[galaxy-dev] Update Galaxy instance with Mercurial error
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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy and Toolshed issues
Hello Shaun, On 7/31/12 09:37:23.000, SHAUN WEBB wrote: Genome indexing: 1. I realise this is just a beta feature and it will be great when fully integrated. I tried to generate bowtie2 indexes for an installed build. I can see the job appear below the table in yellow and it contains the message ...added to the job queue to be indexed with bowtie2. However it seems to just sit there, even after restarting. Should I be able to see the job under 'manage jobs'? No, the indexing jobs are not picked up by that interface. If you click on the job ID under the 'Recent jobs:' heading, you should see a status listing of the indexing job and any sub-jobs it initiated. 2. Where are the generated indexes stored and is the .loc file automatically updated? This can be specified with the genome_data_path option in your universe_wsgi.ini file. Currently, it defaults to tool-data/genome/build/index name/ The .loc files are updated when the job returns from a successful run, if there is no entry for that genome and index already present. --Dave B. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy and Toolshed issues
Hi Shaun, On Jul 31, 2012, at 9:37 AM, SHAUN WEBB wrote: Hi, I have been trying out the latest version of Galaxy and a newly installed local toolshed and I have a few questions/suggestions/bug reports: 1. Tool Versioning: a) As I understand from the wiki, when I create a new version of a tool in a tool shed I must then install the latest version in my Galaxy instance. This is not correct - you can choose to install any valid version of the tool(s). Can you let me know what content of the wiki resulted in this confusion? I'll be sure to make it more clear. This then shows up as two separate tools in my tool menu. Presumably it is best to change the xml description tag to reflect the version number and make tool versions distinguishable in the Galaxy tool menu? b) Would it make more sense to have a single entry for each tool in the tool menu and a drop down to choose which version to run in the tool gui? Similar to when I try to rerun a tool that is no longer installed I get a drop down option to use a derivative of that tool if it exists. Your above recommendation in (b) is exactly what will occur as soon as I get a chance to implement it. c) The toolshed interface allows me to change the name of my tool. If I do this, then go to my Galaxy admin ui and try to get updates for my tool then it fails. Does it make sense to change a tools name after it is created? Is it possible to track previous tool names to avoid this happening? This should not occur. Where are you able to change the name of your tool? You are not even allowed to change the name of the repository if it has been cloned (you can change the name of the repository as long as it has not been cloned). Can you send me a screen shot of hte page that allows you to change the name of your tool in the tool shed? I'll provide a fix as soon as I see where the issue lies. e) Email alerts: I could not find an option to receive email alerts about tool updates when installing via the Galaxy admin ui. Perhaps this should be an option during installation. You can currently set email alerts for specified repositories in the tool shed itself. I will add it to my list to enhance the install process with this feature. Thanks for the request! Running toolshed tools: I have no problems installing tools from toolsheds via Galaxy admin interface, however I can't get these tools to run. They stay Grey forever and look like this in the manage jobs table: 65x...@.xx.ac.uk 0 minutes ago toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools/bedtools_coveragebed_counts/0.1.0 new NoneNoneNone Do I have to set a tool runner or some other option for shed_tools? No special configuration settings are required in your local Galaxy instance to to run tools installed from a tool shed. If they stay in the queued state, there must be an issue in your local Galaxy instance that causes installed tools as well as tools included in the distribution to remain queued. It has nothing to do with the fact they were installed. Migrating tools: I upgraded to the latest dist release of galaxy and when I restarted the server I expected to get a message about migrating freebayes tools. I didn't see this message. Will this be because I restart using --daemon? Is it advisable to therefore restart without --daemon after an upgrade to see if there are any tools to be migrated? It may be best to restart without --daemon after an upgrade. This process works just like the Galaxy database migration process (but you are not forced to perform the tool installs), so you can do whatever you currently do to handle database migrations after you upgrades. Starting with --daemon should still display the exception in your paster log. Do you run multiple front end web servers? If so, the exception will only be thrown from one of them. Shaun Webb Edinburgh University -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Workshop on Extending High-Performance Computing Beyond its Traditional User Communities
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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] .loc files and Reload a tool's configuration
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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Error in loading tools.
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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Error in loading tools.
The problem here is that the public toolshed interface has been updated more recently than the galaxy install on that cloud instance. You should be good to go if you update galaxy (possible through the admin interface at your_ec2_instance/cloud/admin/) to the latest version. -Dannon On Jul 31, 2012, at 12:11 PM, Mohammad Heydarian mheydar...@gmail.com wrote: 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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] August 2012 Galaxy Update
Hello all The August 2012 Galaxy Update is now availablehttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_08at http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_08. Highlights include - GCC2012 GCC2013http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_08#GCC2012_.26_GCC2013: slides are there; video is coming - Other Upcoming Events and Deadlineshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_08#Upcoming_Events_and_Deadlines - Swiss Galaxy Dayhttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_08#Swiss_Galaxy_Day - 29 new papershttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_08#New_Papers - Open Positionshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_08#Who.27s_Hiringat four different institutions - Tool Shed Contributionshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_08#Tool_Shed_Contributions - New Distributionhttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_08#New_Distributions - Other News http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_08#Other_News If you have anything you would like to see in the September *Galaxy Updatehttp://wiki.g2.bx.psu.edu/GalaxyUpdates *, please let me know. Thanks Dave Clements -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] egg distribution error when running galaxy-central
On 1 August 2012 15:28, Clare Sloggett s...@unimelb.edu.au wrote: I can run galaxy-dist without problems and have been working with that (so its eggs are all installed already), but now I want to create a pull request so want to run galaxy-dist. oops, of course I mean 'so want to run galaxy-central.' -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
