Anyone else getting this when trying to upload to a testtoolshed repos?
I'm using the "upload files to repository" function in "repository
actions" and get a blank page with "internal server error".. Worked fine
I am trying to reset metadata on all my repositories at once using the
"Reset metadata on my repositories" button on
https://testtoolshed.g2.bx.psu.edu/ It fails with:
Internal Server Error
Galaxy was unable to successfully complete your request
Module galaxy.web.framework.middleware.error:149 in __call__
>> app_iter = self.application(environ, sr_checker)
Module paste.debug.prints:106 in __call__
>> environ, self.app)
Module paste.wsgilib:543 in intercept_output
>> app_iter = application(environ, replacement_start_response)
Module paste.recursive:84 in __call__
>> return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__
>> return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__
>> return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request
>> body = method( trans, **kwargs )
>> my_writable=True )
Module tool_shed.metadata.repository_metadata_manager:65 in
>> query = self.get_query_for_setting_metadata_on_repositories( my_writable=my_writable,order=True )
Module tool_shed.metadata.repository_metadata_manager:513 in
>> .filter( or_( *clause_list ) )
NameError: global name 'or_' is not defined
I have a new instance of galaxy cloudman running and have added tools from the toolshed to it. When I attempt to run tools like sam-to-bam or any gatk tool I am prompted for a reference genome. However, indices/references not available for these tools. I have added the following line to the sam_fa_indices.loc, but that did nothing:
index hg19 /mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/gh19.fa
I have also added the following three lines to the gatk2_picard_index.loc:
hg19 hg19 Human (hg19) /mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/hg19.fa
GRCh37 GRCh37 Human (GRCh37) /mnt/galaxyIndices/genomes/Hsapiens/GRCh37/seq/GRCh37.fa
mm10 mm10 Mouse (mm10) /mnt/galaxyIndices/genomes/Mmusculus/mm10/seq/mm10.fa
I know I have missed something, but can't seem to figure it out. Could someone point me in the right direction?
Iry T. Witham
Scientific Applications Administrator
Computational Sciences Group
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609
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I installed clustalomega from the galaxy main toolshed using the admin
interface of our local galaxy install. When I run the tool, I get this
Dataset generation errors
Dataset 55: co_alignment.fasta
Tool execution generated the following error message:
Error invoking command:
clustalo --force --threads=1 --maxnumseq=300000 --maxseqlen=15000 -o
/opt/galaxy-dist/database/files/000/dataset_159.dat -v -i
[Errno 2] No such file or directory
I've tried reloading my input file, reloading the tool's configuration,
resetting the metadata on the clustalomega repository, deleting the tool
completely and re-installing. No luck. If I try to rerun the job again, I
get non-sensical errors that seem to originate from other tools, as if the
database was completely garbled. Each of those tools work fine. Only
clustalomega behaves oddly.
I have no access to our galaxy server, so any solution would have to be
implemented from the admin interface.
thanks for any hints,
I'm having trouble after setting up SSL on our Apache proxy for Galaxy.
When I try to import data from UCSC, Galaxy tries to go to the http
(non-ssl) url for UCSC and thus generates a security error in the
browser and the request is blocked. I have added
RequestHeader set X-URL-SCHEME https
to the httpd.conf and that appears to be working. Is there something
else I need to do? Should I patch the data_source tools to use https in
the xml tool definitions? Thanks for any advice.
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
I'm trying to install R/bioconductor packages in galaxy and have trouble
with some of them.
I made a dependency package ("package_qdnaseq_1_0_5" in the
testtoolshed) that should install several R (bioconductor) packages
using "setup_r_environment" and for each package the
It works for many but fails for the package "DNAcopy" with the error
below complaining about gfortran, but that seems to be installed on my
systems (tested two of them, ubuntu 12.04). When I install this with
"install.packages" in my default R installation it installs without
Anyway know how to deal with or debug this?
install_environment.STDOUT DEBUG 2014-10-07 14:04:13,176 Error in
dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object
undefined symbol: _gfortran_os_error
Error: loading failed
Error in dyn.load(file, DLLpath = DLLpath, ...) :
ERROR: loading failed
It would be great to have someone from the Galaxy community involved in
this reproducible science hack-a-thon, as Galaxy is such a positive
contribution to workflows in reproducible science.
Reproducible Science Hackathon:
Curriculum & Workflow Development
Goal: Develop a short course curriculum for tools, resources, and
practices for reproducible science.
Location: NESCent, Durham, NC
Dates and times: December 8 - 11, 2014; 9 am - 5pm each day
To apply: http://goo.gl/GzS118 ; deadline October 10, 2014. Successful
applicants will be notified by October 17th.
Making science more reproducible has enormous potential to accelerate
scientific advance, including for practicing individuals. Despite this,
the tools and approaches that are already available are rarely taught.
To address this, we are organizing a 4-day workshop aimed at developing,
and later teaching, a short course curriculum for tools, resources, and
practices for reproducible science. A part of the workshop will also be
devoted to addressing gaps that hinder the broad adoption of such
resources. The event will be held December 8-11,2014, in Durham, NC, at
the National Evolutionary Synthesis Center (NESCent). We aim to assemble
a diverse and interdisciplinary group of participants, and invite those
interested to apply by Oct 10 at http://goo.gl/GzS118.
The full Call for Participation can be found here: http://goo.gl/IzACr3
I have a local galaxy instance installed on a cluster.
I've been trying to upload data by URL but kept getting this error: *"unable
to fetch <url of data> [Errno socket error] [Errno 110] connection timed
out". *I've tried with and without file compression format and still gives
me that error.
Am I suppose to modify/edit any particular config file?
Can't seem to find a similar thread or answer to this but perhaps I may
have missed. Apologies if I have missed. Would appreciate if anyone can