- galaxy-dev - lists.galaxyproject.org

PBS Server Throwing Errors
by Daniel Patrick Sullivan 01 Aug '12

01 Aug '12

Hi, Galaxy Community, Greetings from The University of Chicago; I hope all who attended the Galaxy conference enjoyed it as much as I did. I have searched the mailing list archives as well as Google to a resolve problem I am seeing, however I am somewhat at a loss as to the next course of action I should be taking to bring this issue to a close. I am hoping that one of the bright minds on this mailing list could help me shed some light on the solution to my problem, or at least help me identify a root cause. I have configured Galaxy to integrate with TORQUE (version 4.0.2) server, and successfully built the PBS python egg as specified in the Galaxy documentation. I am using Python version 2.6 and the latest build of Galaxy. Whenever I launch a job from the Galaxy UI, I get the following error message(s) on the PBS server: 07/30/2012 15:42:48;0080;PBS_Server;Req;dis_request_read;conflicting version numbers, 1 detected, 2 expected 07/30/2012 15:42:48;0080;PBS_Server;Req;req_reject;Reject reply code=15058(Bad DIS based Request Protocol MSG=cannot decode message), aux=0, type=AlternateUserAuthentication, from galaxy@ 07/30/2012 15:42:48;0080;PBS_Server;Req;dis_request_read;conflicting version numbers, 1 detected, 2 expected 07/30/2012 15:42:48;0080;PBS_Server;Req;req_reject;Reject reply code=15058(Bad DIS based Request Protocol MSG=cannot decode message), aux=0, type=QueueJob, from galaxy@ 07/30/2012 15:42:48;0080;PBS_Server;Req;dis_request_read;conflicting version numbers, 1 detected, 2 expected 07/30/2012 15:42:48;0080;PBS_Server;Req;req_reject;Reject reply code=15058(Bad DIS based Request Protocol MSG=cannot decode message), aux=0, type=Disconnect, from galaxy@ 07/30/2012 15:43:01;0002;PBS_Server;Svr;PBS_Server;Torque Server Version = 4.0.2, loglevel = 1 One thing I did notice, that suggests there might be a problem, is that there is no hostname after the galaxy@; most of the other messages in this log file have a host name appended to log entry, i.e.: 07/30/2012 15:43:38;0100;PBS_Server;Req;;Type StatusJob request received from root@sc01, sock=10 I have completed a tcpdump on the schedule node, and I can definitely see bi-directional traffic between the Galaxy server and the scheduler node on TCP port 15001. In addition to this, I have installed the TORQUE client tools on on the Galaxy server, and can spawn an interactive job with qsub -I, as well as check the status of queued jobs using qstat (from the Galaxy server). This suggests to me that there a potential problem with the PBS Egg, although I am not certain. Has anybody seen something like this before, or could somebody point me in the right direction? We do have a support contract with Adaptive Computing, and I am opening a ticket with them as well, however I wanted to reach out to the Galaxy community to cover all of my bases. Thank-you so much for taking the time to read my email. Dan Sullivan

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Local instance and storage space to provide
by Sarah Maman 01 Aug '12

01 Aug '12

Dear all, To purchase equipment related to a local instance of Galaxy, I would like to have your feedback. Did you notice load problems when 10 to 20 users launch jobs at the same time and on a single instance of Galaxy, with mi-RNA or RNA seq data ? What do you recommend in terms of storage space, number of nodes, number of instances? Thank you in advance, Sarah Maman

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Update Galaxy instance with Mercurial error
by Makis Ladoukakis 01 Aug '12

01 Aug '12

Dear Galaxy users, I am running a Galaxy instance in my institution's server and I want to keep it up to date with the latest release. Nevertheless when i try hg incoming i get the following error: abort: There is no Mercurial repository here (.hg not found)! Most probably the administrator of the server has downloaded the Galaxy-dist directory without the use of Mercurial (I was suspicious of that all along as the directory of the Galaxy installation is named galaxy_dist and not galaxy-dist). Is there another way to update my instance? Thank you, Makis Ladoukakis

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Error in loading tools.
by Mohammad Heydarian 01 Aug '12

01 Aug '12

Hi Galaxy Community! Hope all is well. I've been trying to install some tools in my Galaxy Cloudman instance (using image: ami-da58aab3 ) from the main toolshed. When I try to "install to local Galaxy" I get the error: Not Found The resource could not be found. No action for /admin_toolshed/prepare_for_install I have tried to load tools on a couple of different Cloudman instances and tried to load a variety of tools and end up with the same error. Any help would be fantastic. Cheers, Mo Heydarian

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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 31 Jul '12

31 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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