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Help with from_dataset param in Galaxy XML
by SAPET, Frederic 20 Feb '18

20 Feb '18

Hello I try to use the from_dataset param. I have a tabular file with two columns : sequence and ids I would like to let users select some sequences, based on the ids. <param name="seq" type="select" size="120" optional="false" multiple="true" label="Choose your sequences"> <options from_dataset="target"> <column name="name" index="1"/> <column name="value" index="0"/> </options> </param> But I would like to be able to access not only the sequences data, but also the ids. In the <command> tag : name=$seq.name : it give me "seq", the name of my parameter value=$seq.value : it gives me "atcgatcga,tagctacgatcg,aatctactacta", that's fine. I would like to print the id of each sequence. Is it possible ? Thank you. Fred --- Frederic Sapet Bioinformatics Research Engineer BIOGEMMA - Upstream Genomics Group Centre de Recherche de Chappes CS 90126 63720 CHAPPES FRANCE Tel : +33 (0)4 73 67 88 54 Fax : +33 (0)4 73 67 88 99 E-mail : frederic.sapet(a)biogemma.com<mailto:frederic.sapet@biogemma.com>

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Re: [galaxy-dev] Looking for a running example of planemo test with options from_data_table
by nsoranzo＠tiscali.it 15 Feb '18

15 Feb '18

Dear Laure,have a look at https://github.com/galaxyproject/tools-devteam/blob/master/tools/bowtie_wra… Cheers,Nicola ------ Messaggio originale------Da: Laure QUINTRICData: gio 15 feb 2018 16:06A: galaxy-dev(a)lists.galaxyproject.org;CC: Patrick Durand;Olivier Inizan;Oggetto:[galaxy-dev] Looking for a running example of planemo test with options from_data_table Dear list, Is there somewhere in the Galaxy any running example of a planemo test embracing a from_data_table option ? We are trying to reproduce the picard example referenced here: https://github.com/jmchilton/picard/commit/4df8974384081ee1bb0f97e1bb8d7f93… We also have a look on several examples on the IUC, unfortunately it seems to work only with values from history. Many thanks, Laure, Patrick and Olivier. ___________________________________________________________ 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/

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Looking for a running example of planemo test with options from_data_table
by Laure QUINTRIC 15 Feb '18

15 Feb '18

Dear list, Is there somewhere in the Galaxy any running example of a planemo test embracing a from_data_table option ? We are trying to reproduce the picard example referenced here: https://github.com/jmchilton/picard/commit/4df8974384081ee1bb0f97e1bb8d7f93… We also have a look on several examples on the IUC, unfortunately it seems to work only with values from history. Many thanks, Laure, Patrick and Olivier.

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Running toolshed on localhost is broken in release_17.09?
by Peter Briggs 15 Feb '18

15 Feb '18

Hello I'm trying to run a toolshed instance on localhost to test some local tool changes - this works okay in release_17.05, but setting one up using release_17.09 appears to be broken out of the box, at least for me. In release_17.09, after configuration connecting to http://127.0.0.1:9009/ brings up a version which isn't usable - the styles are missing and it it's not possible to navigate, register/login etc. Uncommenting lines like # Serving static files (needed if running standalone) static_enabled: True in the config/tool_shed.yml file don't seem to make any difference. I didn't find anything in the Galaxy Github issue list about this, so has anyone else observed this behaviour? For now I've just gone back to release_17.05 for my local toolshed needs. Thanks Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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Planemo unable to create a shed
by Begusch Florian 12 Feb '18

12 Feb '18

To whom this may concern, I have been trying to create a local shed for my virtual planemo appliance (http://planemo.readthedocs.io/en/latest/appliance.html) using the following command inside the tool's directory (the tool resides under /opt/galaxy/galaxy-app/tools/custom/ an can be added by hand): planemo shed_create --shed_key 'API_KEY' --shed_target local Although I generated this key using an administrator account and added it as the machine's master_api_key I am unable to generate a shed. The error message I receive is as follows: Could not update test_tool GET: error 403: '{"err_msg": "Provided API key is not valid.", "err_code": 403001}', 0 attempts left: {"err_msg": "Provided API key is not valid.", "err_code": 403001} I would appreciate any help and look forward to your reply. Best regards, Florian Begusch Florian Begusch Studierender GEB15 Institut eHealth Department für Angewandte Informatik florian.begusch(a)edu.fh-joanneum.at<mailto:Florian.Begusch@edu.fh-joanneum.at> <mailto:Florian.Begusch@edu.fh-joanneum.at> FH JOANNEUM Gesellschaft mbH Rechtsform/Legal form: GmbH Sitz: Graz Firmenbuchgericht/Court of registry: Landesgericht für ZRS Graz Firmenbuchnummer/Company registration: FN 125888 f DVR: 0813559 UID-Nr.: ATU 42361001 http://www.fh-joanneum.at/hochschule/organisation/impressum

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Re: [galaxy-dev] Predict similar tools for Galaxy tools using text mining and machine learning
by Yvan Le Bras 07 Feb '18

07 Feb '18

Hi Anup, Hello everyone, Thanks for sharing this amazing work! Your project make me remember previous ideas we investigate on a workflow oriented way with notably Mouhamadou Ba, copied. Maybe we can try to go further on it if interested.... Furthermore, I am wondering if this work can help to go further on initiated Galaxy tools translation .... https://github.com/manabuishii/galaxy-translation ... probably not relevant.... Wishing you all a very good week-end. Kind regards, Yvan Envoyé depuis mon smartphone Samsung Galaxy. -------- Message d'origine --------De : anup kumar <anup.rulez(a)gmail.com> Date : 03/02/2018 02:57 (GMT+01:00) À : galaxy-dev(a)lists.galaxyproject.org Objet : [galaxy-dev] Predict similar tools for Galaxy tools using text mining and machine learning Hello everyone, Greetings! I am a contributor to the Galaxy project and currently working on finding similarities in Galaxy tools (a part of my master's thesis). This work aims at finding similar tools for any Galaxy tool based on tools description and their input/output file types. For example, the similar tools for a tool "bowtie2" could be "bwa", "bwameth" or "bwa_mem" among others. To see the results of this project online, please visit the link (works fine on Firefox and Chrome). You should wait for a few seconds before you see a list of tools in the select list as the page loads a big JSON file (~100MB) asynchronously. Once the tools are loaded, please choose a tool and see the similar ones for your favourite tool(s). The similar tools are arranged in the descending order of their probability scores (top 20 are shown). The similar tools that you see are a mixture of tools extracted based on the selected tool's description and file types. It means that sometimes the tools are similar due to their description/kind of functions they have and sometimes due to their file types. Also, there are a few graphics/plots at the end of the page. Here is the code repository to read more about this project. I have followed the following approach to compute the similar tools: Text mining to collect and preprocess the tools' keywords (which represent a tool) - BM25 Matrix factorization to extract important concepts (and not just words) - Latent Semantic Analysis Optimization to combine probability distributions - Gradient Descent and Backtracking Line Search Further, I have plans to include: Deep learning approach to compute similarity between paragraphs inspired from this work Similarity in workflowsIf you have any comment/feedback, please write. It will be immensely helpful. Thanks a lot! Regards, Anup Kumar

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use or convert tool.xml file for database webpage
by Jochen Bick 06 Feb '18

06 Feb '18

Hi, I have a question regarding the layout of each tool. I would like to use the same layout (same xml file) like inside galaxy to build a standalone webpage for a database. Is it possible to convert or use the xml file outside galaxy? My problem is that I have no idea how the xml file get interpreted inside galaxy to generate the interface of a galaxy tool. thanks in advance Jochen

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Predict similar tools for Galaxy tools using text mining and machine learning
by anup kumar 02 Feb '18

02 Feb '18

Hello everyone, Greetings! I am a contributor to the Galaxy project and currently working on finding similarities in Galaxy tools (a part of my master's thesis). This work aims at finding similar tools for any Galaxy tool based on tools description and their input/output file types. For example, the similar tools for a tool "bowtie2" could be "bwa", "bwameth" or "bwa_mem" among others. To see the results of this project online, please visit the link <https://rawgit.com/anuprulez/similar_galaxy_tools/master/viz/similarity_viz…> (works fine on Firefox and Chrome). You should wait for a few seconds before you see a list of tools in the select list as the page loads a big JSON file (~100MB) asynchronously. Once the tools are loaded, please choose a tool and see the similar ones for your favorite tool(s). The similar tools are arranged in the descending order of their probability scores (top 20 are shown). The similar tools that you see are a mixture of tools extracted based on the selected tool's description and file types. It means that sometimes the tools are similar due to their description/kind of functions they have and sometimes due to their file types. Also, there are a few graphics/plots at the end of the page. Here is the code repository <https://github.com/anuprulez/similar_galaxy_tools> to read more about this project. I have followed the following approach to compute the similar tools: 1. Text mining to collect and preprocess the tools' keywords (which represent a tool) - BM25 <https://en.wikipedia.org/wiki/Okapi_BM25> 2. Matrix factorization to extract important concepts (and not just words) - Latent Semantic Analysis <https://en.wikipedia.org/wiki/Latent_semantic_analysis> 3. Optimization to combine probability distributions - Gradient Descent <https://en.wikipedia.org/wiki/Gradient_descent> and Backtracking Line Search <https://en.wikipedia.org/wiki/Backtracking_line_search> Further, I have plans to include: - Deep learning approach to compute similarity between paragraphs inspired from this work <https://cs.stanford.edu/~quocle/paragraph_vector.pdf> - Similarity in workflows If you have any comment/feedback, please write. It will be immensely helpful. Thanks a lot! Regards, Anup Kumar

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Predict similar tools for Galaxy tools using text mining and machine learning
by anup kumar 01 Feb '18

01 Feb '18

Hello everyone, Greetings! I am a contributor to the Galaxy project and currently working on finding similarities in Galaxy tools (a part of my master's thesis). This work aims at finding similar tools for any Galaxy tool based on tools description and their input/output file types. For example, the similar tools for a tool "bowtie2" could be "bwa", "bwameth" or "bwa_mem" among others. To see the results of this project online, please visit the link <https://rawgit.com/anuprulez/similar_galaxy_tools/master/viz/similarity_viz…> (works fine on Firefox and Chrome). You should wait for a few seconds before you see a list of tools in the select list as the page loads a big JSON file (~100MB) asynchronously. Once the tools are loaded, please choose a tool and see the similar ones for your favourite tool(s). The similar tools are arranged in the descending order of their probability scores (top 20 are shown). The similar tools that you see are a mixture of tools extracted based on the selected tool's description and file types. It means that sometimes the tools are similar due to their description/kind of functions they have and sometimes due to their file types. Also, there are a few graphics/plots at the end of the page. Here is the code repository <https://github.com/anuprulez/similar_galaxy_tools> to read more about this project. I have followed the following approach to compute the similar tools: 1. Text mining to collect and preprocess the tools' keywords (which represent a tool) - BM25 <https://en.wikipedia.org/wiki/Okapi_BM25> 2. Matrix factorization to extract important concepts (and not just words) - Latent Semantic Analysis <https://en.wikipedia.org/wiki/Latent_semantic_analysis> 3. Optimization to combine probability distributions - Gradient Descent <https://en.wikipedia.org/wiki/Gradient_descent> and Backtracking Line Search <https://en.wikipedia.org/wiki/Backtracking_line_search> Further, I have plans to include: - Deep learning approach to compute similarity between paragraphs inspired from this work <https://cs.stanford.edu/~quocle/paragraph_vector.pdf> - Similarity in workflows If you have any comment/feedback, please write. It will be immensely helpful. Thanks a lot! Regards, Anup Kumar

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tool IO graph
by Matthias Bernt 01 Feb '18

01 Feb '18

Dear list, I started a little toy project (.. aka procrastination) that I would like to share here. It produces a graph connecting tool ids and input/output formats. As input it takes an arbitrary number of tool xml files https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tool-io-graph I could imagine some use cases: - could be nice for auto-generation of the documentation of a single tool (planemo?) - for tool suites one could easily check if the all tools are connected (I would expect this) - one could explore how tools could be plugged together, find out which tools generate a needed format currently it outputs dot formatted graphs. I can easily see some extensions - filter for subsets of tools / formats - get the surrounding of a tool (e.g. all nodes in distance 2, 4, ...) - filter paths from an available input to a desired output format Cheers, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

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