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

Question about long term goal of Tool Shed usage
by Joel Rosenberg 09 Oct '12

09 Oct '12

Hello, I've been learning about the tool shed, as precipitated by the decision to move the blast tool out of the standard distribution. (I'm having a problem doing so as documented here: http://dev.list.galaxyproject.org/Cannot-install-ncbi-blast-plus-or-other-t… , but that's not the point of this email) Is there a goal to move every tool that's currently included in the EC2 tools snapshot to the public tool shed to keep the standard galaxy distribution leaner? If so, I have two questions/concerns: 1) How will this work with the concept of a tool volume snapshot? I'd have to make a snapshot of my partition every time I installed/removed a tool from a tool shed. Would it make sense to re-characterize the tools volume as a persistent volume (a la the user data volume) instead of it being snapshot driven like it is now? Is it currently possible for me to point to a persistent EC2 tools volume and not a snapshot in my persistent S3 information in order to make the cluster stop/start process simpler? 2) Are there plans to provide ranking or popularity ratings to the public tool shed so I know which tools are the most stable, popular, or perhaps used to be included in the standard distribution? Thanks again for your work, apologies for the verbosity, I'm just getting to know galaxy. -Joel

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Re: [galaxy-dev] Access to https://bitbucket.org/galaxy/galaxy-central/issues
by Greg Von Kuster 09 Oct '12

09 Oct '12

Hi Pieter, We've disabled Bitbucket tickets for now, and we're evaluating better ways to track issues and enhancements. We'll soon have a public form of issue tracking again, and issues you've already submitted should be available there. I'm not sure what the timeline on this is, but we'll communicate information to the community when things are worked out. Thanks, Greg Von Kuster On Oct 9, 2012, at 8:01 AM, Lukasse, Pieter wrote: > Hi Greg, > > I noticed I don’t have access to https://bitbucket.org/galaxy/galaxy-central/issues anymore. I logged some cases there before and I would like to access them. Is that possible? Who can give me access again (at least to the issues logged by me)? > > Regards, > > Pieter. >

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Re: [galaxy-dev] Bismark Wrapper
by Jeremy Goecks 09 Oct '12

09 Oct '12

Bjorn, Please direct all Galaxy development questions to the -dev list (cc'd); this ensures that they get answered quickly and by the right people. > i will put it in the toolshed. I had a few additional questions in the > Issue-Tracker, but unfortunately i can't access it. Is that intentional? Yes, we've disabled Bitbucket tickets for now. We've evaluating better ways to track issues/enhancements, and, one way or another, we'll soon have a public form of issue/enhancement tracking again. > In the pull request was one commit, that includes the > index-infrastructure for bismark indices. Is that also possible with the > toolshed currently? I think so, but I'll let Greg provide the definitive answer. > Bismark is a single perl script, its ok to ship that script with the > wrapper and do not fetch it via tool_dependencies.xml or? Greg is the best person to answer this question. J.

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list of multithreaded tools
by jean-François Taly 09 Oct '12

09 Oct '12

Dear All, Could you please tell where or how I could get the list of multi-threaded tools and the amount of threads they open by default? Thanks a lot Jean-François PS: I have collected the following list by hands: #Tool_id Num_thread gatk_count_covariates 4 gatk_realigner_target_creator 4 gatk_unified_genotyper 4 gatk_variant_eval 4 gatk_variant_recalibrator 4 gatk_variant_select 4 bfast_wrapper 4 bowtie2 4 bowtie_color_wrapper 4 bowtie_wrapper 4 bwa_color_wrapper 4 bwa_wrapper 4 cuffdiff 4 cufflinks 4 cuffmerge 4 tophat2 4 tophat_color 4 tophat 4 -- ##################################### Dr Jean-François Taly Bioinformatician Bioinformatics Core Facility http://biocore.crg.cat CRG - Centre de Regulació Genòmica (Room 439) Parc de Recerca Biomèdica de Barcelona (PRBB) Doctor Aiguader, 88 08003 Barcelona Spain email: jean-francois.taly(a)crg.eu phone: +34 93 316 0202 fax: +34 93 316 0099 #####################################

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Re: [galaxy-dev] Mail galaxy team
by James Taylor 09 Oct '12

09 Oct '12

The Galaxy Web API is documented here: http://wiki.g2.bx.psu.edu/Learn/API -- jt On Tue, Oct 9, 2012 at 6:30 AM, harry humphries <harryhum(a)gmail.com> wrote: > We are trying to develop a plugin for drupal CMS that interacts with the > galaxy api, basically we want to create a control panel for the S3 server > from drupal backend. But we are having trouble finding documentation > related to the galaxy web api. Can you please point us in the right > direction?

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Upload to history via the tool API
by Brad Chapman 08 Oct '12

08 Oct '12

Hi all; I've been thinking about ways to upload into user histories via the API. My goal is to be able to have an analysis platform that works alongside Galaxy and can easily pass files back and forth through the history. The tools API turned out to be a great fit for this, since you can remotely call the upload tool with a URL and stream the file in. I was able to get it working with a couple of small tweaks to the existing code. The pull request to galaxy-central is here: https://bitbucket.org/galaxy/galaxy-central/pull-request/74/tools-api-fixes… Using a Clojure wrapper on top of John's blend4j library, I have a small proof of concept with upload/download from Galaxy histories: https://github.com/chapmanb/clj-blend#usage Dannon, or anyone else who likes to hack on the API, let me know if there is anything I can do to help get these small fixes merged in for the next release. I'd love to be able to demo this with Galaxy main. The API rocks, Brad

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[Patch] Adding interpreter-attribute to the version_command-tag
by Björn Grüning 08 Oct '12

08 Oct '12

Hi all, if we try to wrap a single script-tool, for example bismark [1], it has its own version number and should be included in <version_command>. I would like to ship bismark with the wrapper. That means that bismark is not included in PATH, but exists next to the bismark_wrapper.xml file. That isn't a problem for the <command> tag, but for the <version_command> tag, because it assumes the executed tool in PATH. Attached is a patch that adds the same <command> logic to <version_command> if a interpreter is specified. Regards, Björn [1] http://www.bioinformatics.babraham.ac.uk/projects/bismark/

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L. pneumophila in NGS reference genomes [Main]
by Romain Brunel 08 Oct '12

08 Oct '12

Hello everyone, We are working with Next Generation Sequencing tools on Legionella pneumophila. When trying to use NGS Tools such as Bowtie or BWA on the Main instance of Galaxy, L. pneumophila genomes are not available, although they are listed in the Data Libraries, at http://wiki.g2.bx.psu.edu/Main/Data%20Libraries/Microbes/A-J . Would it be possible to integrate the genome of the Paris strain in order to use it with NGS tools in Main ? NCBI Reference Sequences are : NC_006368.1 (chromosome) and NC_006365.1 (plasmid). Thank you in advance, Romain Brunel

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migrated BWA installed but missing dependencies
by Derrick Lin 08 Oct '12

08 Oct '12

Hi guys, I have updated the galaxy to Oct 5 dist, and BWA has been reinstalled via the migration script. However, I couldn't find any entry has been added in migrated_tools_conf.xml (thus the BWA tools are not display in the tool panel). I check in the admin "Installed tool shed repositories" section and BWA repos status is "Installed, missing dependencies", is that why it didn't get added into the migrated_tools_conf.xml? I have had BWA 0.5.9-r16 in path, and been used by the old BWA wrapper without an issue before. How can I fix this dependencies issue for a Shed Tool? Should I add something like: <tool_dependency_dir>/bowtie/0.12.7/env.sh thanks, Derrick

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Re: [galaxy-dev] [galaxy-user] Cannot install ncbi_blast_plus or other tools from Tool Shed: HTTP 500 error
by Peter Cock 08 Oct '12

08 Oct '12

On Mon, Oct 8, 2012 at 8:26 AM, Joel Rosenberg <thisisjoel(a)hotmail.com> wrote: > So I'm trying to install the recently migrated ncbi_blast_plus tool from the Tool Shed to my local galaxy instance running in EC2 and am getting errors at the installation step. > > After clicking "Install to local Galaxy" I immediately get: "Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)" and an HTTP 500 error code is returned. Chrome tells me the URL it's attempting to request is: > > http://toolshed.g2.bx.psu.edu/repository/install_repositories_by_revision?c… > Trying that URL in Firefox also gives the "Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)" message. It looks like a problem in the public ToolShed. Peter P.S. Problems with local Galaxy installs are normally discussed on the galaxy-dev list (CC'd) rather than galaxy-user list.

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