Newline characters for txt files
by Lawrence, Cris W
I have observed that when I upload a file with CRLF line endings into Galaxy and then later download it, the endings have changed to UNIX (LF only). I also observed that an uploaded file containing CR only line endings in Galaxy downloads to a file again with LF only line endings. These file types are txt. Just want to confirm - does Galaxy scrub line endings?
- Cris
2 years, 11 months
installation error on venv dependencies.xml
by Linda Bakker
Hi All,
I am having some problems with my tool dependencies to setup a python venv.
Dependencies.xml looks like this:
When i install my tool from the toolshed, it fails to install the venv
dependency with this error message:
I am not sure what the problem exactly seems to be. os.py should be a
default python package right or do i need to specify it in the
dependencies file?
Can someone point me in the right direction of what the problem might be.
Thanks!
with regards ,
Linda Bakker
--
Linda Bakker
Bioinformatics Research Assistant
Plant Research International, Wageningen UR
Building 107 (Radix), room W1.Fa.054
Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
tel: +31-317-480756
email: linda.bakker(a)wur.nl
2 years, 11 months
Search Tool Shed
by Matthias Bernt
Dear mailing list,
What is the expected behavior if I click in the Admin area under "Search
Tool Shed" on the "Galaxy Main Tool Shed" button (or any of the Browse
.. or Search .. actions that are available via the black triangle submenu)?
I remember that a new tab with the corresponding Tool Shed page opened
in the browser.
This is currently not happening in my installation. What could be the
problem? As a work around I can trigger the Browse action via right
click and "open link in new tab".
As far as I can see this is not a JavaScript problem.
Best,
Matthias
--
-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.bernt(a)ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------
2 years, 11 months
Re: [galaxy-dev] Shared Data Library, large number of files
by Hans-Rudolf Hotz
this sounds more like a browser issue to me
which browser do you use? what happens when you use a different browser?
and what happens when you just reload the page
Hans-Rudolf
On 03/01/2017 06:17 PM, D K wrote:
> Actually, when I click on the Shared Data-> Data Libraries link I get
> only the Galaxy banner and a blank page, so I'm not even seeing the data
> libraries themselves.
>
> If I use the Admin link and then click Data libraries, I can see the
> actual libraries. But when I try to enter one of the libraries with lots
> of files it hangs.
>
>
> On Wed, Mar 1, 2017 at 9:03 AM, D K <danielfortin86(a)gmail.com
> <mailto:danielfortin86@gmail.com>> wrote:
>
> Hi Hans,
>
> I'm running 16.10. If I'm not mistaken, the old Data Library
> interface is still accessible in the Admin menu isn't it? I have the
> same issue when navigating to a Data Library either from the Admin
> or Shared Data links. I also tried this in 16.07 with the same
> result. If it makes a difference, I'm using PostgreSQL and Apache.
>
> Dwight
>
>
>
> On Tue, Feb 28, 2017 at 11:47 PM, Hans-Rudolf Hotz <hrh(a)fmi.ch
> <mailto:hrh@fmi.ch>> wrote:
>
> Hi Daniel
>
> Just double checking which version of galaxy are you running? In
> other words: are you still using the old Data Library interface?
> (if I remember correctly, the old UI was deprecated in 15.10)
> We had similar issues with the old UI.
>
> The new one works fine and is very fast. E.g. we have a 'MISEQ'
> folder with more than 100 sub folders and a HISEQ folder with
> more than 600 sub folders. Each containing up to 100plus fastq
> and text files.
>
> Regards, Hans-Rudolf
>
>
>
> On 03/01/2017 12:13 AM, D K wrote:
>
> Hi,
>
> I've noticed that the more files / folders (think hundreds
> of folders
> each with 20+ fastq files) I add to a Shared Data Library,
> the longer
> and longer it takes to initially navigate the folder
> structure (after
> clicking on the specific Shared Data Library). Just opening
> up the
> Shared Data Library can take several minutes and often the
> browser times
> out. Is there a way to speed this up?
>
> If it's relevant, when I add shared data, it's linked rather
> than copied
> into Galaxy. Any suggestions would be greatly appreciated
>
> Thanks!
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> https://lists.galaxyproject.org/
> <https://lists.galaxyproject.org/>
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
> <http://galaxyproject.org/search/mailinglists/>
>
>
>
2 years, 11 months
Rg: Galaxy Version
by Anamika Singh
Dear galaxy team,
I am using galaxy platform (old version) in Linux OS which was not
installed by me. I would like to know 'how to check what is the galaxy
version installed currently in my system.
Regards
--
Anamika
2 years, 11 months
tool problems (data_manager_fetch_ncbi_taxonomy & ggplot2)
by Matthias Bernt
Dear mailing list,
I'm experimenting with the tools available at the Tool Shed and ran into
problems with two of the tools.
1. data_manager_fetch_ncbi_taxonomy
If I run the data manager I get an error in the browser: "Uncaught
exception in exposed API method"
The terminal shows the following stack trace:
Traceback (most recent call last):
File "/home/berntm/galaxy/lib/galaxy/web/framework/decorators.py",
line 282, in decorator
rval = func( self, trans, *args, **kwargs )
File "/home/berntm/galaxy/lib/galaxy/webapps/galaxy/api/tools.py",
line 98, in build
return tool.to_json(trans, kwd.get('inputs', kwd))
File "/home/berntm/galaxy/lib/galaxy/tools/__init__.py", line 1853,
in to_json
tools = self.app.toolbox.get_loaded_tools_by_lineage( self.id )
File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line
492, in get_loaded_tools_by_lineage
tool_lineage = self._lineage_map.get( tool_id )
File
"/home/berntm/galaxy/lib/galaxy/tools/toolbox/lineages/factory.py", line
38, in get
lineage = ToolShedLineage.from_tool_id( self.app, tool_id )
File
"/home/berntm/galaxy/lib/galaxy/tools/toolbox/lineages/tool_shed.py",
line 70, in from_tool_id
return ToolShedLineage( app, tool_version )
File
"/home/berntm/galaxy/lib/galaxy/tools/toolbox/lineages/tool_shed.py",
line 53, in __init__
self.tool_version_id = tool_version.id
File
"/home/berntm/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/attributes.py",
line 237, in __get__
return self.impl.get(instance_state(instance), dict_)
File
"/home/berntm/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/attributes.py",
line 578, in get
value = state._load_expired(state, passive)
File
"/home/berntm/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/state.py",
line 474, in _load_expired
self.manager.deferred_scalar_loader(self, toload)
File
"/home/berntm/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/loading.py",
line 610, in load_scalar_attributes
(state_str(state)))
DetachedInstanceError: Instance <ToolVersion at 0x7fc7180b5310> is not
bound to a Session; attribute refresh operation cannot proceed
Any ideas whats going on - and how to fix this?
2. The second tool is ggplot2_2_2_1. Here mingchen0919 is listed as
owner in the Tool Shed -- so I do not know if this mailing list is the
correct address. If not: how do I find contact information to the owner
of a tool in the ToolShed?
Otherwise, the problem is missing dependencies:
In package_fontconfig_2_11_1 (which is a dependency of ggplot) I get
"""
configure: error: in
`/home/berntm/galaxy/database/tmp/tmp-toolshed-mtdBsL0ig/fontconfig-2.11.1':
configure: error: The pkg-config script could not be found or is too
old. Make sure it
is in your PATH or set the PKG_CONFIG environment variable to the full
path to pkg-config.
Alternatively, you may set the environment variables FREETYPE_CFLAGS
and FREETYPE_LIBS to avoid the need to call pkg-config.
See the pkg-config man page for more details.
To get pkg-config, see <http://pkg-config.freedesktop.org/>.
See `config.log' for more details
"""
Is pkg-config supposed to be installed on the computer running galaxy?
Or should this be installed within galaxy?
In addition on the terminal the following error appears after the
pkg-config error:
"""
Exception happened during processing of request from ('127.0.0.1', 42534)
Traceback (most recent call last):
File
"/home/berntm/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
line 1085, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 331, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 654, in __init__
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 713, in finish
self.wfile.close()
File "/usr/lib/python2.7/socket.py", line 283, in close
self.flush()
File "/usr/lib/python2.7/socket.py", line 307, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
"""
Thank you very much for your help.
Best regards,
Matthias
--
-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.bernt(a)ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------
2 years, 11 months
March 2017 News of the Galaxy
by Dave Clements
Hello all,
The <https://gcc2017.sciencesconf.org/>March 2017 Galaxy News
<https://new.galaxyproject.org/galaxy-updates/2017-03/> is out!
- 2017 Galaxy Community Conference
<https://new.galaxyproject.org/galaxy-updates/2017-03/#2017-galaxy-communi...>
early
registration and abstract submission are open.
- Travel fellowships for GCC2017
<https://new.galaxyproject.org/galaxy-updates/2017-03/#gcc2017-travel-fell...>
are
available from the Galaxy Community Fund.
- Metaproteomics of microbiomes at ABRF 2017
<https://new.galaxyproject.org/galaxy-updates/2017-03/#metaproteomics-of-m...>
, Cycle "Bioinformatique par la pratique" 2017
<https://new.galaxyproject.org/galaxy-updates/2017-03/#cycle-bioinformatiq...>
at
INRA in Jouy-en-Josas, and a whole lot more
<https://new.galaxyproject.org/galaxy-updates/2017-03/#all-upcoming-events>
events
are coming up.
- Galaxy is in GSoC 2017
<https://new.galaxyproject.org/galaxy-updates/2017-03/#galaxy-in-google-su...>
- 199 new publications
<https://new.galaxyproject.org/galaxy-updates/2017-03/#new-publications>,
including 11 highlighted pubs.
- Four open positions
<https://new.galaxyproject.org/galaxy-updates/2017-03/#who-s-hiring> in
Europe and North America.
- Two new public servers, RNA-Rocket needs some fuel, and Cancer
Computer upgrades
<https://new.galaxyproject.org/galaxy-updates/2017-03/#public-galaxy-serve...>
- New releases
<https://new.galaxyproject.org/galaxy-updates/2017-03/#releases> of
Galaxy, Planemo, Pulsar, galaxy-lib, Starforge, and (the new)
sequence_utils.
- Over 80 new repos
<https://new.galaxyproject.org/galaxy-updates/2017-03/#toolshed-contributions>
in
the Galaxy Tool Shed.
- And other news
<https://new.galaxyproject.org/galaxy-updates/2017-03/#other-news> too.
Happy March!
Dave C and the Galaxy Team
--
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/
2 years, 11 months
SAML Authentication
by Keith Suderman
Is anyone using SAML for authentication? There is a feature request for SAML support on GitHub ( https://github.com/galaxyproject/galaxy/issues/3146), but it doesn't look like any work has been done.
We need to add the ability for our users to authenticate with a SAML identity provider (IdP), in particular with InCommon/EduRoam/EduCause et al. Looking at the documentation there appears to be "the old way" (configuring Apache/Nginx to do the authentication) and "the new way" where Galaxy handles the authentication. Is it correct to assume that to use the new way I should implement an external authenticator, something like galaxy/auth/providers/saml.py and then some sort of magic to get a config/auth_conf.xml working?
I just want to make sure I am heading down the correct path before investing too much time.
- Keith
Keith Suderman
Research Associate
Department of Computer Science
Vassar College, Poughkeepsie NY
suderman(a)cs.vassar.edu
2 years, 11 months
Deploy on cloud
by Stavros 0 Sachtouris
Hi all,
we are going to deploy galaxy on ~okeanos cloud ( okeanos.grnet.gr ). We
have already developed a working storage backend for our object store
system ( https://github.com/galaxyproject/galaxy/pull/3611 ).
Now we focus on how to make Galaxy run instances/tasks on our VMs and I
would like some advice on how to approach this issue.
What we need is a (potentially large) Galaxy deployment with the ability
to run workflows of dockerized "tasks". Each task should run on a
provisioned VM on our cloud. There are many tools out there to let us
automate VM provisioning, managing docker clusters, scaling, as well as
monitoring and accounting, and we want to provide all of these features
to our partners in European Academia.
The question is, how does Galaxy communicate with a cluster manager like
Apache Mesos or Docker swarm? Any other tools I should look into, which
are known to work with Galaxy? Will we have to drill into Galaxy code
base to provide these features?
Thank you in advance for you suggestions,
Stavros Sachtouris
developer @ www.grnet.gr
2 years, 11 months
Problem with installing tools using Conda
by Ashok Varadharajan
Dear Team,
I have problem with the installation of tools using conda. I am getting
following error message when i try to install tools from galaxy. I tried to
install these tools manually with the same conda used by the galaxy and it
worked. Can anyone help us to solve this issue ?
Traceback (most recent call last):
File "/xxxx/xxxxx/xxxx-xxxx/conda//bin/conda", line 4, in <module>
from conda.cli.main import main
ImportError: No module named conda.cli.main
galaxy.tools.deps.resolvers.conda DEBUG 2017-03-02 17:35:49,759 Removing
failed conda install of samtools, version '1.3.1'
Traceback (most recent call last):
File "/xxxx/xxxxx/xxxx-xxxx/conda//bin/conda", line 4, in <module>
from conda.cli.main import main
ImportError: No module named conda.cli.main
galaxy.tools.deps.resolvers.conda DEBUG 2017-03-02 17:35:49,941 Removing
failed conda install of samtools, version 'None'
Traceback (most recent call last):
File "/xxxx/xxxxx/xxxx-xxxx/conda//bin/conda", line 4, in <module>
from conda.cli.main import main
ImportError: No module named conda.cli.main
galaxy.tools.deps.resolvers.conda DEBUG 2017-03-02 17:35:50,142 Removing
failed conda install of bwa, version '0.7.15'
Traceback (most recent call last):
File "/xxxx/xxxxx/xxxx-xxxx/conda//bin/conda", line 4, in <module>
from conda.cli.main import main
ImportError: No module named conda.cli.main
We are running galaxy-16.07 behind the proxy using nginx, uwsgi and
supervisor in scientific linux 7. Below are the details of galaxy.ini and
supervisor configuration.
*### galaxy.ini *
conda_prefix = /xxxx/xxxxx/xxxx-xxxx/conda/
#conda_exec =
conda_debug = False
conda_ensure_channels = r,bioconda,iuc
#conda_auto_install = False
#conda_verbose_install_check=False
conda_auto_init = True
*### supervisor*
[supervisord]
[program:galaxy_web]
command = $GALAXY_PATH/.venv/bin/uwsgi --virtualenv
$GALAXY_PATH/.venv --ini-paste $GALAXY_PATH/config/galaxy.ini --logdate
--master --processes 3 --threads 6 --logto
$GALAXY_PATH/logs/galaxy.uwsgi.log --socket 127.0.0.1:4001 --pythonpath lib
--stats 127.0.0.1:9191
directory = $GALAXY_PATH
umask = 022
autostart = true
autorestart = true
startsecs = 20
user = galaxy
environment =
PATH=$GALAXY_PATH/.venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin,PYTHONHOME=$GALAXY_PATH/.venv,DRMAA_LIBRARY_PATH=/usr/local/lib/libdrmaa.so
numprocs = 1
stoplight = INT
startretries = 15
process_name = web%(process_num)s
[program:handler]
command = $GALAXY_PATH/.venv/bin/python ./lib/galaxy/main.py -c
$GALAXY_PATH/config/galaxy.ini --server-name=handler%(process_num)s
--log-file=$GALAXY_PATH/logs/
>galaxy_handler%(process_num)s.log
directory = $GALAXY_PATH
process_name = handler%(process_num)s
numprocs = 3
umask = 022
autostart = true
autorestart = true
startsecs = 20
user = galaxy
environment =
PATH=$GALAXY_PATH/.venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin,PYTHONHOME=$GALAXY_PATH/.venv,DRMAA_LIBRARY_PATH=/usr/local/lib/libdrmaa.so
startretries = 15
--
*Thanks and Regards,*
*Ashok Vardharajan*
2 years, 11 months
