Dear All,
The Open Genome Informatics team serves as an “umbrella" organization to support the efforts of many open access open-source bioinformatics projects for Google Summer of Code (GSoC)<https://summerofcode.withgoogle.com/>. Among this list of projects are GMOD and its software projects -- GBrowse, JBrowse; Galaxy; Reactome; WormBase; DockStore; Bioconda; and others.
Call for 2020 Project Ideas and Mentors: We are seeking project ideas to post and attract talented students to this year’s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Robin Haw, Marc Gillespie, Dave Clements, Dannon Baker, and Scott Cain (emails above). You can also submit your ideas here<http://gmod.org/wiki/GSOC_Project_Ideas_2020>.
For more information please refer to the Open Genome Informatics page on the GMOD.org website<http://gmod.org/wiki/GSoC#Google_Summer_of_Code_2020>.
The mentoring organization application deadline with GSoC is February 5th at 2 pm EST. So, if you are interested in taking part with the team please let us know as soon as possible.
Please forward this to others who might be interested in taking part.
If you have any questions please let us know.
Thanks,
Robin, Marc, Dave, Dannon, and Scott.
Robin Haw, PhD
Reactome | JBrowse - Senior Project Manager and Outreach Co-ordinator
robin.haw(a)oicr.on.ca<mailto:robin.haw@oicr.on.ca>
Ontario Institute for Cancer Research
MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
@OICR_news | www.oicr.on.ca | @reactome | reactome.org | @JBrowseGossip | jbrowse.org
Collaborate. Translate. Change lives.
This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.
Dear All,
Sorry for the multiple postings!
The Open Genome Informatics team serves as an “umbrella" organization to support the efforts of many open access open-source bioinformatics projects for Google Summer of Code (GSoC)<https://summerofcode.withgoogle.com/>. Among this list of projects are GMOD and its software projects -- GBrowse, JBrowse; Galaxy; Reactome; WormBase; DockStore; Bioconda; and others.
Call for 2020 Project Ideas and Mentors: We are seeking project ideas to post and attract talented students to this year’s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Robin Haw, Marc Gillespie, Dave Clements, Dannon Baker, and Scott Cain (emails above). You can also submit your ideas here<http://gmod.org/wiki/GSOC_Project_Ideas_2020>.
For more information please refer to the Open Genome Informatics page on the GMOD.org website<http://gmod.org/wiki/GSoC#Google_Summer_of_Code_2020>.
The mentoring organization application deadline with GSoC is February 5th at 2 pm EST. So, if you are interested in taking part with the team please let us know as soon as possible.
Please forward this to others who might be interested in taking part.
If you have any questions please let us know.
Thanks,
Robin, Marc, Dave, Dannon, and Scott.
Robin Haw, PhD
Reactome | JBrowse - Senior Project Manager and Outreach Co-ordinator
robin.haw(a)oicr.on.ca<mailto:robin.haw@oicr.on.ca>
Ontario Institute for Cancer Research
MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
@OICR_news | www.oicr.on.ca | @reactome | reactome.org | @JBrowseGossip | jbrowse.org
Collaborate. Translate. Change lives.
This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.
Hello,
First of all thank you for all of your hard work developing such an
informative and intuitive tool. I have been successful in running the LEfSE
analyses for some of my data, but unfortunately, for the majority I get an
error message when it comes to the step where the Effect size is
calculated. The error message is copied below:
/galaxy_venv/local/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:185:
RRuntimeWarning: Error in (function (file = "", n = NULL, text = NULL,
prompt = "?", keep.source = getOption("keep.source"), :
<text>:1:47: unexpected numeric constant
1: effect.size <- abs(mean(LD[sub_d[,"class"]==""1
^
warnings.warn(x, RRuntimeWarning)
Traceback (most recent call last):
File "/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/run_lefse.py",
line 89, in <module>
if params['rank_tec'] == 'lda': lda_res,lda_res_th =
test_lda_r(cls,feats,class_sl,params['n_boots'],params['f_boots'],params['lda_abs_th'],0.0000000001,params['nlogs'])
File "/export/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/lefse.py",
line 199, in test_lda_r
robjects.r('effect.size <-
abs(mean(LD[sub_d[,"class"]=="'+p[0]+'"]) -
mean(LD[sub_d[,"class"]=="'+p[1]+'"]))')
File "/galaxy_venv/local/lib/python2.7/site-packages/rpy2/robjects/__init__.py",
line 358, in __call__
p = _rparse(text=StrSexpVector((string,)))
rpy2.rinterface.RRuntimeError: Error in (function (file = "", n =
NULL, text = NULL, prompt = "?", keep.source =
getOption("keep.source"), :
<text>:1:47: unexpected numeric constant
1: effect.size <- abs(mean(LD[sub_d[,"class"]==""1
^
For your reference, I am using this tool to analyze human gut microbiome
data.
Also, I cross-posted to the forum (link:
https://help.galaxyproject.org/t/lda-effect-size-error/2840)
Any guidance would be greatly appreciated.
all the best,
Caroline
--
Caroline M. Kelsey
Developmental Psychology Ph.D. Candidate
UVA Babylab: http://uvababylab.org/
The University of Virginia
Hello all
I'm experiencing an issue trying to install the 'dwgsim' from the toolshed:
https://toolshed.g2.bx.psu.edu/view/nilshomer/dwgsim/512671604bab
I've tried installing into a couple of production instances (both running 19.05) as well as local instances running 19.05 and 19.09, but all attempts have failed. Installing other tools e.g. FastQC seems to work ok.
From the log for the 19.09 local instance I'm seeing the following error:
tool_shed.galaxy_install.install_manager ERROR 2020-01-20 14:36:19,721 [p:2159,w:1,m:0] [uWSGIWorker1Core3] Error attempting to retrieve installation information from tool shed https://toolshed.g2.bx.psu.edu/ for revision 512671604bab of repository dwgsim owned by nilshomer
Traceback (most recent call last):
File "lib/tool_shed/galaxy_install/install_manager.py", line 461, in __get_install_info_from_tool_shed
raw_text = util.url_get(tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
File "lib/galaxy/util/__init__.py", line 1677, in url_get
response = urlopener.open(full_url)
File "XXX/python/2.7.10/lib/python2.7/urllib2.py", line 437, in open
response = meth(req, response)
File "XXX/python/2.7.10/lib/python2.7/urllib2.py", line 550, in http_response
'http', request, response, code, msg, hdrs)
File "XXX/apps/python/2.7.10/lib/python2.7/urllib2.py", line 475, in error
return self._call_chain(*args)
File "XXX/apps/python/2.7.10/lib/python2.7/urllib2.py", line 409, in _call_chain
result = func(*args)
File "XXX/apps/python/2.7.10/lib/python2.7/urllib2.py", line 558, in http_error_default
raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
HTTPError: HTTP Error 500: Internal Server Error
Is there something special about this tool which means it can't be installed from the tool shed?
Any help is appreciated
Best wishes
Peter
--
Peter Briggs peter.briggs(a)manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
Hello all,
The January 2020 Galactic News is out!
https://galaxyproject.org/news/2020-01-galaxy-update/
- 13 Upcoming Events
- BCC2020 training topic nominations, Register for Galaxy Admin
Training, Galaxy @ PAG & ABRF, and training @ Earlham and Rennes.
- 172 new publications
- Six highlighted pubs from RT-qPCR to functional genomics
- Two new blog posts
- PGP-UK and Crowdsourcing Science
- Galaxy Platform News
- Three new platforms, UseGalaxy.* news, and platforms in pubs
- Training material and doc updates
- R, RStudio, ATAC-Seq, Scanpy, and Single Cell RNA-Seq
- And other news too
If you have anything to include to next month's newsletter, then
please send it to outreach(a)galaxyproject.org.
And a happy new year too, :-)
Dave C on behalf of the Galaxy community
--
https://galaxyproject.org/