January 2014 - galaxy-dev - lists.galaxyproject.org

A new tool_data_table_conf.xml created under tool-data directory
by Derrick Lin 17 Jan '14

17 Jan '14

Hi guys, After installing the BWA from the Tools Shed, I find there is a new tool_data_table_conf.xml got created under tool-data directory. The file contains the entries of BWA's loc files. I believe the installed BWA still relies on the tool_data_table_conf.xml under galaxy root dir. Anyone can clarify what the one under tool-data dir is for? Regards, Derrick

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moving galaxy instance to different location
by Ido Tamir 17 Jan '14

17 Jan '14

Hi, I have to move my galaxy instance to a different file system location. Is there anything that I have to look out for besides the obvious like absolute paths in some data configs? thank you very much, ido

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Help
by Pasquale Notarangelo 17 Jan '14

17 Jan '14

Hi all, we have installed a Galaxy istance on our server and we developed a new workflow. Also we have published this workflow and now is shared with every user. How can we publish the workflow in only runnable mode and then make this not editable for the other users? Best regards Pasquale & Alfonso ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dott. Pasquale Notarangelo INFN Istituto Nazionale di Fisica Nucleare - Sezione Bari Via Orabona, 4 - 70126 Bari, Italy Tel. ufficio: +39 080-5443194 Interno ufficio: 3194 Mail: pasquale.notarangelo(a)ba.infn.it Skype: pasquale.notarangelo_1985 Msn: pasqualenotarangelo(a)hotmail.it Gmail: notarangelo.pas(a)gmail.com ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Import workflows via API
by Neil.Burdett＠csiro.au 17 Jan '14

17 Jan '14

Hi, I execute workflows via the API. However, if I want another user to use my workflows, I can publish my workflows, but the new user then has to go on to the web browser and import this workflow. Is there a method/script which I can call via the API which can import all available (published) workflows so the user doesn't have to click a button on the web browser "import workflow" ? Thanks for any help Neil

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Pick-you-own columns in BLAST+ tabular output
by Peter Cock 17 Jan '14

17 Jan '14

Hello all, For those interested in more flexible tabular output from BLAST+, please try out the wrappers on the *Test* Tool Shed which I have also just updated to wrap BLAST+ 2.2.29 as well: http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus One open question is should the interface for picking columns include the current column numbers or not? e.g. http://dev.list.galaxyproject.org/attachment/4662771/0/blast-pyo-columns-sp… (Screenshot from this thread last month, where opinion was split) http://dev.list.galaxyproject.org/Including-descriptions-etc-in-extended-BL… In future work we'll add some of the new columns added in the BLAST+ 2.2.28 release like taxonomy fields - but this needs a bit of thought about how to handle the taxonomy database (i.e. should we support multiple versions for full reproducibility, or just use the current version on disk regardless). Most of the time updates to the NCBI taxonomy will simply be additions, which should be harmless to reproducibility - but sometimes taxa can be rearranged. https://github.com/peterjc/galaxy_blast/issues/20 https://github.com/peterjc/galaxy_blast/issues/21 Regards, Peter

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html network
by Lionel Chiron 17 Jan '14

17 Jan '14

Hi all , I am able to write a tool for producing an html file through the network on the Galaxy server but I can't figure out how to watch this html in Galaxy.. I would need to write the address of the pictures(which are on the server) in the html so that it is available through the port 8080 via the network but this is not clear for me how to do that. Lionel

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Re: [galaxy-dev] making tools with Galaxy
by Greg Von Kuster 16 Jan '14

16 Jan '14

Hello Lionel, Please send correspondence like this to the galaxy-dev(a)lists.bx.psu.edu mailing list rather than individual email accounts as doing so will ensure more timely and optimal repoonses. I'm not quite sure what code you are reading, so could you please clarify? In general, though, when you write a Galaxy wrapper to integrate a tool into Galaxy, you will be able to load the tool into the Galaxy tool panel, and the tool UI will display in the main Galaxy panel. When you execute the tool, a Galaxy job will get created which will produce an output in the form of a dataset. This dataset will be displayed in you Galaxy history as the result of excuting the tool. So, in your case, the history item will include the png file and, when clicked , it should display in your main Galaxy panel. There are a lot of details that are calrified in the Galaxy wiki - a good place to start is probably: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Greg Von Kuster On Jan 16, 2014, at 5:56 AM, Lionel Chiron <lionel.chiron(a)nmrtec.com> wrote: > Hi Greg, > > I'm trying to make a tool in Galaxy for implementing our algorithm for mass spectrometry treatment but it is a little tricky for me.. > To make run the algorithm in Python is ok, I produce a png with matplotlib .. but after that I 'm a little lost since I don't know where the picture is produced.. reading your code I can't figure out how you indicate where to produce the png file.. > How can I do?? > Thanks > > Lionel

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creating a hierarchy of students teachers and courses
by Fernandez Edgar 16 Jan '14

16 Jan '14

Hello galaxy team, First and foremost, I would like to thank you for your assistance with my galaxy installation with apache proxy. It works very well. Secondly, I would like your help with creating users, groups, roles and permissions that would allow me to: 1. differentiate a student from a teacher 2. differentiate a student in course A or in course B 3. teachers having read access to students' work 4. teachers sharing with students Right now, I just have created users. There is no group or roles or permissions or datasets. On another note, how can I disable the account of one specific user or a whole group ? Cordialement / Regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication * Bur. : 1-514-343-6111 poste 16568 Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-218

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Re: [galaxy-dev] sanitize_all_html option
by Greg Von Kuster 16 Jan '14

16 Jan '14

Hello Pieter, Please make sure to address items like this to the galaxy-dev(a)lists.bx.psu.edu mailing list rather than individual email accounts as that will ensure more timely responses that include more optimal feedback. Sanitizing values from input text fields on tools and other Galaxy forms is an essential part of ensuring that the values will not wreak havoc within the Galaxy environment. Opening this up to being optional may be a concern to some Galaxy administrators. In any case, the Tool Shed probably should not have the ability to define the use of this feature since it has no affect within any of the Tool Shed environment ( only Galaxy or other applications in which things are installed from the Tool Shed will be affected ). So if it is decided by the Galaxy community that this feature ( i.e., sanitizing form text field values ) should be enhanced or altered, changes should be made within the Galaxy environment rather than the Tool Shed. As input regarding this request comes in from the community, perhaps we can create an appropriate Trello card to capture the direction we should go. Thanks very much for your request on this! Greg Von Kuster On Jan 13, 2014, at 6:16 AM, "Lukasse, Pieter" <pieter.lukasse(a)wur.nl> wrote: > Hi Greg, > > I have some tools which produce HTML and the default setting of the option sanitize_all_html will give problems and/or make the output look ugly. Would it be an option to let the administrator decide, for each tool he installs, whether this option should apply or not? Now is a global setting which applies to all tools, and in practice this results in it being set to “false”....which means that in practice this is a “pseudo security item” as it will not be used that often. > > The alternative I have been thinking about is to add a checkbox to the “manage repository” screen to allow the admin to turn this feature on/off for a specific repository. See also the screenshot below. Maybe you are already working in this direction, but I thought I’d just share this idea with you. > > <image001.png> > > Best regards, > > Pieter Lukasse > > Wageningen UR, Plant Research International > > Departments of Bioscience and Bioinformatics > > Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, > Wageningen, the Netherlands > > +31-317481122; skype: pieter.lukasse.wur > > http://www.pri.wur.nl > >

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Avoid integrated_tool_panel.xml update
by Cristian Alejandro Rojas 16 Jan '14

16 Jan '14

Hi all, There is a setting on somewhere to skip the integrated_tool_panel.xml file update? Best regards, -- *Cristian Alejandro Rojas Quintero* *Estudiante Ingeniería de Sistemas * *Universidad Distrital Francisco José de Caldas* Bogotá - Colombia

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