TypeError with 'dict'
by Martin Christiansen
Hi all,
I'm setting up a local galaxy server and have implemented a tool, but I can't even get it to run.
When I try to run it, the terminal says:
TypeError: unhashable type: 'dict'
The error itself arises from a python egg:
File "~/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/identity.py", line 141 in get
state = dict.get(self, key, default)
Any suggestions of how to solve this?
Best regards,
Martin Christiansen
7 years, 9 months
sql server timeout
by Shrum, Donald C
On occasion I'm getting and 'Internal Server error' on login with my production galaxy server.
If I refresh the page I'm able to login just fine.
This instance of galaxy has an apache frontend and a mysql server on the back end. If I look at my log files I see:
OperationalError: (OperationalError) (2006, 'MySQL server has gone away') 'SELECT galaxy_session.id AS galaxy_session_id.............
It looks like perhaps galaxy is trying to use a stale session or something like that. Has anyone else seen this problem and is there an easy solution aside from having users refresh the page?
Thanks,
Don
FSU Research Computing Center
7 years, 9 months
ToolShed error: samtools installation failure
by Beginner TI
Could someone please take a look?
Thanks,
Rui
On Tue, Aug 5, 2014 at 8:27 PM, Beginner TI <ruiwang.sz(a)gmail.com> wrote:
> Dear Admin,
>
> Since the upgrade, I lost the samtools that I installed myself. Although
> it is still in the tool_conf.xml, it does not show up on the panel. I tried
> to install from toolshed, but failed. Error messages pasted below. Could
> someone take a look?
>
> Thanks,
> Rui
>
> ⇝ AttributeError: 'NoneType' object has no attribute 'strip'
> URL:
> http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...
> Module weberror.evalexception.middleware:*364* in respond
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> view
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> >>
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> app_iter *=* self*.*application*(*environ*,* detect_start_response*)*
> Module paste.recursive:*84* in __call__
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> view
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> >>
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> *return* self*.*application*(*environ*,* start_response*)*
> Module paste.httpexceptions:*633* in __call__
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> view
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> >>
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> *return* self*.*application*(*environ*,* start_response*)*
> Module galaxy.web.framework.base:*132* in __call__
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> view
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> >>
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> *return* self*.*handle_request*(* environ*,* start_response *)*
> Module galaxy.web.framework.base:*190* in handle_request
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> view
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> >>
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> body *=* method*(* trans*,* ****kwargs *)*
> Module galaxy.web.framework:*369* in decorator
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> view
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> >>
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> *return* func*(* self*,* trans*,* ***args*,* ****kwargs *)*
> Module galaxy.webapps.galaxy.controllers.admin_toolshed:*983* in
> prepare_for_install
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> view
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> >>
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> includes_tool_dependencies *)*
> Module tool_shed.util.common_install_util:*97* in
> get_dependencies_for_repository
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> view
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> >>
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> repository *=* suc*.*get_repository_for_dependency_relationship*(* trans
> *.*app*,* tool_shed_url*,* name*,*repository_owner*,* changeset_revision
> *)*
> Module tool_shed.util.shed_util_common:*1036* in
> get_repository_for_dependency_relationship
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> view
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> >>
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> *(* name*,* owner*,* changeset_revision *)* *)*
> Module tool_shed.util.shed_util_common:*1867* in url_join
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> view
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> >>
> <http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=ht...>
> parts*.*append*(* arg*.*strip*(* '/' *)* *)*
> *AttributeError: 'NoneType' object has no attribute 'strip'*
>
>
7 years, 9 months
"The status is being set to Never installed"
by David Hoover
When I install a tool from the toolshed that has type="set_environment" as a requirement, I get this in the main.log:
Creating a new record for version None of tool dependency SCRIPT_PATH for revision 5fed38c7e063 of repository mirdeep2. The status is being set to Never installed.
Consequently, nothing in the tool_dependency directory is created. The tool is shown to have missing dependencies in the 'Manage installed tool shed repositories' panel. Is there something special that must be done to allow a tool to have only an environment setting as a dependency? Is there something that can be done to fix the problem, other than going into the database and changing the tool_dependency.status from 'Never installed' to 'Installed' and manually creating the subdirectories?
--------------------
David Hoover, PhD
Helix Systems Staff
7 years, 9 months
changes to upload.py
by Sajdak, Doris
I'm in an odd situation: I was given an older version of Galaxy with additional tools built into it by a new faculty member. He brought this from his former institutions and wanted us to run his Galaxy instance on our systems. We don't want to support several instances so we agreed to put his tools into our Galaxy implementation. However, we are running into all kinds of snags. The latest issue is that we realized changes have been made to upload.py to allow for additional data types. Here's an example of what I mean:
def check_bam( temp_name ):
return Bam().sniff( temp_name )
def check_sff( temp_name ):
return Sff().sniff( temp_name )
def check_celstgz( temp_name ):
return CelsTgz().sniff( temp_name )
While this doesn't seem like a big deal to add those changes into our installation, I'm concerned that doing so will make us unable to update Galaxy in the future. Can you either confirm or deny that changes to upload.py on our system will be overwritten with Galaxy updates?
Thanks,
Dori
**********************************
Dori Sajdak
Senior Systems Administrator
State University of NY at Buffalo
Center for Computational Research
701 Ellicott St
Buffalo, NY 14203
Phone: (716) 881-8934
Fax: (716) 849-6656
Web: http://ccr.buffalo.edu
**********************************
7 years, 9 months
testtoolshed : python-2.7 installation error
by Geert Vandeweyer
Hi,
I get an installation error on the python 2.7 package in the test
toolshed. I used the 'contact owner' function, but wanted to mention it
here too, as there hasn't been reaction so far. Sorry for double posting
if so.
Error:
tar (child): 5.2.tar.bz2: Cannot open: No such file or directory
A similar error is in the Test run outputs. I believe it is related to
the following (unnecessary) line in the tool_dependency.xml:
<action type="change_directory">..</action>
located just after the download_file action for the 5.2.tar.bz2 file.
Best,
Geert
--
Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandeweyer(a)ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer
7 years, 9 months
condor compute cluster
by Shrum, Donald C
Our galaxy server has an apache front end with ldap authentication.
I've added a condor destination...
<plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner"/>
<destination id="condor" runner="condor"/>
There are some tools I'd like to point to condor but it appears all the jobs will be sent as the user condor.
Is there an existing fix that will submit jobs to our condor cluster as the logged in user?
If not could someone give me a small pointer for a hack fix?
Something along the lines of:
galaxy-dist/lib/galaxy/jobs/runners/util/condor/__init__.py
line 71:
submit = Popen(('condor_submit', submit_file), stdout=PIPE, stderr=STDOUT)
Could be changed to sudo -u xxx -c condor_submit...
Thanks all,
Don
FSU Research Computing Center
7 years, 9 months
August 2014 Galaxy CloudMan release
by Enis Afgan
*We just released an update to Galaxy CloudMan.* CloudMan offers an easy
way to get a personal and completely functional instance of Galaxy in the
cloud in just a few minutes, without any manual configuration.
This is mostly an incremental bug fix release with the following summary of
changes:
-
On AWS, updated *galaxyFS* snapshot (snap-e6e1c04a), which includes the
June 2, 2014 Galaxy release with the July 30th security fix. All the tools
installed via the Tool Shed have been updated and a number of new tools
added, most notably: Tophat2, Bowtie2, FastQC, several FASTQ manipulation
tools, several QC tools.
-
For AWS, added support for VPC
-
For OpenStack clouds, added the ability to automatically recover worker
instances on cluster reboot
-
Added support for creating a file system based on a downloadable archive
-
Do not run Galaxy with multiple processes by default. This is because
Tool Shed installs do not work properly in the multi-process mode. This
feature can be enabled by setting user data option
configure_multiple_galaxy_processes to True when launching an instance.
-
Set SGE slots in each queue to be equal to the number of cores on the
instance
-
Set instance IP in the Galaxy's FTP data upload tool message
-
Added support for Nginx v1.4 and allow it (with the PAM module) to used
as the authentication mechanism when accessing Galaxy Reports app
-
Fixed cluster deletion when performed via the API
-
No longer automatically start Hadoop and HTCondor services
-
On manually-invoked instance reboots, do not increment the instance
reboot count that otherwise eventually leads to instance termination
-
Limit the size of the log message buffer used in the UI to 1000 lines.
Long-running instances had issues with this log growing large and that led
to poor UI performance. The complete log is still available from the Admin
page (or the command line).
-
Automatically delete the bucket/container for Test type (*ie*, 'SGE
only') clusters on cluster termination
For complete details on implemented changes, please see the source code
commits <https://bitbucket.org/galaxy/cloudman/commits/all?search=835%3A903>
.
Enjoy and please let us know what you think,
Enis & Dannon & The Galaxy Team
https://wiki.galaxyproject.org/Cloud
7 years, 9 months
Packaging tools with language specific dependencies
by Renato Alves
Hi everyone,
Is there any standard or commonly used way to package tools that have
language specific dependencies.
I know that with Python libraries one can use setup_virtualenv and with
Java jars the JAVA_JAR_LIB strategy is used.
Is there anything equivalent for R, Perl and Ruby libraries?
Thanks
Renato
7 years, 9 months
Issues with dependencies for toolshed packages
by Iry Witham
Hi Team,
I have been trying to install package_snpEff_3_5 from the Galaxy main tool shed and package_snpEff_3_6 from the Galaxy test tool shed and have the same issue. Once the installer completes it shows that the dependency snpEff.x.x was not installed. When I try to install the dependency it reports that the directory /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/tmp/tmp-toolshed-mtdi48tQV/snpEff does not exist. I have checked to confirm that this is true and discovered that rather then a directory I find a null file named "snpEff and the snpEff_v3.x_core.zip file. I checked my shedtool dependencies folder and the directory for these tools are empty. I have since uninstalled the package. I just tried again to install the snpEff tool and am getting the followig error message:
Internal Server Error
Galaxy was unable to successfully complete your request
URL: http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://t...
Module galaxy.web.framework.middleware.error:149 in __call__
>> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://t...> app_iter = self.application(environ, sr_checker)
Module paste.recursive:84 in __call__
>> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://t...> return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__
>> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://t...> return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__
>> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://t...> return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request
>> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://t...> body = method( trans, **kwargs )
Module galaxy.web.framework:377 in decorator
>> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://t...> return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.admin_toolshed:1035 in prepare_for_install
>> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://t...> raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
Module tool_shed.util.common_util:310 in tool_shed_get
>> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://t...> response = urlopener.open( uri )
Module urllib2:395 in open
>> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://t...> response = meth(req, response)
Module urllib2:508 in http_response
>> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://t...> 'http', request, response, code, msg, hdrs)
Module urllib2:427 in error
>> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://t...> result = self._call_chain(*args)
Module urllib2:367 in _call_chain
>> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://t...> result = func(*args)
Module urllib2:603 in http_error_302
>> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://t...> return self.parent.open(new)
Module urllib2:395 in open
>> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://t...> response = meth(req, response)
Module urllib2:508 in http_response
>> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://t...> 'http', request, response, code, msg, hdrs)
Module urllib2:433 in error
>> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://t...> return self._call_chain(*args)
Module urllib2:367 in _call_chain
>> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://t...> result = func(*args)
Module urllib2:516 in http_error_default
>> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://t...> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
HTTPError: HTTP Error 500: Internal Server Error
extra data<http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://t...>
full traceback<http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://t...>
text version<http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://t...>
This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem.
I appreciate any possible assistance,
Regards,
__________________________________
Iry T. Witham
Scientific Applications Administrator
Scientific Computing Group
Computational Sciences Dept.
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609
Phone: 207-288-6744
email: iry.witham(a)jax.org
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7 years, 9 months
