Hi Vipin and Rui,
please have at the toolshed and test toolshed before developing
wrappers. For deseq2 there are already wrappers that are trying to solve
your issues and it would be nice if you could join that effort. Help
testing and contributing to it.
Ross has a cool wrapper of edgeR, DESeq2
Hi Rui,
I should provide a 'sample metadata table', a tabular file with one
column the names of your samples, the other column the associated
metadata (e.g. type).
This is how I've done it in my DESeq2 wrapper. :-) Feel free to check
the interface at
Wow - that makes at least five Deseq2 wrappers for Galaxy
available or in progress :(
Bjoern's wrapper on the (test) tool shed,
http://testtoolshed.g2.bx.psu.edu/view/bgruening/deseq2
Ross' combined wrapper for edgeR, DESeq2 and voom in one tool:
It is not necessarily bad. If we all test each others tools
(dependencies, interface, output,...) we might get to the best of all
worlds :-) (I have planned to test Björns wrapper)
One of the points of differentiation is also how 'integrated' a tool
needs to be: e.g. Ross' tool for diff
On Wed, Sep 11, 2013 at 10:12 AM, Joachim Jacob | VIB |
joachim.ja...@vib.be wrote:
It is not necessarily bad. If we all test each others tools (dependencies,
interface, output,...) we might get to the best of all worlds :-) (I have
planned to test Björns wrapper)
One of the points of
Am Mittwoch, den 11.09.2013, 10:21 +0100 schrieb Peter Cock:
On Wed, Sep 11, 2013 at 10:12 AM, Joachim Jacob | VIB |
joachim.ja...@vib.be wrote:
It is not necessarily bad. If we all test each others tools (dependencies,
interface, output,...) we might get to the best of all worlds :-) (I
Yes I am agreeing on all statements.
Let me finish my package and will add in one of the toolshed by today
evening. I also willing to test other wrappers to improve the additional
parameter settings.
Tool wrappers Work In Progress from my side:
DEXSeq
edgeR
Scripture
STAR aligner
SAFT multi
Vipin,
Search works pretty well on the toolshed - I'd recommend a search for (eg)
'star' before writing yet another rnastar toolshed wrapper and dependency
package? There's an installable fubar package_rnastar and an rnastar
wrapper based on Jeremy's code mentioned below - but working AFAIK - at
STAR aligner
I have a partial STAR wrapper that may be useful:
https://bitbucket.org/jgoecks/jeremys-code/src/d7096c132657420f08b540c6954b947f648aac80/galaxy/tool-wrappers/star.xml?at=default
Whether you use this code or not, I do have one request: please put the output
in BAM rather than
Hi Joachim,
Thanks for the info! but I could not register on your instance...and thus
could not check your wrapper. :-( Please help!
Thanks,
Rui
On Wed, Sep 11, 2013 at 12:59 AM, Joachim Jacob | VIB |
joachim.ja...@vib.be wrote:
Hi Rui,
I should provide a 'sample metadata table', a
Hey Guys,
It's great to receive so many responses! Thank you all for the
information...
and let me check out each of the masterpiece. :-)
Best,
Rui
On Wed, Sep 11, 2013 at 1:56 AM, Peter Cock p.j.a.c...@googlemail.comwrote:
Wow - that makes at least five Deseq2 wrappers for Galaxy
available
Hi All,
we are making a wrapper for deseq2, and there is a step where
control/experimental conditions
need to be determined. For example, it would be a column like the following
in the input file
Type
CTC
CTC
LM
LM
PT
PT
and we want the select list to contain
CTC
LM
PT
In other words, we want
Hello Rui,
We have DESeq2 wrapper in our oqtans package and you will find this at
https://github.com/ratschlab/oqtans_tools/tree/master/DESeq2
I am currently creating the associated tool_dependency.xml file for dumping
the package in galaxy toolshed. otherwise it requires some manual effort to
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