: Filename and id attributes required for dynamic_links
Note: Cross posted on Galaxy Biostars site:
https://biostar.usegalaxy.org/p/9944/
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Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University
.princeton.edu/tool_runner?tool_id=tophat2>
toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.6
<https://galaxy.princeton.edu/tool_runner?tool_id=tophat2>
toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.7
<https://galaxy.princeton.edu/tool_runner?tool_id=tophat2>
toolsh
nd
may be unlawful. In this case, please notify us by a reply and delete
this email and its contents immediately.
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--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for
ns/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).
--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-
miliar 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 t
it
part of the core galaxy (which would allow multiple tools to share the
same data type definitions) or making it part of a toolshed tool (which
I'm not sure how to do)? BTW, I'm thinking about RSeQC at the moment,
but I know other tools use/require this format.
--
Lance Parsons -
are currently usually created by implicit
datatype converters and are most often used by some external display
applications that need standards conforming files. bed6/12 are
subclasses of bedstrict. They can of course be consumed or created by
any sort of tool. Please let us know if we can provide add
g
these restrictions up, however, and allowing them to function as
'normal' datatypes (users would be free to shoot themselves in the
foot by mis-assigning the datatype). In the meantime, you should be
able to test this by flipping 'allow_datatype_change' in interval.py
to Tru
esire/support on the part of the Galaxy team to allow
tools to use/require the BED12 format?
If not, I'll work on incorporating the conversion(s) within each tool
wrapper, unless someone has an alternate suggestion.
Thanks all,
Lance
Lance Parsons <mailto:lpars...@princeton.edu>
ow I could move over to LDAP, but that is not desirable since it's
less secure than CAS.
Another option would be to implement CAS within Galaxy, but that does
seem like a good bit of work, but perhaps someone is already working on
it or at least interested?
--
Lance Parsons - Scientif
ttempts to
delete it via the toolshed web interface result in internal server
errors. Can an admin take a look?
https://toolshed.g2.bx.psu.edu/view/mrvollger/trtr/13cad5d36301
--
Lance Parsons - Scientific Programmer
Carl C. Icahn Laboratory - Room 136
Lewis-Sigler Institute for Integrative Genomics
ttempts to
delete it via the toolshed web interface result in internal server
errors. Can an admin take a look?
https://toolshed.g2.bx.psu.edu/view/mrvollger/trtr/13cad5d36301
--
Lance Parsons - Scientific Programmer
Carl C. Icahn Laboratory - Room 136
Lewis-Sigler Institute for Integrative Genomics
if
anyone had any advice on a better way to query job parameters. See the
function here:
https://gist.github.com/lparsons/a4724b51afd9027e3c0e
Thanks in advance for any suggestions or comments.
--
Lance Parsons - Scientific Programmer
Carl C. Icahn Laboratory - Room 136
Lewis-Sigler Institute
I've had requests from users to install Kallisto as Galaxy tool. I
didn't see any wrappers or evidence of wrappers in my searching, but I
thought I'd ask here to see if anyone is working on or interested in
working on such a thing.
--
Lance Parsons - Scientific Programme
I've had requests from users to install Kallisto as Galaxy tool. I
didn't see any wrappers or evidence of wrappers in my searching, but I
thought I'd ask here to see if anyone is working on or interested in
working on such a thing.
--
Lance Parsons - Scientific Programme
Hi Lance,
Kallisto has some licensing issues and the IUC decided to not offer it
as IUC tool.
Some related thread:
https://groups.google.com/forum/#!topic/kallisto-sleuth-users/oVRg69Zmots
Cheers,
Bjoern
Am 29.04.2016 um 16:37 schrieb Lance Parsons:
I've had requests from users to inst
t. 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/
Lance Parsons <mailto:lpars...@princeton.edu>
April 29, 2016
hat do others see when running the above
query? Has anyone run into this or a similar issue? Thanks.
--
Lance Parsons - Scientific Programmer
Carl C. Icahn Laboratory - Room 136
Lewis-Sigler Institute for Integrative Genomics
Princeton University
__
n see what
datasets were deleted and which were not at the time of deletion).
There is a separate hda.purged column that indicates that an HDA is no
longer user-recoverable by the user. I have 699 datasets that are
d.deleted but not hda.purged, this number should be 0.
--nate
Lance Parsons <
t; are hda.purged, the next
cleanup step is to mark d.deleted. Then after d.deleted, it's marked
d.purged and the file(s) are actually removed from disk. It's a bit of
a failsafe so that datasets can be intercepted if unintentionally deleted.
--nate
Lance Parsons <mailto:lpars...@pr
clean those up?
In general, I’m running into disk issues with my Galaxy server and I’d
like to try and tighten up disk usage where ever I can. Thanks in advance.
--
Lance Parsons - Scientific Programmer
Carl C. Icahn Laboratory - Room 136
Lewis-Sigler Institute for Integrative Genomics
s for Galaxy
documentation and training these days…
--
Lance Parsons - Scientific Programmer
Carl C. Icahn Laboratory - Room 136
Lewis-Sigler Institute for Integrative Genomics
Princeton University
___
Please keep all replies on the list by usin
action terms (/e.g./ |condition:genotype|) to the DESeq2
wrapper? Does this functionality exist in a different Galaxy tool?
Thanks in advance.
--
Lance Parsons - Scientific Programmer
Carl C. Icahn Laboratory - Room 136
Lewis-Sigler Institute for Integrative Genomics
Pr
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