galaxy-dev August 2012

galaxy-dev@lists.galaxyproject.org

95 participants
171 discussions

Using the tools API
by Clare Sloggett 28 Aug '12

28 Aug '12

Hi guys, The Tools API is currently working for me from galaxy-central, but I'm not sure how to correctly run a tool. Are there any example scripts, as there are for some other parts of the API? Specifically I want to find out what the expected payload fields are when I post to CREATE to run a tool. Some of the fields are clear to me just from the api/tools.py code (e.g. 'tool_id') but others are not (e.g. how the input datasets and parameters are specified). A separate question: How do we specify "Advanced" or conditional-dependent fields for a tool? Some of these fields are necessary to run the tool at all. For instance, on my system, calling http://localhost:8080/api/tools/tophat?key=.... returns { "description": "Find splice junctions using RNA-seq data", "id": "tophat", "inputs": [ { "html": "%3Cselect%20name%3D%22input1%22%3E%0A%3C/select%3E", "label": "RNA-Seq FASTQ file", "name": "input1", "type": "data" }, { "label": "Conditional (refGenomeSource)", "name": "refGenomeSource" }, { "label": "Conditional (singlePaired)", "name": "singlePaired" } ], "name": "Tophat for Illumina", "version": "1.5.0" } This is obviously only some of the inputs you see in the UI. I think that all the Advanced fields are missing, and more importantly, any input which is dependent on a conditional is missing. So the refGenomeSource conditional is there, but the actual reference genome field is not. The type of the reference genome field also presumably depends on which value is supplied for the referenceGenomeSource conditional. Is there currently a way to specify (or see) these missing fields? Thanks, Clare -- 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

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Pull request, and missing step connections
by Clare Sloggett 28 Aug '12

28 Aug '12

Hi guys, I made a very small code change so that the workflows API will display all the steps in a workflow, not just the inputs (these are still displayed separately, as before). I made a pull request even though the change is small, just to learn what I'm doing: https://bitbucket.org/galaxy/galaxy-central/pull-request/68/show-workflow-s… But in doing so I noticed something in the workflows I don't understand. I can't see a connection between workflow "input datasets" and the steps they are inputting to. I doubt this is a bug, I just don't know how it's supposed to work, so I'm not sure if my API change is sufficient. So for instance, if I create a small workflow with steps Input Dataset -> TopHat (accepted_hits bam file) -> Cufflinks and call the API on this workflow, I now see { "id": "f2db41e1fa331b3e", "inputs": { "1": { "label": "Input SE fastq", "value": "" } }, "name": "Tophat + cufflinks", "steps": { "1": { "id": 1, "input_steps": {}, "tool_id": null, "type": "data_input" }, "2": { "id": 2, "input_steps": {}, "tool_id": "tophat", "type": "tool" }, "3": { "id": 3, "input_steps": { "input": { "source_step": 2, "step_output": "accepted_hits" } }, "tool_id": "cufflinks", "type": "tool" } }, "url": "/api/workflows/f2db41e1fa331b3e" } The "inputs" field was there before, the "steps" field is the new bit. So as expected, step 3 lists step 2 as an input. However step 2 does not list step 1 as an input, even though the GUI shows that they are connected and the workflow works. From other testing it seems that "Input Dataset" steps never appear wired up in my API response. I'm just iterating over all input_connections, so apparently steps of type data_input are not in the list of WorkflowStep.input_connections . Is this how it should be? How can I find out which steps an Input Dataset is connected to? Thanks, Clare -- 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

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DataTypes
by Alfredo Guilherme Silva Souza 28 Aug '12

28 Aug '12

Good Afternoon. I need to create a new data type in the galaxy, because I need to import a file in the format. Pdb. Someone already had to create a new kind of data? Can you help? Thank you. -- *Alfredo Guilherme* * *

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problems with labels in the tool box and order of the tools
by Hans-Rudolf Hotz 28 Aug '12

28 Aug '12

HI We have been struggling with this problem since we updated to "changeset:6799:40f1816d6857" (March 12, 2012 release). We never had the time to figure out whether it was a bug or whether we made a mistake. Unfortunately, it now has reached a point where we have a serious problem with our production server. I managed to reproduce the error on a new galaxy-dist clone "changeset:7404:ec29ce8e27a1" (July 20, 2012 release): I modify the top of "tool_conf.xml" in the following way (ie: adding a label): <?xml version="1.0"?> <toolbox> <section name="Get Data" id="getext"> <tool file="data_source/upload.xml"/> <label text="external" id="external_data" /> <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" /> ... and it works, after restart, I get the label (see attachment "ss2.tiff") I add a new tool definition: "load_abi_reads.xml": <?xml version="1.0"?> <toolbox> <section name="Get Data" id="getext"> <tool file="data_source/upload.xml"/> <tool file="hrh/load_abi_reads.xml"/> <label text="external" id="external_data" /> <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" /> ... and it works, after restart, I get the new tool (see attachment "ss3.tiff") Now, I don't like the label anymore <toolbox> <section name="Get Data" id="getext"> <tool file="data_source/upload.xml"/> <tool file="hrh/load_abi_reads.xml"/>  <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" /> but, after restart, the label is still there. Even worse, I add a second tool ("load_novaseq_reads.xml") before the first added tool <?xml version="1.0"?> <toolbox> <section name="Get Data" id="getext"> <tool file="data_source/upload.xml"/> <tool file="hrh/load_novaseq_reads.xml"/> <tool file="hrh/load_abi_reads.xml"/>  <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" /> and after restart, the second tool is put below the first added tool (and the label is also still there, see attachment "ss4.tiff") The display in the web browser corresponds to the file "integrated_tool_panel.xml", eg: <?xml version="1.0"?> <toolbox> <section id="getext" name="Get Data" version=""> <tool id="upload1" /> <tool id="load_abi_reads" /> <tool id="load_novaseq_reads" /> <label id="external_data" text="external" version="" /> <tool id="ucsc_table_direct1" /> <tool id="ucsc_table_direct_test1" /> <tool id="ucsc_table_direct_archaea1" /> What do I need to change, in order to have the same information in the "integrated_tool_panel.xml" file as in the "tool_conf.xml" file with regard to order of the tools and removal of labels? Any help appreciated Thank you very much Regards, Hans -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

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Re-starting Galaxy
by kauerbach＠comcast.net 28 Aug '12

28 Aug '12

Hello, If I were to stop and re-start the Galaxy server with the run.sh script would jobs that are aleady running or are in the queue be lost when the server is re-started? If so, is there another method to use which would not lose the running or queued jobs? Thank you.

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ToolShed enhancement for repository lists
by Peter Cock 28 Aug '12

28 Aug '12

Hi all, This is an idea I mentioned to Dannon (off list during discussion about moving the NCBI BLAST+ wrappers to the Tool Shed), and he seemed positive about it. Currently the left hand pane of the ToolShed (once logged in) looks like this: Search * Search for valid tools * Search for workflows Repositories * Browse by category * Browse my repositories * Browse my invalid tools * Create new repository I would find it useful to add another entry listing those repositories where I have contributor rights. This could be included under the existing "Browse my repositories", but perhaps a separate entry is better - if anyone has a concise description for this (so far I've not come up with a short way of phrasing this). Should I file this as an enhancement issue on BitBucket? Regards, Peter

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potential operate on genomic intervals-intersect bug
by Michael Wilson 28 Aug '12

28 Aug '12

Dear Galaxy, Last night (1AM) and today (10:45AM) I have not been able to return results with the operate on genomic intervals, intersect tool. For example if I upload ChIP-seq peak replicates in .gz format (downloaded directly from ENCODE), no results are returned when they are intersected with each other (or with themselves). If I use the Join tool I indeed am able to join many intervals as would be expected. Not sure if I am doing something wrong this time..... Here is a shared history link to give an example: https://main.g2.bx.psu.edu/u/mdwilson/h/intersect-test Best regards, Mike

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Possible bug in dynamic options
by Mutlu Dogruel 28 Aug '12

28 Aug '12

Hi, I wrote a script for dynamically populating a user form. It works but it's slow. When I checked the Galaxy log, I saw that the method called by my custom tool's xml is being run twice (the same debugging lines appear twice in the log, and that happens consistently). Is there any explanation for this? The script returns a list of strings fetched from a remote server. It's running a bit slow, taking up to 6 seconds, so it would be great if I can half that! For testing purposes, I wrote a dummy method that returns a few characters in a list of tuples. Again, my print statement in the Python script is called twice. Has anyone noticed such behaviour? Could it be related to this Galaxy bug: https://bitbucket.org/galaxy/galaxy-central/issue/491/data_column-parameter… The Galaxy script shown on that page says: "NOTE: This is wasteful since dynamic options and dataset collection happens twice (here and when generating HTML)." Thanks. Best regards, -- Mutlu

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Galaxy wiki is throwing errors during edit commit
by Tomithy Too 27 Aug '12

27 Aug '12

Hi Devs, The galaxy wiki is throwing error whenever I try to commit an edit change to it. I have attached a screenshot for your reference. Cheers Tomithy

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Galaxy-France -- Communauté française de Galaxy (French Galaxy Community)
by Dave Clements 27 Aug '12

27 Aug '12

Bonjour à tous, Avec l'aide et le soutien de l'équipe Galaxy, nous venons de mettre en ligne la liste de diffusion Galaxy France. Cette liste a pour but de partager et communiquer sur nos différentes expériences avec Galaxy au sein de l'hexagone. La langue officielle de cette liste est le français. Vous avez besoin d'aide dans l'utilisation de Galaxy, Vous hébergez un serveur public Galaxy, Vous maintenez une instance locale de Galaxy, Vous venez de déposer un outil sur le toolshed, Vous avez des trucs et astuces pouvant interresser la communauté, Vous organisez des formations avec Galaxy, Rejoignez nous en vous inscrivant à http://lists.bx.psu.edu/listinfo/galaxy-france Les archives de cette liste sont disponibles à http://france.list.galaxyproject.org A très bientôt sur la liste Galaxy France, Les administrateurs: Alban Lermine, Olivier Inizan, Rémi Marenco, Dave Clements & Jennifer Jackson ------------------------------ --------------------- Hi everyone, With the help and the support of the Galaxy team, we just put online the Galaxy French mailing list. The aim of this list is to share and communicate on our different experiences with Galaxy in France. * The main language is French. * Topics include, but are not limited to: You need help in the use of Galaxy, You're hosting a Galaxy public server, You're maintaining a local instance of Galaxy, You just add a new tool on the toolshed, You have some tips that could interested the community, You organize workshops with Galaxy, Join us by subscribing at http://lists.bx.psu.edu/listinfo/galaxy-france The list's archives are also available at http://france.list.galaxyproject.org See you soon on the Galaxy-France list, The administrators: Alban Lermine, Olivier Inizan, Rémi Marenco, Dave Clements & Jennifer Jackson -- <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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galaxy-dev August 2012