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.gruen...@gmail.com> À: "Lance Parsons"
<lpars...@princeton.edu>, "Daniel Blankenberg" <d...@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:d...@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:d...@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:lpars...@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_9_1).
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--
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
___________________________________________________________
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and other Galaxy lists, please use the interface at:
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