Bypassing Data Managers?
by Raymond Wan
Dear all,
I'm a bit new at being a Galaxy administrator, so apologies for the
basic question.
I need to install some bowtie and bowtie2 indices. I have the indices
already but came across this page:
https://wiki.galaxyproject.org/Admin/DataPreparation
which says the steps mentioned on that page have been replaced with
Data Managers. I'm having problems with installing Data Managers
(accessing ToolShed right now and some errors which I guess I need to
sort out later) and was wondering if there was a way to bypass Data
Managers?
Are Data Managers the only way of installing reference data? With the
indices already pre-calculated, can I install them without having to
go through re-calculating them within Galaxy?
Thank you!
Ray
6 years, 11 months
18 February GalaxyAdmins Meetup: Ansible, Python Wheels
by Hans-Rudolf Hotz
Hello all,
The next GalaxyAdmins online meetup is next week, on Thursday, February
18 at 5PM CET (see your local time to know when to connect:
http://bit.ly/1nDGAkZ)
https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2016_02_18
The featured topics are:
- Automating Galaxy deployment @ artbio.fr: the pros and cons of
Ansible, presented by Marius van den Beek
- The Wheels on the Galaxy go round and round: Python Wheels in
Galaxy, presented by Nate Coraor
The meetup will use the same Adobe Connect technology used on previous
calls. The 'Meeting Room Link' will be provided on the wiki page in
time. It takes a couple of minutes to connect, so you are encouraged to
start connecting a few minutes early.
Looking forward to our first gathering in 2016
Dave C and Hans-Rudolf
--
Hans-Rudolf Hotz, PhD
Bioinformatics Support
Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
6 years, 11 months
copy/import shared history
by Le-Shin Wu
Hi,
I’ve recently installed a new galaxy server and I found some weird behaviors of admin jobs.
First, a shared history can not be copied as a new history. For example, user A shared one of his history with user B. User B can see this shared history through “histories shred with me” link, but when user B clicks “copy” of this history nothing happened. However, user B can view this history if he clicks “view” but if he then clicks “import history”, a new galaxy home page will be displayed on the center panel (as shown in the attached screenshot).
Second, the administer can only delete groups but he can not purge those deleted groups. In other words, when the administer clicks the “purge” button of a deleted group, nothing will happen on this group. It still shows on the table with status as “deleted”
Third, when installed the “package_fontconfig_2_11_1” through tool shed, the status of this package always shows as “installing tool dependencies”. We restarted our galaxy server several times but this message never went away (it always shows on the “monitor installing repositories” page).
We really have no idea how to fix these strange behaviors and the web log file also don’t have any error message. Any suggestion? Thank you.
Best
LW
6 years, 11 months
Fwd: [GMOD-devel] Google Summer of Code - Open Genome Informatics group
by Dave Clements
Hello all,
I know it's late in the game (I meant to email about this last week)
but *Galaxy
is applying to the 2016 Google Summer of Code as part of the Open Genome
Informatics group*. That group includes GMOD, Reactome, Wormbase, OICR,
and if we get some ideas in, Galaxy.
*The application goes in on Friday, which means ideas are due by the end of
Thursday* (which may be today, by the time you read this).
If you have ideas, please post 'em. Details and links are below.
Thanks, and again I apologize for the late notice,
Dave C
---------- Forwarded message ----------
From: Robin Haw <Robin.Haw(a)oicr.on.ca>
Date: Tue, Feb 16, 2016 at 1:25 PM
Subject: [GMOD-devel] Google Summer of Code - Open Genome Informatics group
To: "gmod-devel(a)lists.sourceforge.net" <gmod-devel(a)lists.sourceforge.net>
Dear All,
I’ve updated the Open Genome Informatics page: http://gmod.org/wiki/GSoC.,
in preparation for applying for this year’s Google Summer of Code.
If you are interested in participating, please
1. Let me, Scott and Marc (cc’d) know.
2. Post your project ideas on
http://gmod.org/wiki/GSOC_Project_Ideas_2016 over the next week; the
application process has started.
Last year’s project idea page is
http://gmod.org/wiki/GSOC_Project_Ideas_2015
Scott, Marc and I will work on the application.
Please take a look over the pages and provide any feedback?
Questions? Please let me know!
Thanks,
Robin
6 years, 11 months
stage_data_in_history ValueError: No JSON object could be decoded
by Peter Cock
Hi all,
Occasionally I've seen TravisCI tool tests fail with an exeception
ValueError: No JSON object could be decoded, e.g.
https://travis-ci.org/peterjc/galaxy_blast/jobs/107255016
...
galaxy.jobs INFO 2016-02-16 14:17:41,118 Collecting metrics for Job 139
galaxy.jobs DEBUG 2016-02-16 14:17:41,143 job 139 ended (finish()
executed in (1049.363 ms))
galaxy.model.metadata DEBUG 2016-02-16 14:17:41,154 Cleaning up
external metadata files
...
======================================================================
ERROR: NCBI BLAST+ blastn ( ncbi_blastn_wrapper ) > Test-2
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test/functional/test_toolbox.py",
line 291, in test_tool
self.do_it( td )
File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test/functional/test_toolbox.py",
line 40, in do_it
stage_data_in_history( galaxy_interactor, testdef.test_data(),
test_history, shed_tool_id )
File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test/base/interactor.py",
line 41, in stage_data_in_history
upload_wait()
File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test/base/interactor.py",
line 278, in wait
while not self.__history_ready( history_id ):
File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test/base/interactor.py",
line 297, in __history_ready
history_json = self._get( "histories/%s" % history_id ).json()
File "/home/travis/virtualenv/python2.6.9/lib/python2.6/site-packages/requests/models.py",
line 805, in json
return complexjson.loads(self.text, **kwargs)
File "/opt/python/2.6.9/lib/python2.6/json/__init__.py", line 307, in loads
return _default_decoder.decode(s)
File "/opt/python/2.6.9/lib/python2.6/json/decoder.py", line 319, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/opt/python/2.6.9/lib/python2.6/json/decoder.py", line 338, in
raw_decode
raise ValueError("No JSON object could be decoded")
ValueError: No JSON object could be decoded
-------------------- >> begin captured stdout << ---------------------
...
On this run there was no sign of an SQLite locking issue. This JSON problem
went away on a re-run, sadly instead the test-set failed further on with an
SQLite locking problem, see:
https://github.com/galaxyproject/galaxy/issues/1158#issuecomment-168714547
Does this "No JSON object could be decoded" point at a file system issue
(perhaps a race condition)? From searching the email archive this exception
(although not necessarily from the same area of the code) seems to occur
most often where Galaxy is being used with a cluster. But here this is all
running on a single TravisCI VM with the local job runner.
I appreciate there probably isn't enough information here to solve this,
but perhaps we need better logging here - are the JSON files simply
empty for example?
Regards,
Peter
6 years, 11 months
Gemini installation error
by Sebastian Schaaf
Hey all,
I am currently trying to install Gemini (v0.18.1) via the test toolshed.
It finally fails in dependencies as 'package_gemini_0_18_1' finds
dependency 'gemini' to end in error state. There the message looks like
the following:
---
2016-02-11 16:34:47 (72.4 MB/s) - `Miniconda-latest-Linux-x86_64.sh' saved
[25416725/25416725]
Python 2.7.11 :: Continuum Analytics, Inc.
Traceback (most recent call last):
File "gemini_install.py", line 190, in <module>
main(parser.parse_args())
File "gemini_install.py", line 80, in main
gemini = install_conda_pkgs(anaconda, remotes, args)
File "gemini_install.py", line 97, in install_conda_pkgs
urllib.urlretrieve(remotes["requirements_conda"], filename=req_file)
File "/home/galaxy/tool_libs/python2.7/lib/python2.7/urllib.py", line
98, in urlretrieve
return opener.retrieve(url, filename, reporthook, data)
File "/home/galaxy/tool_libs/python2.7/lib/python2.7/urllib.py", line
245, in retrieve
fp = self.open(url, data)
File "/home/galaxy/tool_libs/python2.7/lib/python2.7/urllib.py", line
213, in open
return getattr(self, name)(url)
File "/home/galaxy/tool_libs/python2.7/lib/python2.7/urllib.py", line
443, in open_https
h.endheaders(data)
File "/home/galaxy/tool_libs/python2.7/lib/python2.7/httplib.py", line
1049, in endheaders
self._send_output(message_body)
File "/home/galaxy/tool_libs/python2.7/lib/python2.7/httplib.py", line
893, in _send_output
self.send(msg)
File "/home/galaxy/tool_libs/python2.7/lib/python2.7/httplib.py", line
855, in send
self.connect()
File "/home/galaxy/tool_libs/python2.7/lib/python2.7/httplib.py", line
1274, in connect
server_hostname=server_hostname)
File "/home/galaxy/tool_libs/python2.7/lib/python2.7/ssl.py", line 352,
in wrap_socket
_context=self)
File "/home/galaxy/tool_libs/python2.7/lib/python2.7/ssl.py", line 579,
in __init__
self.do_handshake()
File "/home/galaxy/tool_libs/python2.7/lib/python2.7/ssl.py", line 808,
in do_handshake
self._sslobj.do_handshake()
IOError: [Errno socket error] [SSL: UNKNOWN_PROTOCOL] unknown protocol
(_ssl.c:590)
---
Some browsing at Google brought hints on three common cases where this
could appear *plus* a fourth one which looks by error code pretty much
what I got:
http://blog.techstacks.com/2010/03/3-common-causes-of-unknown-ssl-protoco...
So, may I be right that there is a typo in an URL needed for downloading
during the setup process? Or is it, according to
http://stackoverflow.com/questions/10667960/python-requests-throwing-up-s...
due to some failed SSL certificate check?
Some help (or ideas for targeted checking) would be great :).
Cheers,
Sebastian
--
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
6 years, 11 months
NGS.plot script freeze
by Philipp Rathert
Dear All,
we are trying to use NGS-plot on our local docker-galaxy-stable instance.
The script freezes whenever we click on the tool.
Does anybody have an idea what is wrong and how to fix this?
There is no error message or anything.
Thank you very much.
Kind regards,
Philipp
6 years, 11 months
REGISTRATION OF GALAXY
by martin perez
Hello;
How are you, I am from Panamá i try registrer for Galaxy /galaxeast, program but i dont know as do.
Do you can help me?
I am student in the university.
Martin Perez
Panamá, Panamá.
6 years, 11 months
