Re: [galaxy-dev] regarding tool dependencies
Hello Nir, the tool publishing process looks like this: tools for Galaxy are contributed by developers like you to the Tool Shed https://toolshed.g2.bx.psu.edu/ which serves as an 'appstore' for Galaxies worldwide. Any Galaxy administrator can then instal the tool. Some tools have dependencies, yours seem to depend on R. The recommended way to have Galaxy installed these dependencies for you is to use Conda (list of some available R packages here: https://anaconda.org/r/repo?type=conda). To learn more about Conda please visit https://docs.galaxyproject.org/en/master/admin/conda_faq.html Alternatively, when you do not care about sharing your tool, and you do not need to track reproducibility you can add any tool to Galaxy locally (add the .xml wrapper and point tool_conf.xml at it and restart Galaxy). When the tool is executed and no dependencies are found Galaxy will look for its executable and if it is on the $PATH it will just use it. Please let us know if you have more questions. Thanks for using Galaxy, Martin On Thu, Feb 9, 2017 at 11:01 AM Nir Shachaf wrote: > Dear Galaxy-dev team, > > As a research scientist in the dept. of Plant Sciences I would like to > contribute a tool to the 'Metabolomics' tool-box under Galaxy. The tool is > principally written in R, with some dependencies (namely: R>=3.x, and > several R packages). Following the documentation in: > > https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies > > https://wiki.galaxyproject.org/Admin/Config/ToolDependencies > > I admit I get confused by the numerous possibilities offered by the > framework. My main concern is to be able to link the Galaxy server to tools > already installed on my development environment, and NOT to depend on the > tools available in the tool-shed repository (as many are not there, and > there are specific versions requirements). > > Could you kindly direct me to the relevant solution, or a user's-list > post, if applicable? > > Many thanks in advance, > Nir Shachaf, > Plant Sciences Dept., > Weizmann Inst. of Science, > Rehovot, Israel. > ___ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] regarding tool dependencies
Dear Galaxy-dev team, As a research scientist in the dept. of Plant Sciences I would like to contribute a tool to the 'Metabolomics' tool-box under Galaxy. The tool is principally written in R, with some dependencies (namely: R>=3.x, and several R packages). Following the documentation in: https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies https://wiki.galaxyproject.org/Admin/Config/ToolDependencies I admit I get confused by the numerous possibilities offered by the framework. My main concern is to be able to link the Galaxy server to tools already installed on my development environment, and NOT to depend on the tools available in the tool-shed repository (as many are not there, and there are specific versions requirements). Could you kindly direct me to the relevant solution, or a user's-list post, if applicable? Many thanks in advance, Nir Shachaf, Plant Sciences Dept., Weizmann Inst. of Science, Rehovot, Israel. ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Newline characters for txt files
I have observed that when I upload a file with CRLF line endings into Galaxy and then later download it, the endings have changed to UNIX (LF only). I also observed that an uploaded file containing CR only line endings in Galaxy downloads to a file again with LF only line endings. These file types are txt. Just want to confirm - does Galaxy scrub line endings? - Cris ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Configuring Galaxy, Pulsar and Conda
Hi John, thank you for your help. Now it works! Il 07/02/2017 21:20, John Chilton ha scritto: Hello, Thanks for working on this - Pulsar still hasn't quite caught up with Galaxy in terms of support for Conda but we are getting there. So I noticed two things that should help today when I was trying to recreate your problem - the first is that Conda support in Pulsar requires this PR (https://github.com/galaxyproject/pulsar/pull/126) which isn't part of 0.7.3 - the pulsar you are targeting. I did an update of Pulsar though so that should help - release 0.7.4 should be available as of today. Additionally, I noticed that the default for the Pulsar client option "dependency_resolution" in Galaxy was broken. So to get this to work at all - you will need to update your job_conf.xml and specify that Pulsar should resolve dependencies and not Galaxy. This means adding remote to your Pulsar destination. I opened a Pull Request here for the Galaxy change - so hopefully this will be the default by the time 17.01 is released. The logs should make it clear if there are additional problems after those changes I think. One think I would recommend is adding a versionless Conda resolver also - so you may want to make that dependency resolvers file look like this instead: This may not be strictly needed based on the tools you are attempting to get this to work for though. Thanks for your patience and let me know how it goes. -John On Fri, Feb 3, 2017 at 6:18 AM, ric wrote: Hi, I'm tryng to configure a Pulsar server to resolve dependencies using Conda but unfortunately it does not work. When I try to execute, for example, bowtie2, the standard error in the Galaxy machine says: "/home/galaxy/pulsar/files/staging/67/command.sh: line 60: bowtie2-build: command not found" because Conda in the Pulsar machine does not download this dependency. Here is my app.yml: dependency_resolvers_config_file: dependency_resolvers_conf.xml My dependency_resolvers_conf.xml The log of the Galaxy server: galaxy.tools DEBUG 2017-01-19 14:50:18,910 Validated and populated state for tool request (97.265 ms) galaxy.tools.actions INFO 2017-01-19 14:50:19,069 Handled output named output for tool toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.0 (81.926 ms) galaxy.tools.actions INFO 2017-01-19 14:50:19,113 Added output datasets to history (43.950 ms) galaxy.tools.actions INFO 2017-01-19 14:50:19,179 Verified access to datasets for Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.0] (33.690 ms) galaxy.tools.actions INFO 2017-01-19 14:50:19,180 Setup for job Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.0] complete, ready to flush (66.261 ms) galaxy.tools.actions INFO 2017-01-19 14:50:19,240 Flushed transaction for job Job[id=67,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.0] (59.840 ms) galaxy.tools.execute DEBUG 2017-01-19 14:50:19,240 Tool [toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.0] created job [67] (296.972 ms) galaxy.tools.execute DEBUG 2017-01-19 14:50:19,266 Executed 1 job(s) for tool toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.0 request: (355.402 ms) 156.148.160.117 - - [19/Jan/2017:14:50:18 +0200] "POST /api/tools HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 Safari/537.36" 156.148.160.117 - - [19/Jan/2017:14:50:19 +0200] "GET /api/webhooks/tool HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 Safari/537.36" 156.148.160.117 - - [19/Jan/2017:14:50:19 +0200] "GET /api/histories/1cd8e2f6b131e891/contents?details=b847e822bdc195d0%2C40876639881ca029%2C915ae9a80309f157%2Cfd767e8b7355e21a%2C9ce617df390851fc%2C3cc0effd29705aa3%2Cb701da857886499b&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2017-01-19T12%3A11%3A40.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://156.148.120.96:8080/"; "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 Safari/537.36" galaxy.jobs DEBUG 2017-01-19 14:50:19,912 (67) Working directory for job is: /home/galaxy/galaxy_test_pulsar/database/jobs_directory/000/67 galaxy.jobs.handler DEBUG 2017-01-19 14:50:19,931 (67) Dispatching to pulsar runner galaxy.jobs DEBUG 2017-01-19 14:50:20,013 (67) Persisting job destination (destination id: remote_cluster) galaxy.jobs.runners DEBUG 2017-01-19 14:50:20,044 Job [67] queued (112.446 ms) galaxy.jobs.handler INFO 2017-01-19 14:50:20,090 (67) Job dispatched galaxy.jobs.runners.pulsar INFO 2017-01-19 14:50:20,205 pulsar_version is 0.7.3 galaxy.util.object_wrapper WARNING 2017-01-19 14:50:20,644 Unable to create dynamic subclass for , None: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases galaxy.tools.deps DEBUG 2017-01-19 14:50:20,8
Re: [galaxy-dev] Create a new datatype svg
Hmm. I wonder if a composite datatype would work here? https://wiki.galaxyproject.org/Admin/Datatypes/Composite%20Datatypes Peter On Thu, Feb 9, 2017 at 9:25 AM, Jochen Bick wrote: > Hi Dan, > > I understand the option with this specific flag. What I mean is that for > example the file format bam has two file in one save button. So if you > click on save you can either save the bam file or the bai file. I would > liek to have the same feature with my png and svg. So that I have just > one item in the history showing the png and if you click on save you > have the option to also save svg. > > Cheers Jochen > ___ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Create a new datatype svg
Hi Dan, I understand the option with this specific flag. What I mean is that for example the file format bam has two file in one save button. So if you click on save you can either save the bam file or the bai file. I would liek to have the same feature with my png and svg. So that I have just one item in the history showing the png and if you click on save you have the option to also save svg. Cheers Jochen ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/