[galaxy-dev] Share history (or change history ownership) through the Galaxy API?
Hello, Is it possible to share a history with a user (by user name) or change ownership through the Galaxy API? I didn't see any example doing this. Thanks. Cheers, Daniel -- Daniel Sobral, Bioinformatics Unit Instituto Gulbenkian de Ciência ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Share history (or change history ownership) through the Galaxy API?
Thanks Martin, I saw that you can upload a file directly to a history using the API through the upload tool, but then it has limitations in terms of file size, no? Would it be useable with large files? Thanks, Daniel On 01/15/2014 07:05 PM, Martin Čech wrote: Hi Daniel, I am sorry but Galaxy API doesn't support sharing of histories yet. For further notice these two parts of the API documentation are the most relevant for the histories API: https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.histories https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.history_contents Martin, Galaxy Team On Wed, Jan 15, 2014 at 1:36 PM, Daniel Sobral dsob...@igc.gulbenkian.pt mailto:dsob...@igc.gulbenkian.pt wrote: Hello, Is it possible to share a history with a user (by user name) or change ownership through the Galaxy API? I didn't see any example doing this. Thanks. Cheers, Daniel -- Daniel Sobral, Bioinformatics Unit Instituto Gulbenkian de Ciência ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Daniel Sobral, Bioinformatics Unit Instituto Gulbenkian de Ciência ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Uploading gzipped fastq files through the API
Just an update: when I set it to copy, it works fine as expected. So I guess the only alternatives alternatives I have are: - link the file, but as unzipped fastq - copy the file (which copies the unzipped data to galaxy) Would be nice to have a way of working with gzipped fastq files, since most tools now work with them routinely. I'm probably missing something here? Thanks, Daniel On 12/30/2013 10:18 PM, dsob...@igc.gulbenkian.pt wrote: Hello, I have been using the galaxy API to upload files into a library (using a local folder for library import) and running a workflow into a history. I have been following the example scripts that come with galaxy. When I upload a gzipped fastq file, in autodetection mode (linking the file and not copying, to be faster), the file is not detected as fastq. Even if I explicitly say that it is a fastq, the file is uploaded as a fastq but with its contents gzipped (so downstream analysis fail). Nonetheless, if I do this manually through the interface, the file is unzipped correctly. Any idea how can I upload the gzipped fastq through the API so that it can be used properly? Thank you. = Daniel Sobral Next Generation Sequencing Data Analyst IGC - Instituto Gulbenkian de Ciencias e-mail dsob...@igc.gulbenkian.pt = -- Daniel Sobral, Bioinformatics Unit Instituto Gulbenkian de Ciência ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Restrict tool usage by certain users
Hello, At the moment I don't think there is a way to restrict usage of specific tool(s) to specific user(s). Is anyone thinking on developing this kind of functionality? I guess it might be a bit complicated to implement? I guess an easier alternative is to have different galaxy instances running, each one with a different tool set? Thanks, Daniel ___ 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] Fixed Thread number in certain tools
Hello, For certain tools, like bwa or blast, there is a non-configurable number of threads to use inside the tool xml. This is inconvenient for certain cluster configurations, where what we want is division of a job into multiple jobs (I guess this is what is intended by the parallel tag), and not creation of threads that may wreak havoc in a cluster. Is there any reason why bwa and blast have --num-threads=8 pre-configured in the xml file? Thanks, Daniel ___ 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] Hard-links and sshfs
Hello, My instance of galaxy is running on an sshfs mount. The problem comes when I set the new_file_path in the universe_wsgi.ini to be a folder within that sshfs. When I upload something, the hard link in the mkstemp_ln function fails because of apparent limitations of sshfs with hard links. It works if I replace that hard link by a file copy, but I would appreciate an alternative that would avoid me messing around the internals of the code. Thanks, Daniel ___ 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] Local Toolshed misbehaviours?
Hello, I've installed a local toolshed server in http://myserver/toolshed/ (served by Apache) I am able to run it and create a repository with a tool. In my local galaxy server (http://myserver/galaxy/) I am able to see the repositories in that toolshed server, but when I try to install the tool, it gives me: abort: HTTP Error 404: Not Found . I can install tools from the main galaxy toolshed without problems. I've also uploaded a test tool to the test toolshed server http://testtoolshed.g2.bx.psu.edu and I could install the tools in my galaxy server. Any ideas of what I may be doing wrong here with my toolshed server? From the galaxy Toolshed wiki I cannot see anything to give me a clue about what's going on... Thanks, Daniel ___ 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] Local Toolshed misbehaviours?
Hi Greg, The paster log from the toolshed server does not tells me much: 172.22.50.249 - - [16/Mar/2012:12:27:31 +0100] GET /toolshed/repository/preview_tools_in_changeset?repository_id=2bccd98f7ba1e82achangeset_revision=a42c4c034c26webapp=galaxy HTTP/1.1 200 - http://myserver/toolshed//repository/browse_valid_repositories?galaxy_url=http://myserver/galaxy/webapp=galaxy; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2 172.22.50.249 - - [16/Mar/2012:12:27:44 +0100] GET /toolshed/repository/install_repository_revision?repository_id=2bccd98f7ba1e82achangeset_revision=a42c4c034c26webapp=galaxy HTTP/1.1 302 - http://myserver/toolshed/repository/preview_tools_in_changeset?repository_id=2bccd98f7ba1e82achangeset_revision=a42c4c034c26webapp=galaxy; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2 But the galaxy paster indicates a failure: 172.22.50.249 - - [16/Mar/2012:12:28:03 +0100] GET /galaxy/admin_toolshed/browse_repositories?status=errormessage=abort%3A+HTTP+Error+404%3A+Not+Found%0A%3Cbr%2F%3E HTTP/1.1 200 - http://myserver/galaxy/admin_toolshed/install_repository?tool_shed_url=http://myserver/toolshed/repo_info_dict=f16fe1e576e5fb5fdc3c94b320b0d6447be8ac7d:7b2267656e657269635f7574696c73223a205b2247656e65726963205574696c73222c2022687474703a2f2f64736f6272616c406d6e656d6f73796e652f7265706f732f64736f6272616c2f67656e657269635f7574696c73222c2022613432633463303334633236225d7dincludes_tools=True; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2 Nothing that helps me much. I have has some problems with permissions in the tmp dir, but I reconfigured it and it still does not work. Daniel On 03/16/2012 11:04 AM, Greg Von Kuster wrote: Hi Daniel, What does your tool shed paster log say when you get the 404 error trying to install? You can see the paster log by running the following from your Galaxy installation directory when your tool shed is running. tail -f community_webapp.log Greg Von Kuster On Mar 16, 2012, at 4:34 AM, Daniel Sobral wrote: Hello, I've installed a local toolshed server in http://myserver/toolshed/ (served by Apache) I am able to run it and create a repository with a tool. In my local galaxy server (http://myserver/galaxy/) I am able to see the repositories in that toolshed server, but when I try to install the tool, it gives me: abort: HTTP Error 404: Not Found . I can install tools from the main galaxy toolshed without problems. I've also uploaded a test tool to the test toolshed server http://testtoolshed.g2.bx.psu.edu and I could install the tools in my galaxy server. Any ideas of what I may be doing wrong here with my toolshed server? From the galaxy Toolshed wiki I cannot see anything to give me a clue about what's going on... Thanks, Daniel ___ 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/
Re: [galaxy-dev] Variable number of inputs in Workflow (or optional inputs)
Hi Jennifer, Thanks for the reply. However, my question was not about building tools. My question was about building a workflow (using the workflow editor with existing tools), as a user of galaxy. Using the workflow editor, when I create a workflow using a tool that allows a variable number of inputs, it seems that I have to define the number of inputs during workflow creation and not when I run the workflow. I was just asking if it would be feasible to have a variable number of inputs (only defined when a running instance of a workflow is created). It feels to me that the answer is no. Thanks again, Daniel On Mon 05 Mar 2012 05:56:16 PM WET, Jennifer Jackson wrote: Hello Daniel, Examining existing tools that have multiple/optional inputs can be a good way to see how this is done. One example is the tool: NGS: QC and manipulation - Manipulate FASTQ. The 'Manipulate FASTQ' tool source is here: http://bitbucket.org/galaxy/galaxy-central/src/e58a87c91bc4/tools/fastq/ fastq_manipulation.py fastq_manipulation.xml The tool tag set is defined in this wiki; http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax See repeat, conditional, and when for more details and examples. Questions about tools are best sent to the galaxy-...@bx.psu.edu mailing list (the galaxy-user list is primarily for questions about data/tools usages on the main public instance). I am going to forward your question over there so that the development community can add to my reply in case they have a simpler way of doing this or other advice. Best, Jen Galaxy team On 3/5/12 7:32 AM, Daniel Sobral wrote: Hi, I wanted to build a workflow where the first step would be a tool that can have a variable number of inputs (e.g. a series). It seems that I need to predefine apriori the number of inputs to give to the tool. Is there a way to define the number of inputs at runtime? E.g. a series-like input? Thanks, Daniel ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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] Running galaxy in a cluster as if it was local
Hi, We're trying to setup a galaxy server, but where we want some of the tools to run on a cluster. This cluster is supporting mosix so at the moment we cannot use any of the drmaa stuff available (or can we?). The way we're setting it up at the moment is to run the command we want to run on the cluster through a remote mosix run. This works (almost) fine if we do it for specific command line tools (e.g. samtools). But now I've tried to run the whole python wrapper instead of only the command-line tool. In this case the problem we have is that the libraries on the end of the compute node are not set in the environment, since the environment is set only on the machine running the frontend. Is there any way I can set up the PYTHONPATH or other environment variables so that this would work in the compute node? Thanks, Daniel ___ 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] Tool that outputs html report
Hello, I want to develop a galaxy wrapper for a tool that outputs an html report (with images inside specific subfolders). Do I need to do like the FastQC galaxy wrapper that reconstructs the html so that they are all in the same folder? Or is there a way to circumvent this so that I can keep the original html structure? One way of cheating is maybe zipping the output and provide the zip file as data? Thanks, Daniel Sobral ___ 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/
