How Do I Add Ray To Galaxy Central In The Tool Shed ?

Question: How Do I Add Ray To Galaxy Central In The Tool Shed ?

5.5 years ago by

Hello, I want to add Ray (a scalable de novo assembler for genomes and metagenomes) to Galaxy. Ray is GPLv3 [1]. I have read http://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial and I understand that I have to write a Tool Definition File in XML. I also visited the source code here: https://bitbucket.org/galaxy/galaxy-central/src/5de636ce68faededc52d7b 0c16167fbef98be786/tools/sr_assembly?at=default I will also have to write a wrapper for Ray to prepare the command line from the options provided by the Galaxy API. But where is stored the executable (in my case, where is sdtored Ray) ? Does Galaxy include the specs to build all the tools available in Galaxy-Central ? [1] http://denovoassembler.sourceforge.net/

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modified 5.5 years ago by James Taylor ♦ 470 • written 5.5 years ago by Sébastien Boisvert • 40

5.5 years ago by

James Taylor ♦ 470

United States

James Taylor ♦ 470 wrote:

And I really want you to do this! No, we are gradually moving all the tools out of galaxy-central into the Tool Shed. You probably want to look at this page: http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-p arty_tool_dependency_installation_and_compilation_with_installed_repos itories Which describes how you can add a recipe to the toolshed that will install the Ray binaries.

ADD COMMENT • link written 5.5 years ago by James Taylor ♦ 470

So we are at least two ! So Ray needs a C++ 1998 compiler and a MPI library (let's say g++ and openmpi-bin). Are those already installed in Galaxy deployments ? Also, when is tool_dependencies.xml processed (I assume it is procesed when re-loading the content of the shed into Galaxy ? Thanks !

ADD REPLY • link written 5.5 years ago by Sébastien Boisvert • 40

Am Donnerstag, den 06.06.2013, 14:42 -0400 schrieb SĂŠbastien Boisvert: Joining the party! Make three out of it! You can assume that gcc is installed. Nevertheless, openmpi-bin needs to be installed. I would suggest to create a orphan-tool-dependency for openmpi-bin. For example have a look at: http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_boost_1_53 And than make that orphan-tool-dep a requirement of your repository. I don't understand the question, but if you install Ray the tool_dependency file is read and at that time it will be installed and the openmpi dependency. Cheers, BjĂśrn

ADD REPLY • link written 5.5 years ago by Björn Grüning • 350

On some platforms (like DNANexus), when you launch an app, it launches an instance from an image (let's say Debian). Then, the system install the software (let's say MUMmer) on the instance, fetch the data (from S3 or Azure or something else), launch the software (let's say MUMmer). When the software completes, the results are pushed by to cloud storage, and the instance is killed. So in this kind of platform, the installation occurs independently for each job you launch. I don't know if Galaxy works like that -- that was my question (I am reading the 3 important Galaxy papers today !). So the question becomes "When Ray get installed ?" Answers may include: A) Ray is installed once by a sysadmin. B) Ray is installed automatically by Galaxy when it starts if Ray is not already installed. C) Ray is installed each time someone uses it because an instance is spawned. D) Ray is not installed because it ships with the operating system, just like ls, pwd and so on. E) the Galaxy user needs to upload a static Ray executable just like he/she uploads their data. -Sébastien.

ADD REPLY • link written 5.5 years ago by Sébastien Boisvert • 40

Am Donnerstag, den 06.06.2013, 15:19 -0400 schrieb Sébastien Boisvert: I think that is the best answer. Replace sysadmin with galaxy-admin. Because Ray will be installed by him. If you have different Ray versions that will be handled by the toolshed to enable reproducibility. Possible, but you loose reproducibility, but maybe a good starting point to write the wrapper, the installation instruction can be hooked up later.

ADD REPLY • link written 5.5 years ago by Björn Grüning • 350

From what I understand, I need to write 2 XML files in order to allow people to add Ray to their Galaxy instances: * ray.xml * tool_dependencies.xml These two files are self-contained -- that is Galaxy will install everything using tool_dependencies.xml (in my case, Open-MPI and Ray will be installed from source using the GNU compiler). Can I put these files directly in galaxy-dist/tools/sr_assembly/ray/ ? I suppose these 2 XML files will be distributed in galaxy-dist, but like Velvet, Ray won't be enabled by default in tool_conf.xml as assembly is more costly than mapping. Then, I need to add this to galaxy-dist/tool_conf.xml: <section name="NGS: Assembly" id="ngs_assembly"> <label text="Ray" id="ray"/> <tool file="sr_assembly/ray/ray.xml"/> </section> And finally, I just need to restart Galaxy. Is that correct ?

ADD REPLY • link written 5.5 years ago by Sébastien Boisvert • 40

Hi Sébastien, This all looks fine, except for the part about including this in the distribution. As James stated, we are moving to a model where eventually all tools will be sourced from the Tool Shed. That is where you should create your repository. Whether or not to have the repo binaries self-install & config or not will be up to you. Going forward, you probably will want to start up a new thread for new questions and have discussions on the galaxy-dev@bx.psu.edu mailing list. This will give your questions the most exposure to the development community. http://wiki.galaxyproject.org/MailingLists#The_lists Take care, Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

ADD REPLY • link written 5.5 years ago by Jennifer Hillman Jackson ♦ 25k

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