July 2012 - galaxy-dev - lists.galaxyproject.org

Upload local files
by Sascha Kastens 01 Aug '12

01 Aug '12

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.

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August 2012 Galaxy Update
by Dave Clements 31 Jul '12

31 Jul '12

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.loc files and Reload a tool's configuration
by Julian Pradinuk 31 Jul '12

31 Jul '12

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

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Workshop on Extending High-Performance Computing Beyond its Traditional User Communities
by James Taylor 31 Jul '12

31 Jul '12

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

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galaxy cloudMan failed
by jiesheng＠bioteam.net 30 Jul '12

30 Jul '12

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

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bcftools
by Hongkyun Kim 30 Jul '12

30 Jul '12

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

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GFF tools
by Sarah Maman 30 Jul '12

30 Jul '12

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_filter…> using simple expressions OR Filter GFF data by feature count <http://sig-workbench.toulouse.inra.fr/galaxy/tool_runner?tool_id=gff_filter…> using simple expressions OR Filter GTF data by attribute values_list <http://sig-workbench.toulouse.inra.fr/galaxy/tool_runner?tool_id=gtf_filter…>) , 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

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Jobs waiting in job queue
by Edward Hills 29 Jul '12

29 Jul '12

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.

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Make a tool visible/available only to certain users ?
by Greg Edwards 27 Jul '12

27 Jul '12

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

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Getting syntax error on Join + environment_setup_file not read
by Pete Schmitt 27 Jul '12

27 Jul '12

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