- galaxy-dev - lists.galaxyproject.org

Programming error in tool finish method
by James Boocock 15 Jan '13

15 Jan '13

ProgrammingError: (ProgrammingError) You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings. u'UPDATE job SET update_time=?, state=?, stdout=?, stderr=? WHERE job.id = ?' ['2013-01-14 07:17:20.417990', 'error', '', '\n\n\x1b[33mS\x1b[0megmented \x1b[33mHAP\x1b[0mlotype \x1b[33mE\x1b[0mstimation & \x1b[33mI\x1b[0mmputation \x1b[33mT\x1b[0mool\ That is just a sample of the stdout that I think it is failing on. I think that shapeit is using 8 bit character codes in the stdout and galaxy is failing on adding to the database. Has anyone experienced this problem and could help me. Cheers James

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Errors in browser: unknown css properties
by Joachim Jacob 15 Jan '13

15 Jan '13

Hello all, Trying to fix Trackster on our Galaxy, I noticed that my browser (Firefox) catches a lot of warnings, also on properties of CSS that I thought would be especially for Firefox. Can this cause lagging while using Galaxy? (some of our users experience slow browsing on our Galaxy). Timestamp: 01/14/2013 10:13:19 AM Warning: Unknown property '-moz-border-radius'. Declaration dropped. Source File: https://main.g2.bx.psu.edu/static/style/base.css?v=1357902839 Line: 314 Timestamp: 01/14/2013 10:13:19 AM Warning: Unknown property '-moz-border-radius-topright'. Declaration dropped. Source File: https://main.g2.bx.psu.edu/static/style/base.css?v=1357902839 Line: 315 Timestamp: 01/14/2013 10:13:19 AM Warning: Unknown property '-moz-border-radius-topleft'. Declaration dropped. Source File: https://main.g2.bx.psu.edu/static/style/base.css?v=1357902839 Line: 315 Timestamp: 01/14/2013 10:13:19 AM Warning: Unknown property '-moz-border-radius-bottomright'. Declaration dropped. Source File: https://main.g2.bx.psu.edu/static/style/base.css?v=1357902839 Line: 316 Timestamp: 01/14/2013 10:13:19 AM Warning: Error in parsing value for 'filter'. Declaration dropped. Source File: https://main.g2.bx.psu.edu/static/style/base.css?v=1357902839 Line: 329 Thanks for the clarifications, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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text manipulation Compute tool error
by mark.rose＠syngenta.com 14 Jan '13

14 Jan '13

Hello On a local install of galaxy I am getting seemingly erroneous behavior from the text manipulation tool "Compute". It will compute the expression I set (c3-c2+1) but will concatenate it to the last column rather that create a new column. Also the job errors and is shown in red. I can get around the concatenation problem by using the Add Column tool but subsequent use of Compute also errors and its results are unavailable for further analysis though the output appears correct. Can you help? Mark This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.

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GalaxyAdmins Meetup -- January 16 at 10 AM Central
by IIHG Galaxy Administrator 14 Jan '13

14 Jan '13

Hello, The next GalaxyAdmins Meetup will be Wednesday, January 16, 2013 from 10 AM to 11 AM US Central time. John Chilton of the Minnesota Supercomputing Institute will cover "Deploying Production Galaxy Environments on OpenStack with CloudBioLinux and CloudMan". You can join the meetup at https://globalcampus.uiowa.edu/join_meeting.html?meetingId=1262341808106. We use the Blackboard Collaborate Web Conferencing system for the meetup. Downloading the required applets in advance and using a headphone with microphone to prevent audio feedback during the call is recommended. Thank you. -- Srinivas Maddhi Senior Systems Administrator Iowa Institute for Human Genetics The University of Iowa

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welcome.html
by Anatoliy Pandorin 14 Jan '13

14 Jan '13

Hi. Thanks for your help! I have a few questions: "Is it possible to display different content of central area (welcome.html) according to user - registered or guest? If guest - page with offer to register, if registered user - page with another info. And how I can get the email of this user?" Best regards, Anatoly

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Anonymous use of workflows and visualization?
by Sveinung Gundersen 14 Jan '13

14 Jan '13

Hello all, We are wondering if it is possible to activate anonymous use of the workflows and the visualization (trackster) features of Galaxy, somehow? This is a strict requirement for the acceptance of our new paper in a specific journal. Hack solutions are also welcome! Thanks, Sveinung Gundersen

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Anonymous use of workflows and visualization?
by Sveinung Gundersen 14 Jan '13

14 Jan '13

Hello all, We are wondering if it is possible to activate anonymous use of the workflows and the visualization (trackster) features of Galaxy, somehow? This is a strict requirement for the acceptance of our new paper in a specific journal. Hack solutions are also welcome! Thanks, Sveinung Gundersen

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Issues with Trello, and enhancement request
by Joachim Jacob 14 Jan '13

14 Jan '13

Hi all, I cannot post to Trello today. Actually, this problem exists from last friday already. My enhancement request (which was not yet posted on Trello - at least not in a way I could find it...): """ Some files I upload have a first line containing the column names. Sometimes I need to first strip of that line, before continuing analyses. Afterward, I need to paste that line back on top. Perhaps it would be more efficient to have an option set in the 'Edit attributes' of a dataset: column names from first line? Or something similar. The first line would disappear, and the content would be set as metadata on the tabular file. """ Thanks, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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Vizualisation broken after updating
by Joachim Jacob 14 Jan '13

14 Jan '13

Hi all, In general, updating Galaxy works very smooth. But I got some strange unresolved merges after the last update (files affecting galaxy-dist/static/scripts/packed/viz) After resolving the conflicts (to the correct latest files), the visualisation component is not working anymore. Symptoms: I see the list of saved visualisations, but clicking on a visualisation just returns an empty screen. Creating a new visualisation: the box to name the visualisation appears, but after filling in and proceeding, again a blank screen with just the Galaxy Bar on top. Any help how to fix this? Thanks, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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Uploading files to history via API
by Neil.Burdett＠csiro.au 14 Jan '13

14 Jan '13

Hi, It seems the API documentation is a bit scarce. I'd like to upload a file from the command line using the API rather than the GUI, but would like to see the file in the history. Does anyone have any information how to do this/ any tools that are available. Thanks Neil

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