Upload local files
by Sascha Kastens
Hi devs,
when using the upload tool it would be nice to let the user
specify paths to files stored on our internal servers like the admin
can when choosing to add data to a library. Also it would be nice
to be able to link to these files.
Unfortunately I was not able to find the "tool" for uploading
files into a library so it would be nice if you can give me a hint.
With this information I should be able to extend the normal upload
tool.
Thanks in advance!
Cheers,
Sascha Kastens
Project Manager
GATC Biotech AG
Jakob-Stadler-Platz 7
D-78467 Konstanz
Phone: +49 (0) 7531-81604110
Fax: +49 (0) 7531-816081
Email: s.kastens(a)gatc-biotech.com
http://www.gatc-biotech.com
http://www.twitter.com/gatcbiotech
http://www.facebook.com/gatcbiotech
http://www.xing.com/companies/gatcbiotechag
GATC Biotech AG
Chairman Supervisory Board: Fritz Pohl
Board of Directors: Peter Pohl, Thomas Pohl, Dr. Marcus Benz
UID: DE 142 315 733 | Registration: Konstanz, HRB 1757 | Registered Office: Konstanz
The information contained in this email is intended solely for the addressee. Access to this email by anyone else unauthorized. If you are not the intended recipient, any form of disclosure, reproduction, distribution or any action taken or refrained from in reliance on it, is prohibited and may be unlawful. Please notify the sender immediately. The content of this email is not legally binding unless confirmed by letter.
9 years, 5 months
.loc files and Reload a tool's configuration
by Julian Pradinuk
Hi all,
I'm puzzled by the following:
Edits to blastdb.loc are reflected when I reload NCBI BLAST+ blastn from
Admin tools. This is great.
HOWEVER, edits to bowtie_indices.loc, bwa_index.loc, etc. are not reflected
when their respective tools are reloaded.
Is this an error with my configuration or has this feature not yet been
implemented for NGS tools?
Thanks!
Julian
9 years, 6 months
Workshop on Extending High-Performance Computing Beyond its Traditional User Communities
by James Taylor
Galaxy developers,
There is an upcoming workshop on accessible HPC that might be of interest to many of you. It would be great to see the Galaxy community perspective included in these discussions. Details follow.
Thanks,
James
--
http://www.psc.edu/index.php/escience-2012-workshop
Extending High-Performance Computing Beyond its Traditional User Communities
Co-located with the 8th IEEE International Conference on eScience,
Chicago, USA
October 8, 2012
Call for Papers:
Papers submission due: Aug. 6, 2012
Historically, high-performance computing (HPC) has enabled computationally intensive simulations performed in batch mode on a small number of standalone supercomputers, shared among users selected for their computing skills as much as for expertise in their own disciplines. There has been a sustained effort over the past decade to broaden this model by deploying a wider variety of HPC systems tied into emerging national and global cyber-infrastructure (CI), yet only a small fraction of the resources fielded by HPC-based CI programs such as the eXtreme Science and Engineering Discovery Environment (XSEDE) is currently used by people who are not members of communities that have used supercomputing centers since the 1980’s.
Given the digital instruments and methods that are revolutionizing biological, environmental, and physical sciences, as well as the promise of important benefits to social sciences and the arts and humanities, XSEDE is undertaking a proactive effort to work with members of these communities to identify barriers and to develop projects that show how to effectively overcome them.
In this context, the goal of the proposed workshop is to discuss examples of successful projects as well as barriers and practical approaches to overcoming them. After the presentation of selected papers, there will be a discussion among all the participants. The desired outcome is an improved understanding of actions that should be taken by the various stakeholders in order to enable a wide spectrum of practitioners to use HPC resources as part of their work and data flows, and to establish an informal network of people and communities interested in this outcome.
We invite papers that describe projects that have already used HPC systems, or whose requirements analysis indicates a need for HPC systems as part of the infrastructure for their implementation – if specific topics of concern are satisfactorily addressed.
Disciplines of study include, but are not limited to:
• Genomics and bioinformatics
• Social, behavioral and economic sciences
• Digital humanities
• Public Health
• Citizen science
• Computational linguistics
• Machine learning
• Digital arts
Topics of concern include, but are not limited to:
• Campus, Cloud and HPC resources: tradeoffs and interoperation
• Security and privacy of HPC environments
• Data management, integration and visualization from Lab to HPC and back
• Parallelization of compute- or data-intensive tasks
• Programming paradigms, tools and programming environments
• Access to and scheduling of HPC environments
• Community portals and gateways
• Workflow management and remote collaboration
• System level support for workflows that include HPC
• Fault-tolerance of distributed applications
• Scalability of infrastructures and applications
• Training and education of current and future practitioners
9 years, 6 months
galaxy cloudMan failed
by jiesheng＠bioteam.net
Hi, all
I just tried installing galaxy in amazon cloud following the instruction
here:http://wiki.g2.bx.psu.edu/CloudMan.
Using this ami-da58aab3, I do not have http service after the instance
is started. I logined into the instance and confirmed it. How should I
troubleshoot it?
Could your guys ask Amazon to remove
ami-561bc93f, 072133624695/galaxy-cloudman-2012-02-26 ? If it is not
from galaxy, it is risky to have it. If user selects it, user most
likely will give access key and secret key at launch time as is in
instruction. I used this one before I went to section 5 to find out I
am not supposed to use it.
thanks
--
jason zhang
The BioTeam, Inc.
jason(a)bioteam.net
9 years, 6 months
bcftools
by Hongkyun Kim
Dear all,
I am not sure whether the following issue is related to development or
bug report. In main galaxy website, I generated bcf files using
mpileup, and now would like to convert bcf files to vcf files.
However, I cannot find this conversion tool. Oddly, I find this tool
in test galaxy website. Is this bug or in the process of the
development?
Thank you,
HK
9 years, 6 months
GFF tools
by Sarah Maman
Hello,
When I use one of GFF tool (
Filter GFF data by attribute
<http://sig-workbench.toulouse.inra.fr/galaxy/tool_runner?tool_id=gff_filt...>
using simple expressions OR
Filter GFF data by feature count
<http://sig-workbench.toulouse.inra.fr/galaxy/tool_runner?tool_id=gff_filt...>
using simple expressions OR
Filter GTF data by attribute values_list
<http://sig-workbench.toulouse.inra.fr/galaxy/tool_runner?tool_id=gtf_filt...>)
, I have this message :
Traceback (most recent call last):
File "/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/filters/gff/gff_filter_by_attribute.py", line 55, in <module>
attribute_types = from_json_string( sys.argv[4] )
File "/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/__init__.py", line 384, in loads
File "/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py", line 402, in decode
File "/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py", line 420, in raw_decode
simplejson.decoder.JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0)
Could you please help me ?
Thanks in advance,
Sarah Maman
9 years, 6 months
Jobs waiting in job queue
by Edward Hills
Hi Galaxy team,
This is going to be a very unhelpful message but I hope you have some
ideas to point me in the right direction!
For some reason our local Galaxy instance (set up with the production
server guide on the wiki minus all the fancy cluster stuff) is
refusing to run jobs except after a restart.
So we wish to execute our particular tool, it shows up in the history
as grey and will remain that way.
I have investigated all the logs and there are no error messages and
for some reason the handler is not receiving the message to execute
the tool.
Once we reset Galaxy as soon as it has gone through its initial
start-up process it executes our tool we wanted it to with no
problems.
We are operating with the latest version of galaxy-dist as of 30/07/12.
I have investigated the web and manager logs as well as my apache logs
just in case and have come up short.
Any tips or ideas would be much appreciated!
Cheers,
Ed
Department of Biochemistry,
University of Otago,
Dunedin,
New Zealand.
9 years, 6 months
Make a tool visible/available only to certain users ?
by Greg Edwards
Hi,
I'd like to make a tool or tool category visible only to certain users on a
Galaxy installation. I've trawled the Galaxy Wiki/Searches a fair bit for
this but didn't see it, hope it's not obvious.
Context is: a Galaxy Cloudman installation running on AWS, with a category
of extra custom tools added to the standard menu. One of them is the latest
"development" version of a tool which should ideally be only visible and
runnable for the developer.
I've got a temporary solution where the development version checks the
Galaxy login id, eg. fred(a)someplace.com and exits with an error if fred is
not one of the privileged id's. I'm trusting that the standard security in
Galaxy will be enough to prevent any determined workaround to make it run
(and indeed view the code).
However it would be better if non-privilged users couldn't even see the
tool. Any way to do that ?
Thanks,
Greg E
--
Greg Edwards,
Port Jackson Bioinformatics
gedwards2(a)gmail.com
9 years, 6 months
