Re: [galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)
Hi Lance, I looked at this a bit ago and had similar concerns, particularly with the outputs and inputs not being well-defined. In addition to the output tar ball —> local, extract —> upload not being great, as you mention, the input datatypes, etc, could use some work — in the very least, we should definitely create a nice biom datatype and have some converters available (import and export). Definitely worth spending some extra time to make sure that we have the data flowing well between each of the different parts/tools, and even better to make sure that its done in a way that allows mixing and matching with other non-qiime tools. One thing that we want to avoid is large amounts of manual massaging of the automatically generated xml; fixing things up once might not be too bad, but having to do it with each new tool version can be “frustrating". Although perhaps having a good starting point and only needing to manually modify for any updates could be good enough (I’m not very familiar with the extent of typical changes between qiime versions to make a call on how much changes). Dan (resending since I received a message bounce from list) On Oct 6, 2015, at 9:59 AM, Daniel Blankenberg <dan@bx.psu.edu> wrote:
Hi Lance,
I looked at this a bit ago and had similar concerns, particularly with the outputs and inputs not being well-defined. In addition to the output tar ball —> local, extract —> upload not being great, as you mention, the input datatypes, etc, could use some work — in the very least, we should definitely create a nice biom datatype and have some converters available (import and export).
Definitely worth spending some extra time to make sure that we have the data flowing well between each of the different parts/tools, and even better to make sure that its done in a way that allows mixing and matching with other non-qiime tools.
One thing that we want to avoid is large amounts of manual massaging of the automatically generated xml; fixing things up once might not be too bad, but having to do it with each new tool version can be “frustrating". Although perhaps having a good starting point and only needing to manually modify for any updates could be good enough (I’m not very familiar with the extent of typical changes between qiime versions to make a call on how much changes).
Dan
On Oct 5, 2015, at 5:26 PM, Lance Parsons <lparsons@princeton.edu> wrote:
I was recently asked if I could provide a QIIME analysis pipeline for 16S data in Galaxy using tools in the QIIME pipeline (http://qiime.org/).
I did a bit of looking around for existing Galaxy wrappers and found an application that generates the wrappers for QIIME scripts for Galaxy (https://github.com/qiime/qiime-galaxy). This is a very well written application that does a great job of wrapping the QIIME scripts for Galaxy. However, there are a few things about it that don't quite fit my needs.
1. The tools output tgz files of all of the output files. This means that to execute a pipeline, the user would have to download the tgz files, untar, and then upload whichever file(s) are needed for the next step. 2. There is no toolshed repository to install the dependencies for these tools, making it a tricky for administrators to automate and also maintain various versions of QIIME going forward. 3. There are no toolshed versions of the tools themselves, which also makes installation and integration a bit tricky and makes it hard to me to create and manage updates, fixes, tweaks, etc. There are also no tests, etc.
For these reasons I decided to investigate the feasibility of using the generated wrappers as a basis for a "toolshed" version of QIIME. If anyone is interested in helping, or has suggestions, or is working on something related, I'd be very happy to collaborate.
The repository for the WIP is at https://github.com/lparsons/galaxy_tools/tree/qiime/tools/qiime1.9.0. There is also a package on the testtoolshed as well as a first pass at package_qiime_1_9_1 (https://github.com/lparsons/galaxy_tools/tree/qiime/packages/package_qiime_1...).
-- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University
___________________________________________________________ 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 agree that it would be very nice to get the data flowing between each of the tools and to be able to mix/match with other tools. That is an area of Galaxy tool-dev that I'm less familiar with, so any help would be greatly appreciated. As for the manual massaging, I agree, however, at this point I'm really hoping that the changes between Qiime versions are manageable, esp. once we have the data types and basic framework of the tools down. Along that front, I would very much like to get something usable (at least for some specific workflows) done sooner rather than later, then be able to iterate, adding new tools, datatypes, etc. as we move forward. Does that sound reasonable? I love the idea of a Metagenomics toolfest (https://github.com/galaxyproject/tools-iuc/issues/299). One thing I would like to do soon then, would be to define some functionality for the first round. What would be very helpful would be if you, Bjoern, etc. could help make sure the first round lays the proper groundwork so I/we don't have to redo things for later iterations, but we can build on a solid foundation. Thanks so much for the input, help, etc. It is very much appreciated. - Lance
Daniel Blankenberg <mailto:dan@bx.psu.edu> October 6, 2015 at 10:21 AM Hi Lance,
I looked at this a bit ago and had similar concerns, particularly with the outputs and inputs not being well-defined. In addition to the output tar ball —> local, extract —> upload not being great, as you mention, the input datatypes, etc, could use some work — in the very least, we should definitely create a nice biom datatype and have some converters available (import and export).
Definitely worth spending some extra time to make sure that we have the data flowing well between each of the different parts/tools, and even better to make sure that its done in a way that allows mixing and matching with other non-qiime tools.
One thing that we want to avoid is large amounts of manual massaging of the automatically generated xml; fixing things up once might not be too bad, but having to do it with each new tool version can be “frustrating". Although perhaps having a good starting point and only needing to manually modify for any updates could be good enough (I’m not very familiar with the extent of typical changes between qiime versions to make a call on how much changes).
Dan
(resending since I received a message bounce from list)
Daniel Blankenberg <mailto:dan@bx.psu.edu> October 6, 2015 at 9:59 AM Hi Lance,
I looked at this a bit ago and had similar concerns, particularly with the outputs and inputs not being well-defined. In addition to the output tar ball —> local, extract —> upload not being great, as you mention, the input datatypes, etc, could use some work — in the very least, we should definitely create a nice biom datatype and have some converters available (import and export).
Definitely worth spending some extra time to make sure that we have the data flowing well between each of the different parts/tools, and even better to make sure that its done in a way that allows mixing and matching with other non-qiime tools.
One thing that we want to avoid is large amounts of manual massaging of the automatically generated xml; fixing things up once might not be too bad, but having to do it with each new tool version can be “frustrating". Although perhaps having a good starting point and only needing to manually modify for any updates could be good enough (I’m not very familiar with the extent of typical changes between qiime versions to make a call on how much changes).
Dan
Lance Parsons <mailto:lparsons@princeton.edu> October 5, 2015 at 5:26 PM I was recently asked if I could provide a QIIME analysis pipeline for 16S data in Galaxy using tools in the QIIME pipeline (http://qiime.org/).
I did a bit of looking around for existing Galaxy wrappers and found an application that generates the wrappers for QIIME scripts for Galaxy (https://github.com/qiime/qiime-galaxy). This is a very well written application that does a great job of wrapping the QIIME scripts for Galaxy. However, there are a few things about it that don't quite fit my needs.
1. The tools output tgz files of all of the output files. This means that to execute a pipeline, the user would have to download the tgz files, untar, and then upload whichever file(s) are needed for the next step. 2. There is no toolshed repository to install the dependencies for these tools, making it a tricky for administrators to automate and also maintain various versions of QIIME going forward. 3. There are no toolshed versions of the tools themselves, which also makes installation and integration a bit tricky and makes it hard to me to create and manage updates, fixes, tweaks, etc. There are also no tests, etc.
For these reasons I decided to investigate the feasibility of using the generated wrappers as a basis for a "toolshed" version of QIIME. If anyone is interested in helping, or has suggestions, or is working on something related, I'd be very happy to collaborate.
The repository for the WIP is at https://github.com/lparsons/galaxy_tools/tree/qiime/tools/qiime1.9.0. There is also a package on the testtoolshed as well as a first pass at package_qiime_1_9_1 (https://github.com/lparsons/galaxy_tools/tree/qiime/packages/package_qiime_1...).
-- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University
Hi Lance, I will help if I can. I also think we should begin too write 2-3 nice tools in the beginning to test the handshake between them and lay the ground work. This will also help to get familiar with the tool. I still hope some one else from the community shows interest! :) Thanks, Bjoern Am 06.10.2015 um 20:33 schrieb Lance Parsons:
I agree that it would be very nice to get the data flowing between each of the tools and to be able to mix/match with other tools. That is an area of Galaxy tool-dev that I'm less familiar with, so any help would be greatly appreciated.
As for the manual massaging, I agree, however, at this point I'm really hoping that the changes between Qiime versions are manageable, esp. once we have the data types and basic framework of the tools down.
Along that front, I would very much like to get something usable (at least for some specific workflows) done sooner rather than later, then be able to iterate, adding new tools, datatypes, etc. as we move forward. Does that sound reasonable? I love the idea of a Metagenomics toolfest (https://github.com/galaxyproject/tools-iuc/issues/299). One thing I would like to do soon then, would be to define some functionality for the first round. What would be very helpful would be if you, Bjoern, etc. could help make sure the first round lays the proper groundwork so I/we don't have to redo things for later iterations, but we can build on a solid foundation.
Thanks so much for the input, help, etc. It is very much appreciated.
- Lance
Daniel Blankenberg <mailto:dan@bx.psu.edu> October 6, 2015 at 10:21 AM Hi Lance,
I looked at this a bit ago and had similar concerns, particularly with the outputs and inputs not being well-defined. In addition to the output tar ball —> local, extract —> upload not being great, as you mention, the input datatypes, etc, could use some work — in the very least, we should definitely create a nice biom datatype and have some converters available (import and export).
Definitely worth spending some extra time to make sure that we have the data flowing well between each of the different parts/tools, and even better to make sure that its done in a way that allows mixing and matching with other non-qiime tools.
One thing that we want to avoid is large amounts of manual massaging of the automatically generated xml; fixing things up once might not be too bad, but having to do it with each new tool version can be “frustrating". Although perhaps having a good starting point and only needing to manually modify for any updates could be good enough (I’m not very familiar with the extent of typical changes between qiime versions to make a call on how much changes).
Dan
(resending since I received a message bounce from list)
Daniel Blankenberg <mailto:dan@bx.psu.edu> October 6, 2015 at 9:59 AM Hi Lance,
I looked at this a bit ago and had similar concerns, particularly with the outputs and inputs not being well-defined. In addition to the output tar ball —> local, extract —> upload not being great, as you mention, the input datatypes, etc, could use some work — in the very least, we should definitely create a nice biom datatype and have some converters available (import and export).
Definitely worth spending some extra time to make sure that we have the data flowing well between each of the different parts/tools, and even better to make sure that its done in a way that allows mixing and matching with other non-qiime tools.
One thing that we want to avoid is large amounts of manual massaging of the automatically generated xml; fixing things up once might not be too bad, but having to do it with each new tool version can be “frustrating". Although perhaps having a good starting point and only needing to manually modify for any updates could be good enough (I’m not very familiar with the extent of typical changes between qiime versions to make a call on how much changes).
Dan
Lance Parsons <mailto:lparsons@princeton.edu> October 5, 2015 at 5:26 PM I was recently asked if I could provide a QIIME analysis pipeline for 16S data in Galaxy using tools in the QIIME pipeline (http://qiime.org/).
I did a bit of looking around for existing Galaxy wrappers and found an application that generates the wrappers for QIIME scripts for Galaxy (https://github.com/qiime/qiime-galaxy). This is a very well written application that does a great job of wrapping the QIIME scripts for Galaxy. However, there are a few things about it that don't quite fit my needs.
1. The tools output tgz files of all of the output files. This means that to execute a pipeline, the user would have to download the tgz files, untar, and then upload whichever file(s) are needed for the next step. 2. There is no toolshed repository to install the dependencies for these tools, making it a tricky for administrators to automate and also maintain various versions of QIIME going forward. 3. There are no toolshed versions of the tools themselves, which also makes installation and integration a bit tricky and makes it hard to me to create and manage updates, fixes, tweaks, etc. There are also no tests, etc.
For these reasons I decided to investigate the feasibility of using the generated wrappers as a basis for a "toolshed" version of QIIME. If anyone is interested in helping, or has suggestions, or is working on something related, I'd be very happy to collaborate.
The repository for the WIP is at https://github.com/lparsons/galaxy_tools/tree/qiime/tools/qiime1.9.0. There is also a package on the testtoolshed as well as a first pass at package_qiime_1_9_1 (https://github.com/lparsons/galaxy_tools/tree/qiime/packages/package_qiime_1...).
___________________________________________________________ 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/
Hi Lance, Björn, Dan We are several scientists working on metagenomics in France and at a previous GUGGO (western France User Group) meeting, we mention the fact to "benchmark" our Galaxy pipelines. One is using new Qiime tools integration, one Mothur and the last one, the recently developped FROGS (Find Rapidly OTU with Galaxy Solution) pipeline using Swarm. We already have had some exchanges with Björn concerning metagenomics flavours on Docker, and I think it will be particularly interesting to exchange one with each other. The Qiime integration was started in march by colleagues from Brest Ifremer centre. I was just trying to install and test FROGS from Toulouse and Jouy-en-Josas INRA labs. If they are not on the list, I can contact them. All the best, Yvan ----- Mail original -----
De: "Björn Grüning" <bjoern.gruening@gmail.com> À: "Lance Parsons" <lparsons@princeton.edu>, "Daniel Blankenberg" <dan@bx.psu.edu> Cc: "Galaxy Dev List" <galaxy-dev@lists.galaxyproject.org> Envoyé: Mercredi 7 Octobre 2015 14:25:38 Objet: Re: [galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)
Hi Lance,
I will help if I can. I also think we should begin too write 2-3 nice tools in the beginning to test the handshake between them and lay the ground work. This will also help to get familiar with the tool.
I still hope some one else from the community shows interest! :)
Thanks, Bjoern
Am 06.10.2015 um 20:33 schrieb Lance Parsons:
I agree that it would be very nice to get the data flowing between each of the tools and to be able to mix/match with other tools. That is an area of Galaxy tool-dev that I'm less familiar with, so any help would be greatly appreciated.
As for the manual massaging, I agree, however, at this point I'm really hoping that the changes between Qiime versions are manageable, esp. once we have the data types and basic framework of the tools down.
Along that front, I would very much like to get something usable (at least for some specific workflows) done sooner rather than later, then be able to iterate, adding new tools, datatypes, etc. as we move forward. Does that sound reasonable? I love the idea of a Metagenomics toolfest (https://github.com/galaxyproject/tools-iuc/issues/299). One thing I would like to do soon then, would be to define some functionality for the first round. What would be very helpful would be if you, Bjoern, etc. could help make sure the first round lays the proper groundwork so I/we don't have to redo things for later iterations, but we can build on a solid foundation.
Thanks so much for the input, help, etc. It is very much appreciated.
- Lance
Daniel Blankenberg <mailto:dan@bx.psu.edu> October 6, 2015 at 10:21 AM Hi Lance,
I looked at this a bit ago and had similar concerns, particularly with the outputs and inputs not being well-defined. In addition to the output tar ball —> local, extract —> upload not being great, as you mention, the input datatypes, etc, could use some work — in the very least, we should definitely create a nice biom datatype and have some converters available (import and export).
Definitely worth spending some extra time to make sure that we have the data flowing well between each of the different parts/tools, and even better to make sure that its done in a way that allows mixing and matching with other non-qiime tools.
One thing that we want to avoid is large amounts of manual massaging of the automatically generated xml; fixing things up once might not be too bad, but having to do it with each new tool version can be “frustrating". Although perhaps having a good starting point and only needing to manually modify for any updates could be good enough (I’m not very familiar with the extent of typical changes between qiime versions to make a call on how much changes).
Dan
(resending since I received a message bounce from list)
Daniel Blankenberg <mailto:dan@bx.psu.edu> October 6, 2015 at 9:59 AM Hi Lance,
I looked at this a bit ago and had similar concerns, particularly with the outputs and inputs not being well-defined. In addition to the output tar ball —> local, extract —> upload not being great, as you mention, the input datatypes, etc, could use some work — in the very least, we should definitely create a nice biom datatype and have some converters available (import and export).
Definitely worth spending some extra time to make sure that we have the data flowing well between each of the different parts/tools, and even better to make sure that its done in a way that allows mixing and matching with other non-qiime tools.
One thing that we want to avoid is large amounts of manual massaging of the automatically generated xml; fixing things up once might not be too bad, but having to do it with each new tool version can be “frustrating". Although perhaps having a good starting point and only needing to manually modify for any updates could be good enough (I’m not very familiar with the extent of typical changes between qiime versions to make a call on how much changes).
Dan
Lance Parsons <mailto:lparsons@princeton.edu> October 5, 2015 at 5:26 PM I was recently asked if I could provide a QIIME analysis pipeline for 16S data in Galaxy using tools in the QIIME pipeline (http://qiime.org/).
I did a bit of looking around for existing Galaxy wrappers and found an application that generates the wrappers for QIIME scripts for Galaxy (https://github.com/qiime/qiime-galaxy). This is a very well written application that does a great job of wrapping the QIIME scripts for Galaxy. However, there are a few things about it that don't quite fit my needs.
1. The tools output tgz files of all of the output files. This means that to execute a pipeline, the user would have to download the tgz files, untar, and then upload whichever file(s) are needed for the next step. 2. There is no toolshed repository to install the dependencies for these tools, making it a tricky for administrators to automate and also maintain various versions of QIIME going forward. 3. There are no toolshed versions of the tools themselves, which also makes installation and integration a bit tricky and makes it hard to me to create and manage updates, fixes, tweaks, etc. There are also no tests, etc.
For these reasons I decided to investigate the feasibility of using the generated wrappers as a basis for a "toolshed" version of QIIME. If anyone is interested in helping, or has suggestions, or is working on something related, I'd be very happy to collaborate.
The repository for the WIP is at https://github.com/lparsons/galaxy_tools/tree/qiime/tools/qiime1.9.0. There is also a package on the testtoolshed as well as a first pass at package_qiime_1_9_1 (https://github.com/lparsons/galaxy_tools/tree/qiime/packages/package_qiime_1...).
___________________________________________________________ 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/
___________________________________________________________ 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/
-- ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Yvan Le Bras, PhD @Yvan2935 <°))))>< e-Biogenouest project http://www.e-biogenouest.org CNRS UMR 6074 IRISA-INRIA, Campus de Beaulieu, 35042 Rennes Cedex tél.: +33 (0) 2 99 84 71 79 / +33 (0) 6.10.43.96.51 yvan.le_bras@irisa.fr
Hi Yvan,
Hi Lance, Björn, Dan
We are several scientists working on metagenomics in France and at a previous GUGGO (western France User Group) meeting, we mention the fact to "benchmark" our Galaxy pipelines. One is using new Qiime tools integration, one Mothur and the last one, the recently developped FROGS (Find Rapidly OTU with Galaxy Solution) pipeline using Swarm. We already have had some exchanges with Björn concerning metagenomics flavours on Docker, and I think it will be particularly interesting to exchange one with each other. The Qiime integration was started in march by colleagues from Brest Ifremer centre. I was just trying to install and test FROGS from Toulouse and Jouy-en-Josas INRA labs. If they are not on the list, I can contact them.
Please do so. This is great to know. Please also consider to join our hackathon: https://github.com/galaxyproject/tools-iuc/issues/299 We are always open for new ideas. Would be great to get a nice suite and a few workflows for metagenomic in the near future! :) Thanks, Bjoern
All the best,
Yvan
----- Mail original -----
De: "Björn Grüning" <bjoern.gruening@gmail.com> À: "Lance Parsons" <lparsons@princeton.edu>, "Daniel Blankenberg" <dan@bx.psu.edu> Cc: "Galaxy Dev List" <galaxy-dev@lists.galaxyproject.org> Envoyé: Mercredi 7 Octobre 2015 14:25:38 Objet: Re: [galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)
Hi Lance,
I will help if I can. I also think we should begin too write 2-3 nice tools in the beginning to test the handshake between them and lay the ground work. This will also help to get familiar with the tool.
I still hope some one else from the community shows interest! :)
Thanks, Bjoern
Am 06.10.2015 um 20:33 schrieb Lance Parsons:
I agree that it would be very nice to get the data flowing between each of the tools and to be able to mix/match with other tools. That is an area of Galaxy tool-dev that I'm less familiar with, so any help would be greatly appreciated.
As for the manual massaging, I agree, however, at this point I'm really hoping that the changes between Qiime versions are manageable, esp. once we have the data types and basic framework of the tools down.
Along that front, I would very much like to get something usable (at least for some specific workflows) done sooner rather than later, then be able to iterate, adding new tools, datatypes, etc. as we move forward. Does that sound reasonable? I love the idea of a Metagenomics toolfest (https://github.com/galaxyproject/tools-iuc/issues/299). One thing I would like to do soon then, would be to define some functionality for the first round. What would be very helpful would be if you, Bjoern, etc. could help make sure the first round lays the proper groundwork so I/we don't have to redo things for later iterations, but we can build on a solid foundation.
Thanks so much for the input, help, etc. It is very much appreciated.
- Lance
Daniel Blankenberg <mailto:dan@bx.psu.edu> October 6, 2015 at 10:21 AM Hi Lance,
I looked at this a bit ago and had similar concerns, particularly with the outputs and inputs not being well-defined. In addition to the output tar ball —> local, extract —> upload not being great, as you mention, the input datatypes, etc, could use some work — in the very least, we should definitely create a nice biom datatype and have some converters available (import and export).
Definitely worth spending some extra time to make sure that we have the data flowing well between each of the different parts/tools, and even better to make sure that its done in a way that allows mixing and matching with other non-qiime tools.
One thing that we want to avoid is large amounts of manual massaging of the automatically generated xml; fixing things up once might not be too bad, but having to do it with each new tool version can be “frustrating". Although perhaps having a good starting point and only needing to manually modify for any updates could be good enough (I’m not very familiar with the extent of typical changes between qiime versions to make a call on how much changes).
Dan
(resending since I received a message bounce from list)
Daniel Blankenberg <mailto:dan@bx.psu.edu> October 6, 2015 at 9:59 AM Hi Lance,
I looked at this a bit ago and had similar concerns, particularly with the outputs and inputs not being well-defined. In addition to the output tar ball —> local, extract —> upload not being great, as you mention, the input datatypes, etc, could use some work — in the very least, we should definitely create a nice biom datatype and have some converters available (import and export).
Definitely worth spending some extra time to make sure that we have the data flowing well between each of the different parts/tools, and even better to make sure that its done in a way that allows mixing and matching with other non-qiime tools.
One thing that we want to avoid is large amounts of manual massaging of the automatically generated xml; fixing things up once might not be too bad, but having to do it with each new tool version can be “frustrating". Although perhaps having a good starting point and only needing to manually modify for any updates could be good enough (I’m not very familiar with the extent of typical changes between qiime versions to make a call on how much changes).
Dan
Lance Parsons <mailto:lparsons@princeton.edu> October 5, 2015 at 5:26 PM I was recently asked if I could provide a QIIME analysis pipeline for 16S data in Galaxy using tools in the QIIME pipeline (http://qiime.org/).
I did a bit of looking around for existing Galaxy wrappers and found an application that generates the wrappers for QIIME scripts for Galaxy (https://github.com/qiime/qiime-galaxy). This is a very well written application that does a great job of wrapping the QIIME scripts for Galaxy. However, there are a few things about it that don't quite fit my needs.
1. The tools output tgz files of all of the output files. This means that to execute a pipeline, the user would have to download the tgz files, untar, and then upload whichever file(s) are needed for the next step. 2. There is no toolshed repository to install the dependencies for these tools, making it a tricky for administrators to automate and also maintain various versions of QIIME going forward. 3. There are no toolshed versions of the tools themselves, which also makes installation and integration a bit tricky and makes it hard to me to create and manage updates, fixes, tweaks, etc. There are also no tests, etc.
For these reasons I decided to investigate the feasibility of using the generated wrappers as a basis for a "toolshed" version of QIIME. If anyone is interested in helping, or has suggestions, or is working on something related, I'd be very happy to collaborate.
The repository for the WIP is at https://github.com/lparsons/galaxy_tools/tree/qiime/tools/qiime1.9.0.
There is also a package on the testtoolshed as well as a first pass at
package_qiime_1_9_1 (https://github.com/lparsons/galaxy_tools/tree/qiime/packages/package_qiime_1...).
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/
___________________________________________________________ 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/
Hey there, Any news on this? My colleague Aarif made me aware of the discussion, because one of our students, Ashok, worked on this months ago. QIIME was requested by a project which never started and therefore the developed codes did not gain priority. Basically we faced the same issues, and at least the 'dead end' problem with the resulting tgz archives was solved. We are currently assembling the codes into a toolshed entry, but I need to ask Ashok tomorrow about the current progress. Is there still interest on it or is everything already on the move..? Cheers, Sebastian Björn Grüning schrieb:
Hi Yvan,
Hi Lance, Björn, Dan
We are several scientists working on metagenomics in France and at a previous GUGGO (western France User Group) meeting, we mention the fact to "benchmark" our Galaxy pipelines. One is using new Qiime tools integration, one Mothur and the last one, the recently developped FROGS (Find Rapidly OTU with Galaxy Solution) pipeline using Swarm. We already have had some exchanges with Björn concerning metagenomics flavours on Docker, and I think it will be particularly interesting to exchange one with each other. The Qiime integration was started in march by colleagues from Brest Ifremer centre. I was just trying to install and test FROGS from Toulouse and Jouy-en-Josas INRA labs. If they are not on the list, I can contact them. Please do so. This is great to know. Please also consider to join our hackathon:
https://github.com/galaxyproject/tools-iuc/issues/299
We are always open for new ideas. Would be great to get a nice suite and a few workflows for metagenomic in the near future! :)
Thanks, Bjoern
All the best,
Yvan
----- Mail original -----
De: "Björn Grüning" <bjoern.gruening@gmail.com> À: "Lance Parsons" <lparsons@princeton.edu>, "Daniel Blankenberg" <dan@bx.psu.edu> Cc: "Galaxy Dev List" <galaxy-dev@lists.galaxyproject.org> Envoyé: Mercredi 7 Octobre 2015 14:25:38 Objet: Re: [galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)
Hi Lance,
I will help if I can. I also think we should begin too write 2-3 nice tools in the beginning to test the handshake between them and lay the ground work. This will also help to get familiar with the tool.
I still hope some one else from the community shows interest! :)
Thanks, Bjoern
Am 06.10.2015 um 20:33 schrieb Lance Parsons:
I agree that it would be very nice to get the data flowing between each of the tools and to be able to mix/match with other tools. That is an area of Galaxy tool-dev that I'm less familiar with, so any help would be greatly appreciated.
As for the manual massaging, I agree, however, at this point I'm really hoping that the changes between Qiime versions are manageable, esp. once we have the data types and basic framework of the tools down.
Along that front, I would very much like to get something usable (at least for some specific workflows) done sooner rather than later, then be able to iterate, adding new tools, datatypes, etc. as we move forward. Does that sound reasonable? I love the idea of a Metagenomics toolfest (https://github.com/galaxyproject/tools-iuc/issues/299). One thing I would like to do soon then, would be to define some functionality for the first round. What would be very helpful would be if you, Bjoern, etc. could help make sure the first round lays the proper groundwork so I/we don't have to redo things for later iterations, but we can build on a solid foundation.
Thanks so much for the input, help, etc. It is very much appreciated.
- Lance
Daniel Blankenberg <mailto:dan@bx.psu.edu> October 6, 2015 at 10:21 AM Hi Lance,
I looked at this a bit ago and had similar concerns, particularly with the outputs and inputs not being well-defined. In addition to the output tar ball —> local, extract —> upload not being great, as you mention, the input datatypes, etc, could use some work — in the very least, we should definitely create a nice biom datatype and have some converters available (import and export).
Definitely worth spending some extra time to make sure that we have the data flowing well between each of the different parts/tools, and even better to make sure that its done in a way that allows mixing and matching with other non-qiime tools.
One thing that we want to avoid is large amounts of manual massaging of the automatically generated xml; fixing things up once might not be too bad, but having to do it with each new tool version can be “frustrating". Although perhaps having a good starting point and only needing to manually modify for any updates could be good enough (I’m not very familiar with the extent of typical changes between qiime versions to make a call on how much changes).
Dan
(resending since I received a message bounce from list)
Daniel Blankenberg <mailto:dan@bx.psu.edu> October 6, 2015 at 9:59 AM Hi Lance,
I looked at this a bit ago and had similar concerns, particularly with the outputs and inputs not being well-defined. In addition to the output tar ball —> local, extract —> upload not being great, as you mention, the input datatypes, etc, could use some work — in the very least, we should definitely create a nice biom datatype and have some converters available (import and export).
Definitely worth spending some extra time to make sure that we have the data flowing well between each of the different parts/tools, and even better to make sure that its done in a way that allows mixing and matching with other non-qiime tools.
One thing that we want to avoid is large amounts of manual massaging of the automatically generated xml; fixing things up once might not be too bad, but having to do it with each new tool version can be “frustrating". Although perhaps having a good starting point and only needing to manually modify for any updates could be good enough (I’m not very familiar with the extent of typical changes between qiime versions to make a call on how much changes).
Dan
Lance Parsons <mailto:lparsons@princeton.edu> October 5, 2015 at 5:26 PM I was recently asked if I could provide a QIIME analysis pipeline for 16S data in Galaxy using tools in the QIIME pipeline (http://qiime.org/).
I did a bit of looking around for existing Galaxy wrappers and found an application that generates the wrappers for QIIME scripts for Galaxy (https://github.com/qiime/qiime-galaxy). This is a very well written application that does a great job of wrapping the QIIME scripts for Galaxy. However, there are a few things about it that don't quite fit my needs.
1. The tools output tgz files of all of the output files. This means that to execute a pipeline, the user would have to download the tgz files, untar, and then upload whichever file(s) are needed for the next step. 2. There is no toolshed repository to install the dependencies for these tools, making it a tricky for administrators to automate and also maintain various versions of QIIME going forward. 3. There are no toolshed versions of the tools themselves, which also makes installation and integration a bit tricky and makes it hard to me to create and manage updates, fixes, tweaks, etc. There are also no tests, etc.
For these reasons I decided to investigate the feasibility of using the generated wrappers as a basis for a "toolshed" version of QIIME. If anyone is interested in helping, or has suggestions, or is working on something related, I'd be very happy to collaborate.
The repository for the WIP is at https://github.com/lparsons/galaxy_tools/tree/qiime/tools/qiime1.9.0.
There is also a package on the testtoolshed as well as a first pass at
package_qiime_1_9_1 (https://github.com/lparsons/galaxy_tools/tree/qiime/packages/package_qiime_1...).
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/
___________________________________________________________ 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/
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/
-- Sebastian Schaaf, M.Sc. Bioinformatics Faculty Coordinator NGS Infrastructure Chair of Biometry and Bioinformatics Department of Medical Informatics, Biometry and Epidemiology (IBE) University of Munich DKTK Munich Marchioninistr. 15, K U1 808 D-81377 Munich (Germany) Tel: +49 89 4400 77499
Hi Sebastian, I think we try to work on this during our upcoming hackathon. https://github.com/galaxyproject/tools-iuc/issues/299 It would be nice to join and contribute your work to it. Thanks, Bjoern Am 13.10.2015 um 15:03 schrieb Sebastian Schaaf:
Hey there,
Any news on this?
My colleague Aarif made me aware of the discussion, because one of our students, Ashok, worked on this months ago. QIIME was requested by a project which never started and therefore the developed codes did not gain priority. Basically we faced the same issues, and at least the 'dead end' problem with the resulting tgz archives was solved. We are currently assembling the codes into a toolshed entry, but I need to ask Ashok tomorrow about the current progress.
Is there still interest on it or is everything already on the move..?
Cheers,
Sebastian
Björn Grüning schrieb:
Hi Yvan,
Hi Lance, Björn, Dan
We are several scientists working on metagenomics in France and at a previous GUGGO (western France User Group) meeting, we mention the fact to "benchmark" our Galaxy pipelines. One is using new Qiime tools integration, one Mothur and the last one, the recently developped FROGS (Find Rapidly OTU with Galaxy Solution) pipeline using Swarm. We already have had some exchanges with Björn concerning metagenomics flavours on Docker, and I think it will be particularly interesting to exchange one with each other. The Qiime integration was started in march by colleagues from Brest Ifremer centre. I was just trying to install and test FROGS from Toulouse and Jouy-en-Josas INRA labs. If they are not on the list, I can contact them. Please do so. This is great to know. Please also consider to join our hackathon:
https://github.com/galaxyproject/tools-iuc/issues/299
We are always open for new ideas. Would be great to get a nice suite and a few workflows for metagenomic in the near future! :)
Thanks, Bjoern
All the best,
Yvan
----- Mail original -----
De: "Björn Grüning" <bjoern.gruening@gmail.com> À: "Lance Parsons" <lparsons@princeton.edu>, "Daniel Blankenberg" <dan@bx.psu.edu> Cc: "Galaxy Dev List" <galaxy-dev@lists.galaxyproject.org> Envoyé: Mercredi 7 Octobre 2015 14:25:38 Objet: Re: [galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)
Hi Lance,
I will help if I can. I also think we should begin too write 2-3 nice tools in the beginning to test the handshake between them and lay the ground work. This will also help to get familiar with the tool.
I still hope some one else from the community shows interest! :)
Thanks, Bjoern
Am 06.10.2015 um 20:33 schrieb Lance Parsons:
I agree that it would be very nice to get the data flowing between each of the tools and to be able to mix/match with other tools. That is an area of Galaxy tool-dev that I'm less familiar with, so any help would be greatly appreciated.
As for the manual massaging, I agree, however, at this point I'm really hoping that the changes between Qiime versions are manageable, esp. once we have the data types and basic framework of the tools down.
Along that front, I would very much like to get something usable (at least for some specific workflows) done sooner rather than later, then be able to iterate, adding new tools, datatypes, etc. as we move forward. Does that sound reasonable? I love the idea of a Metagenomics toolfest (https://github.com/galaxyproject/tools-iuc/issues/299). One thing I would like to do soon then, would be to define some functionality for the first round. What would be very helpful would be if you, Bjoern, etc. could help make sure the first round lays the proper groundwork so I/we don't have to redo things for later iterations, but we can build on a solid foundation.
Thanks so much for the input, help, etc. It is very much appreciated.
- Lance
Daniel Blankenberg <mailto:dan@bx.psu.edu> October 6, 2015 at 10:21 AM Hi Lance,
I looked at this a bit ago and had similar concerns, particularly with the outputs and inputs not being well-defined. In addition to the output tar ball —> local, extract —> upload not being great, as you mention, the input datatypes, etc, could use some work — in the very least, we should definitely create a nice biom datatype and have some converters available (import and export).
Definitely worth spending some extra time to make sure that we have the data flowing well between each of the different parts/tools, and even better to make sure that its done in a way that allows mixing and matching with other non-qiime tools.
One thing that we want to avoid is large amounts of manual massaging of the automatically generated xml; fixing things up once might not be too bad, but having to do it with each new tool version can be “frustrating". Although perhaps having a good starting point and only needing to manually modify for any updates could be good enough (I’m not very familiar with the extent of typical changes between qiime versions to make a call on how much changes).
Dan
(resending since I received a message bounce from list)
Daniel Blankenberg <mailto:dan@bx.psu.edu> October 6, 2015 at 9:59 AM Hi Lance,
I looked at this a bit ago and had similar concerns, particularly with the outputs and inputs not being well-defined. In addition to the output tar ball —> local, extract —> upload not being great, as you mention, the input datatypes, etc, could use some work — in the very least, we should definitely create a nice biom datatype and have some converters available (import and export).
Definitely worth spending some extra time to make sure that we have the data flowing well between each of the different parts/tools, and even better to make sure that its done in a way that allows mixing and matching with other non-qiime tools.
One thing that we want to avoid is large amounts of manual massaging of the automatically generated xml; fixing things up once might not be too bad, but having to do it with each new tool version can be “frustrating". Although perhaps having a good starting point and only needing to manually modify for any updates could be good enough (I’m not very familiar with the extent of typical changes between qiime versions to make a call on how much changes).
Dan
Lance Parsons <mailto:lparsons@princeton.edu> October 5, 2015 at 5:26 PM I was recently asked if I could provide a QIIME analysis pipeline for 16S data in Galaxy using tools in the QIIME pipeline (http://qiime.org/).
I did a bit of looking around for existing Galaxy wrappers and found an application that generates the wrappers for QIIME scripts for Galaxy (https://github.com/qiime/qiime-galaxy). This is a very well written application that does a great job of wrapping the QIIME scripts for Galaxy. However, there are a few things about it that don't quite fit my needs.
1. The tools output tgz files of all of the output files. This means that to execute a pipeline, the user would have to download the tgz files, untar, and then upload whichever file(s) are needed for the next step. 2. There is no toolshed repository to install the dependencies for these tools, making it a tricky for administrators to automate and also maintain various versions of QIIME going forward. 3. There are no toolshed versions of the tools themselves, which also makes installation and integration a bit tricky and makes it hard to me to create and manage updates, fixes, tweaks, etc. There are also no tests, etc.
For these reasons I decided to investigate the feasibility of using the generated wrappers as a basis for a "toolshed" version of QIIME. If anyone is interested in helping, or has suggestions, or is working on something related, I'd be very happy to collaborate.
The repository for the WIP is at https://github.com/lparsons/galaxy_tools/tree/qiime/tools/qiime1.9.0.
There is also a package on the testtoolshed as well as a first pass at
package_qiime_1_9_1 (https://github.com/lparsons/galaxy_tools/tree/qiime/packages/package_qiime_1...).
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/
___________________________________________________________ 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/
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/
Hi Björn, The discussion looks good, although (or right because?) it gained a somewhat more generic scope, where QIIME is one of several construction sites in the metagenomics field. Do I get it right that the date for the hackathon is tba? Will there be a notification? I think we would like to join :). Anyhow we discussed yesterday in the office and came up the following: 1. Ashok collected all dependencies (names/versions of tools/libraries), he also formalized them in recipes. The community has to check whether it fits the needs/expectations, as we are relatively new to tool sheds and started to load a private one recently with tools. But the plain list should already save some work. As we run SLES as OS (which is close to blank in terms of up to date software...) the dependency list should go quite far. 2. The codes which were written by him for an internship will anyhow get some improvements: currently the "qiime_connector" is simply a kind of archive extractor which makes an arbitrary file from a QIIME tool output archive available in the Galaxy history, so that there is neither a dead end nor the need for a "download/upload" step. For user who know QIIME from the command line (and therefore know how the modules work) this may be a suitable solution, but not for beginners who start with metagenomics. Somehow it does not feel "galaxy'sh"... So far, looking forward to joining forces :). Cheers, Sebastian Björn Grüning schrieb:
Hi Sebastian,
I think we try to work on this during our upcoming hackathon.
https://github.com/galaxyproject/tools-iuc/issues/299
It would be nice to join and contribute your work to it.
Thanks, Bjoern
Am 13.10.2015 um 15:03 schrieb Sebastian Schaaf:
Hey there,
Any news on this?
My colleague Aarif made me aware of the discussion, because one of our students, Ashok, worked on this months ago. QIIME was requested by a project which never started and therefore the developed codes did not gain priority. Basically we faced the same issues, and at least the 'dead end' problem with the resulting tgz archives was solved. We are currently assembling the codes into a toolshed entry, but I need to ask Ashok tomorrow about the current progress.
Is there still interest on it or is everything already on the move..?
Cheers,
Sebastian
Björn Grüning schrieb:
Hi Yvan,
Hi Lance, Björn, Dan
We are several scientists working on metagenomics in France and at a previous GUGGO (western France User Group) meeting, we mention the fact to "benchmark" our Galaxy pipelines. One is using new Qiime tools integration, one Mothur and the last one, the recently developped FROGS (Find Rapidly OTU with Galaxy Solution) pipeline using Swarm. We already have had some exchanges with Björn concerning metagenomics flavours on Docker, and I think it will be particularly interesting to exchange one with each other. The Qiime integration was started in march by colleagues from Brest Ifremer centre. I was just trying to install and test FROGS from Toulouse and Jouy-en-Josas INRA labs. If they are not on the list, I can contact them. Please do so. This is great to know. Please also consider to join our hackathon:
https://github.com/galaxyproject/tools-iuc/issues/299
We are always open for new ideas. Would be great to get a nice suite and a few workflows for metagenomic in the near future! :)
Thanks, Bjoern
All the best,
Yvan
----- Mail original -----
De: "Björn Grüning" <bjoern.gruening@gmail.com> À: "Lance Parsons" <lparsons@princeton.edu>, "Daniel Blankenberg" <dan@bx.psu.edu> Cc: "Galaxy Dev List" <galaxy-dev@lists.galaxyproject.org> Envoyé: Mercredi 7 Octobre 2015 14:25:38 Objet: Re: [galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)
Hi Lance,
I will help if I can. I also think we should begin too write 2-3 nice tools in the beginning to test the handshake between them and lay the ground work. This will also help to get familiar with the tool.
I still hope some one else from the community shows interest! :)
Thanks, Bjoern
Am 06.10.2015 um 20:33 schrieb Lance Parsons:
I agree that it would be very nice to get the data flowing between each of the tools and to be able to mix/match with other tools. That is an area of Galaxy tool-dev that I'm less familiar with, so any help would be greatly appreciated.
As for the manual massaging, I agree, however, at this point I'm really hoping that the changes between Qiime versions are manageable, esp. once we have the data types and basic framework of the tools down.
Along that front, I would very much like to get something usable (at least for some specific workflows) done sooner rather than later, then be able to iterate, adding new tools, datatypes, etc. as we move forward. Does that sound reasonable? I love the idea of a Metagenomics toolfest (https://github.com/galaxyproject/tools-iuc/issues/299). One thing I would like to do soon then, would be to define some functionality for the first round. What would be very helpful would be if you, Bjoern, etc. could help make sure the first round lays the proper groundwork so I/we don't have to redo things for later iterations, but we can build on a solid foundation.
Thanks so much for the input, help, etc. It is very much appreciated.
- Lance
> Daniel Blankenberg <mailto:dan@bx.psu.edu> October 6, 2015 at > 10:21 AM Hi Lance, > > I looked at this a bit ago and had similar concerns, > particularly with the outputs and inputs not being > well-defined. In addition to the output tar ball —> local, > extract —> upload not being great, as you mention, the input > datatypes, etc, could use some work — in the very least, we > should definitely create a nice biom datatype and have some > converters available (import and export). > > Definitely worth spending some extra time to make sure that we > have the data flowing well between each of the different > parts/tools, and even better to make sure that its done in a > way that allows mixing and matching with other non-qiime > tools. > > > One thing that we want to avoid is large amounts of manual > massaging of the automatically generated xml; fixing things up > once might not be too bad, but having to do it with each new > tool version can be “frustrating". Although perhaps having a > good starting point and only needing to manually modify for any > updates could be good enough (I’m not very familiar with the > extent of typical changes between qiime versions to make a call > on how much changes). > > > > > Dan > > (resending since I received a message bounce from list) > > > > Daniel Blankenberg <mailto:dan@bx.psu.edu> October 6, 2015 at > 9:59 AM Hi Lance, > > I looked at this a bit ago and had similar concerns, > particularly with the outputs and inputs not being > well-defined. In addition to the output tar ball —> local, > extract —> upload not being great, as you mention, the input > datatypes, etc, could use some work — in the very least, we > should definitely create a nice biom datatype and have some > converters available (import and export). > > Definitely worth spending some extra time to make sure that we > have the data flowing well between each of the different > parts/tools, and even better to make sure that its done in a > way that allows mixing and matching with other non-qiime > tools. > > > One thing that we want to avoid is large amounts of manual > massaging of the automatically generated xml; fixing things up > once might not be too bad, but having to do it with each new > tool version can be “frustrating". Although perhaps having a > good starting point and only needing to manually modify for any > updates could be good enough (I’m not very familiar with the > extent of typical changes between qiime versions to make a call > on how much changes). > > > > > Dan > > > > Lance Parsons <mailto:lparsons@princeton.edu> October 5, 2015 > at 5:26 PM I was recently asked if I could provide a QIIME > analysis pipeline for 16S data in Galaxy using tools in the > QIIME pipeline (http://qiime.org/). > > I did a bit of looking around for existing Galaxy wrappers and > found an application that generates the wrappers for QIIME > scripts for Galaxy (https://github.com/qiime/qiime-galaxy). > This is a very well written application that does a great job > of wrapping the QIIME scripts for Galaxy. However, there are a > few things about it that don't quite fit my needs. > > 1. The tools output tgz files of all of the output files. This > means that to execute a pipeline, the user would have to > download the tgz files, untar, and then upload whichever > file(s) are needed for the next step. 2. There is no toolshed > repository to install the dependencies for these tools, making > it a tricky for administrators to automate and also maintain > various versions of QIIME going forward. 3. There are no > toolshed versions of the tools themselves, which also makes > installation and integration a bit tricky and makes it hard to > me to create and manage updates, fixes, tweaks, etc. There are > also no tests, etc. > > For these reasons I decided to investigate the feasibility of > using the generated wrappers as a basis for a "toolshed" > version of QIIME. If anyone is interested in helping, or has > suggestions, or is working on something related, I'd be very > happy to collaborate. > > The repository for the WIP is at > https://github.com/lparsons/galaxy_tools/tree/qiime/tools/qiime1.9.0. > > There is also a package on the testtoolshed as well as a first pass at > package_qiime_1_9_1 > (https://github.com/lparsons/galaxy_tools/tree/qiime/packages/package_qiime_1...). > > >
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/
___________________________________________________________ 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/
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/
-- Sebastian Schaaf, M.Sc. Bioinformatics Faculty Coordinator NGS Infrastructure Chair of Biometry and Bioinformatics Department of Medical Informatics, Biometry and Epidemiology (IBE) University of Munich DKTK Munich Marchioninistr. 15, K U1 808 D-81377 Munich (Germany) Tel: +49 89 4400 77499
Am 15.10.2015 um 09:46 schrieb Sebastian Schaaf:
Hi Björn,
The discussion looks good, although (or right because?) it gained a somewhat more generic scope, where QIIME is one of several construction sites in the metagenomics field. Do I get it right that the date for the hackathon is tba? Will there be a notification? I think we would like to join :).
Yes, we are trying find a schedule :) Subscribe to the github issue and you will know. We will also announce it via twitter and this ML.
Anyhow we discussed yesterday in the office and came up the following:
1. Ashok collected all dependencies (names/versions of tools/libraries), he also formalized them in recipes. The community has to check whether it fits the needs/expectations, as we are relatively new to tool sheds and started to load a private one recently with tools. But the plain list should already save some work. As we run SLES as OS (which is close to blank in terms of up to date software...) the dependency list should go quite far.
Awesome. Please see also this one here: https://github.com/galaxyproject/tools-iuc/pull/297 It takes care of all python libs. Testing and enhancements are welcome! Depending on how far we will get with wrapping tools we also need the other dependencies.
2. The codes which were written by him for an internship will anyhow get some improvements: currently the "qiime_connector" is simply a kind of archive extractor which makes an arbitrary file from a QIIME tool output archive available in the Galaxy history, so that there is neither a dead end nor the need for a "download/upload" step. For user who know QIIME from the command line (and therefore know how the modules work) this may be a suitable solution, but not for beginners who start with metagenomics. Somehow it does not feel "galaxy'sh"...
Also a nice ideas. I guess we discuss this in more detail during the hackathon and trying to get some proper filetypes into Galaxy for this.
So far, looking forward to joining forces :).
!!! Greetings to Munich! Bjoern
Cheers, Sebastian
Björn Grüning schrieb:
Hi Sebastian,
I think we try to work on this during our upcoming hackathon.
https://github.com/galaxyproject/tools-iuc/issues/299
It would be nice to join and contribute your work to it.
Thanks, Bjoern
Am 13.10.2015 um 15:03 schrieb Sebastian Schaaf:
Hey there,
Any news on this?
My colleague Aarif made me aware of the discussion, because one of our students, Ashok, worked on this months ago. QIIME was requested by a project which never started and therefore the developed codes did not gain priority. Basically we faced the same issues, and at least the 'dead end' problem with the resulting tgz archives was solved. We are currently assembling the codes into a toolshed entry, but I need to ask Ashok tomorrow about the current progress.
Is there still interest on it or is everything already on the move..?
Cheers,
Sebastian
Björn Grüning schrieb:
Hi Yvan,
Hi Lance, Björn, Dan
We are several scientists working on metagenomics in France and at a previous GUGGO (western France User Group) meeting, we mention the fact to "benchmark" our Galaxy pipelines. One is using new Qiime tools integration, one Mothur and the last one, the recently developped FROGS (Find Rapidly OTU with Galaxy Solution) pipeline using Swarm. We already have had some exchanges with Björn concerning metagenomics flavours on Docker, and I think it will be particularly interesting to exchange one with each other. The Qiime integration was started in march by colleagues from Brest Ifremer centre. I was just trying to install and test FROGS from Toulouse and Jouy-en-Josas INRA labs. If they are not on the list, I can contact them. Please do so. This is great to know. Please also consider to join our hackathon:
https://github.com/galaxyproject/tools-iuc/issues/299
We are always open for new ideas. Would be great to get a nice suite and a few workflows for metagenomic in the near future! :)
Thanks, Bjoern
All the best,
Yvan
----- Mail original -----
De: "Björn Grüning" <bjoern.gruening@gmail.com> À: "Lance Parsons" <lparsons@princeton.edu>, "Daniel Blankenberg" <dan@bx.psu.edu> Cc: "Galaxy Dev List" <galaxy-dev@lists.galaxyproject.org> Envoyé: Mercredi 7 Octobre 2015 14:25:38 Objet: Re: [galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)
Hi Lance,
I will help if I can. I also think we should begin too write 2-3 nice tools in the beginning to test the handshake between them and lay the ground work. This will also help to get familiar with the tool.
I still hope some one else from the community shows interest! :)
Thanks, Bjoern
Am 06.10.2015 um 20:33 schrieb Lance Parsons: > I agree that it would be very nice to get the data flowing > between each of the tools and to be able to mix/match with other > tools. That is an area of Galaxy tool-dev that I'm less familiar > with, so any help would be greatly appreciated. > > As for the manual massaging, I agree, however, at this point I'm > really hoping that the changes between Qiime versions are > manageable, esp. once we have the data types and basic framework > of the tools down. > > Along that front, I would very much like to get something usable > (at least for some specific workflows) done sooner rather than > later, then be able to iterate, adding new tools, datatypes, etc. > as we move forward. Does that sound reasonable? I love the idea > of a Metagenomics toolfest > (https://github.com/galaxyproject/tools-iuc/issues/299). One > thing I would like to do soon then, would be to define some > functionality for the first round. What would be very helpful > would be if you, Bjoern, etc. could help make sure the first > round lays the proper groundwork so I/we don't have to redo > things for later iterations, but we can build on a solid > foundation. > > Thanks so much for the input, help, etc. It is very much > appreciated. > > - Lance > >> Daniel Blankenberg <mailto:dan@bx.psu.edu> October 6, 2015 at >> 10:21 AM Hi Lance, >> >> I looked at this a bit ago and had similar concerns, >> particularly with the outputs and inputs not being >> well-defined. In addition to the output tar ball —> local, >> extract —> upload not being great, as you mention, the input >> datatypes, etc, could use some work — in the very least, we >> should definitely create a nice biom datatype and have some >> converters available (import and export). >> >> Definitely worth spending some extra time to make sure that we >> have the data flowing well between each of the different >> parts/tools, and even better to make sure that its done in a >> way that allows mixing and matching with other non-qiime >> tools. >> >> >> One thing that we want to avoid is large amounts of manual >> massaging of the automatically generated xml; fixing things up >> once might not be too bad, but having to do it with each new >> tool version can be “frustrating". Although perhaps having a >> good starting point and only needing to manually modify for any >> updates could be good enough (I’m not very familiar with the >> extent of typical changes between qiime versions to make a call >> on how much changes). >> >> >> >> >> Dan >> >> (resending since I received a message bounce from list) >> >> >> >> Daniel Blankenberg <mailto:dan@bx.psu.edu> October 6, 2015 at >> 9:59 AM Hi Lance, >> >> I looked at this a bit ago and had similar concerns, >> particularly with the outputs and inputs not being >> well-defined. In addition to the output tar ball —> local, >> extract —> upload not being great, as you mention, the input >> datatypes, etc, could use some work — in the very least, we >> should definitely create a nice biom datatype and have some >> converters available (import and export). >> >> Definitely worth spending some extra time to make sure that we >> have the data flowing well between each of the different >> parts/tools, and even better to make sure that its done in a >> way that allows mixing and matching with other non-qiime >> tools. >> >> >> One thing that we want to avoid is large amounts of manual >> massaging of the automatically generated xml; fixing things up >> once might not be too bad, but having to do it with each new >> tool version can be “frustrating". Although perhaps having a >> good starting point and only needing to manually modify for any >> updates could be good enough (I’m not very familiar with the >> extent of typical changes between qiime versions to make a call >> on how much changes). >> >> >> >> >> Dan >> >> >> >> Lance Parsons <mailto:lparsons@princeton.edu> October 5, 2015 >> at 5:26 PM I was recently asked if I could provide a QIIME >> analysis pipeline for 16S data in Galaxy using tools in the >> QIIME pipeline (http://qiime.org/). >> >> I did a bit of looking around for existing Galaxy wrappers and >> found an application that generates the wrappers for QIIME >> scripts for Galaxy (https://github.com/qiime/qiime-galaxy). >> This is a very well written application that does a great job >> of wrapping the QIIME scripts for Galaxy. However, there are a >> few things about it that don't quite fit my needs. >> >> 1. The tools output tgz files of all of the output files. This >> means that to execute a pipeline, the user would have to >> download the tgz files, untar, and then upload whichever >> file(s) are needed for the next step. 2. There is no toolshed >> repository to install the dependencies for these tools, making >> it a tricky for administrators to automate and also maintain >> various versions of QIIME going forward. 3. There are no >> toolshed versions of the tools themselves, which also makes >> installation and integration a bit tricky and makes it hard to >> me to create and manage updates, fixes, tweaks, etc. There are >> also no tests, etc. >> >> For these reasons I decided to investigate the feasibility of >> using the generated wrappers as a basis for a "toolshed" >> version of QIIME. If anyone is interested in helping, or has >> suggestions, or is working on something related, I'd be very >> happy to collaborate. >> >> The repository for the WIP is at >> https://github.com/lparsons/galaxy_tools/tree/qiime/tools/qiime1.9.0. >> >> >> There is also a package on the testtoolshed as well as a first pass at >> package_qiime_1_9_1 >> (https://github.com/lparsons/galaxy_tools/tree/qiime/packages/package_qiime_1...). >> >> >> >> > >
> 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/ > ___________________________________________________________ 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/
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/
participants (5)
-
Björn Grüning -
Daniel Blankenberg -
Lance Parsons -
Sebastian Schaaf -
Yvan Le Bras