried creating two different XML files with the same tool id, but that
didn't work. And how would I make sure the wrapper scripts pointed to the correct version... it seems like I would have to tailor each script with an absolute path to the specific version....?
No you need to have the Tool Shed managing that for you. Each version is a separate tool with the same tool-id. Galaxy keeps track of every dependency of a certain tool. So the same tool with different versions with different dependencies will be working over time.
Please read more about all of that in the galaxy wiki, especially about Tools and the Tool Shed:
https://wiki.galaxyproject.org/ToolShed
Cheers, Bjoern
- Nik.
On Mon, Jul 7, 2014 at 11:56 PM, Björn Grüning <bjoern.gruening@gmail.com
wrote:
Hi Nik,
you can hack to tool rendering and omit the version string, but I would not recommend that. The version will be a selectbox as soon as you have multiple versions from the same tools installed. This is important for reproducibility. The best approach would be to fix the version string. Do you have any suggestions? For my wrappers I try to go with that version scheme: {Tool-Version}.{wrapper-version}.
Cheers, Bjoern
Am 08.07.2014 08:51, schrieb Nikhil Joshi:
Hi all,
So I am trying to remove the version info (at the top of a tool page) entirely for all the tools. As I understand, those versions are the versions of the wrappers and not the tools themselves. Although I could change that, I would rather just not have the versions on the tool pages at all. We currently show all the versions of our tools on our landing page. Is there any way to remove the version part of the tool title entirely? I.e., if it originally says "Map with BWA for Illumina (version 1.0.0)", I just want it to say "Map with BWA for Illumina".
- Nik.
___________________________________________________________ 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/
-- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w)
Hi Nik, sorry for my late response. Am 09.07.2014 01:23, schrieb Nikhil Joshi:
Hi Bjorn,
So I actually don't use the toolshed at all, we have a galaxy AMI that I update and maintain. We have many of the canonical tools, but we also have many custom tool interfaces on there, some of which I wrote. We also use the latest version of the tool if possible. All of the XML files are local to the instance and are not from the toolshed. I am referring to the version that is used in the "<tool>" tag. That version number seems arbitrary and the students that use our Galaxy are constantly confused as to why the tool page has a different version than the tool itself.However, it seems like there is no easy way to remove that part, so I think I will just have to update the version numbers myself.
Please remember you are then forced to maintain the tools all by your own and integrate changes from upstream by your own. I'm not sure that is worth the effort.
What would be the best way to have multiple versions of a tool *without* using the toolshed? Any help is highly appreciated. Thanks!
I don't think that is possible at all. In the end that is one reason the Tool Shed project was started. To make it possible to have many different tool versions and to spread the maintenance burden over the entire community. Have a look at the galaxytools repository, maintained by several people: https://github.com/bgruening/galaxytools We accept PR and you are very welcome to work with us to improve the tools, in the end I really think it will save you some time. An other really easy possibility is ... just remove the tool-version from the HTML rendering. If you are not afraid of maintaining in house patches, that should be fine and will take time, I guess. Cheers, Bjoern
- Nik.
On Tue, Jul 8, 2014 at 1:12 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Nik,
Hi Bjorn,
Thanks for your response. It seems to me that the wrapper version is not really that useful... the thing that is important is the version of the underlying tool.
Sure, I agree. But on the other side the user should not care about the version, and is on most cases not interested as long as it works :) But as pointed out I would also like to shift to a more useful numbering, that the arbitrary one we are using now.
I can certainly update the versions to be the versions of
the tool, if need be.
That will break many thing, if you combining your tools with the toolshed and updates would be more complicated. Don't do that, at least not for tools from the ToolShed. Try to convince the Tool Maintainers.
However, I wasn't aware that you could have multiple
versions of the same tool to choose from. How do I get that to work?
You can simply install multiple versions (revisions) from the same tool from the Tool Shed. For example multimple Blast version.
I tried creating two different XML files with the same tool id, but that
didn't work. And how would I make sure the wrapper scripts pointed to the correct version... it seems like I would have to tailor each script with an absolute path to the specific version....?
No you need to have the Tool Shed managing that for you. Each version is a separate tool with the same tool-id. Galaxy keeps track of every dependency of a certain tool. So the same tool with different versions with different dependencies will be working over time.
Please read more about all of that in the galaxy wiki, especially about Tools and the Tool Shed:
https://wiki.galaxyproject.org/ToolShed
Cheers, Bjoern
- Nik.
On Mon, Jul 7, 2014 at 11:56 PM, Björn Grüning <bjoern.gruening@gmail.com
wrote:
Hi Nik,
you can hack to tool rendering and omit the version string, but I would not recommend that. The version will be a selectbox as soon as you have multiple versions from the same tools installed. This is important for reproducibility. The best approach would be to fix the version string. Do you have any suggestions? For my wrappers I try to go with that version scheme: {Tool-Version}.{wrapper-version}.
Cheers, Bjoern
Am 08.07.2014 08:51, schrieb Nikhil Joshi:
Hi all,
So I am trying to remove the version info (at the top of a tool page) entirely for all the tools. As I understand, those versions are the versions of the wrappers and not the tools themselves. Although I could change that, I would rather just not have the versions on the tool pages at all. We currently show all the versions of our tools on our landing page. Is there any way to remove the version part of the tool title entirely? I.e., if it originally says "Map with BWA for Illumina (version 1.0.0)", I just want it to say "Map with BWA for Illumina".
- Nik.
___________________________________________________________ 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 (2)
-
Björn Grüning -
Nikhil Joshi