May 2013 - galaxy-dev - lists.galaxyproject.org

"login to ftp server failed" or "Problem with ftp connexion to Galaxy"
by Danni Yu 01 Jun '13

01 Jun '13

To whom this may concern, This is Danni Yu, a Galaxy user starting to use Galaxy since 2011. I was able to upload large files through ftp in 2011 and 2012. Now, I am facing the same problem as the other users (such as Barbara Sixt on May 27, 2013 and Fabrice Besnard on May 22, 2013). The error message is "530 login incorrect". Ms. Jennifer Hillman-Jackson in Galaxy Support and Training team very kindly mentioned that "Please feel free to contact us for an update if this is still a problem by next Friday" on May 24, 2013. Since it is already Friday but the problem still exists, I am hoping to learn whether a solution has been provided. Thanks very much and Sincerely, Danni

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Getting example_watch_folder.py to work...
by Neil.Burdett＠csiro.au 31 May '13

31 May '13

Hi, I'm trying to get the example_watch_folder.py to run but it seems to fail, and I'm not sure why? I run: ./example_watch_folder.py 64f3209856a3cf4f2d034a1ad5bf851c http://barium-rbh/csiro/api/ /home/galaxy/galaxy-drop/input /home/galaxy/galaxy-drop/output "My API Import" f597429621d6eb2b I got the workflow Id from : http://barium-rbh/csiro/api/workflows which gave me: [ { "id": "f597429621d6eb2b", "name": "extract", "url": "/csiro/api/workflows/f597429621d6eb2b" }, { "id": "f2db41e1fa331b3e", "name": "FULL CTE", "url": "/csiro/api/workflows/f2db41e1fa331b3e" } ] The output I get from the command line is: {'outputs': ['ba0fa2aed4052bce'], 'history': 'ba03619785539f8c'} The files I put into /home/galaxy/galaxy-drop/input get copied to /home/galaxy/galaxy-drop/output But nothing else happens. If I go to http://barium-rbh/csiro/api/histories I can see: { "id": "ba03619785539f8c", "name": "colin.nii.gz - extract", "url": "/csiro/api/histories/ba03619785539f8c" }, However when I go to: http://barium-rbh/csiro/api/histories/ba03619785539f8c I get: { "contents_url": "/csiro/api/histories/ba03619785539f8c/contents", "id": "ba03619785539f8c", "name": "colin.nii.gz - extract", "state": "error", "state_details": { "discarded": 0, "empty": 0, "error": 1, "failed_metadata": 0, "new": 0, "ok": 0, "queued": 0, "running": 0, "setting_metadata": 0, "upload": 0 } } Any ideas much appreciated Thanks Neil

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Re: [galaxy-dev] Multi File upload api
by Alex.Khassapov＠csiro.au 31 May '13

31 May '13

Hi John, Can you please have a look at Neil's question. Thank you, -Alex From: Burdett, Neil (ICT Centre, Herston - RBWH) Sent: Thursday, 30 May 2013 4:30 PM To: Khassapov, Alex (CSIRO IM&T, Clayton) Subject: Multi File upload api Hi Alex, The file "galaxy-dist/scripts/api/example_watch_folder.py" allows us to watch a folder then upload files that arrive in a specified input folder into the database and history. Can you ask your friend (who implemented the multi file upload tool), what changes are necessary to this file so we can upload multiple files as we do from the GUI. I assume he would know quite quickly what to do and hopefully quite simple.... Thanks Neil

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June 2013 Galaxy Update
by Dave Clements 31 May '13

31 May '13

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Status of Galaxy Cloud Instance dev
by Joachim Jacob | VIB | 31 May '13

31 May '13

Hi all, I am planning to launch a Galaxy Cloud Instance, to run for about one month. But I believe I've read somewhere a new image of Galaxy on AWS is being prepared right now. Can somebody update me on the status? Perhaps it is smart to wait a few days with launching through CloudLaunch until the new release is there? Thanks, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team

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[GSoC 2013] Introduction
by Saket Choudhary 31 May '13

31 May '13

Hi Everyone! I have been selected to work on the eQTL pipeline and visualisation for the Galaxy Project as part of the Google Summer of Code 2013 ( http://www.google-melange.com/gsoc/homepage/google/gsoc2013) I am pursuing my fourth year of undergraduate studies at Indian Institute of Technology Bombay(http://www.iitb.ac.in/). My areas of interest are broadly Bioinformatics and of lately I have been working on NGS problems. I have created a blog here : http://galaxy-gsoc2013.blogspot.com/ . The first post should be up soon. My proposal is here : http://www.google-melange.com/gsoc/proposal/review/google/gsoc2013/saketkc/…. I would love to know your suggestions/comments. I am relatively new to Galaxy, and some of my questions in the process might be elementary, so kindly bear with it :) Thanks Saket Choudhary

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Making Public a Data Library Gives Internal Server Error
by Rodolfo Aramayo 31 May '13

31 May '13

Hi, As Admin, I uploaded a set of files from filesystems paths Uploading is successful but when I try to make the datasets public I get the following error: Internal Server Error Galaxy was unable to sucessfully complete your request <==By The Way...NOTE how sucessfully is misspelled!! URL: http://galaxy.tamu.edu/library_common/make_library_item_public?library_id=8… File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 128 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 184 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/library_common.py', line 1626 in make_library_item_public self._check_access( trans, cntrller, is_admin, ldda.library_dataset, current_user_roles, use_panels, library_id, show_deleted ) AttributeError: 'NoneType' object has no attribute 'library_dataset' Help will be appreciated Thanks --R

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import Workflow from public Galaxy to local instance
by Andreas Kuntzagk 30 May '13

30 May '13

Hi, I want to make workflows published on usegalaxy.org available for users on our local instance. How do I do this? regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich

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Creating tool shed repository: installation of dependencies fails.
by Joachim Jacob | VIB | 30 May '13

30 May '13

Hi all, I am building a wrapper around BLAT, and have put it locally in a toolshed. However, the automatic installation of dependencies fails: ************************* Tool dependency installation error: [Errno 2] No such file or directory: '/home/galaxy/galaxy-dist/database/tmp/tmp2J7K_L/database/tmp/tmp2J7K_L/blat ************************* Note that there is a strange duplication in the path. Furthermore, on that Galaxy instance, the database is on /mnt/testgalaxydb/database instead of path mentioned in the error. The tool_dependencies.xml matches the wrapper xml. blat is just downloaded from its url. ************************* <?xml version="1.0"?> <tool_dependency> <package name="blat" version="1.0.0"> <install version="1.0"> <actions> <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat</action> <action type="move_file"> <source>blat</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> The BLAT binary for linux x86_64 is retrieved from UCSC. </readme> </package> </tool_dependency> ************************* Thanks for helping me further. Cheers, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team

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Setting up Galaxy interface to motif finding software
by Tom Hait . 30 May '13

30 May '13

Dear Galaxy developers, I hope you could help me with the following issue. I wish to use galaxy tools in our AMADEUS motif finding software: http://acgt.cs.tau.ac.il/amadeus/ AMADEUS helps many users who wish to find motifs in their sequences. AMADEUS has 2 limitations: 1. It can find motifs vs all organism's genome. 2. If the user don't want to find motif vs all organism's genome then The user itself will have to supply the sequences for the motif finding according to his chipSeq peaks he got. We would like that the user won't be troubled with the second limitation by adding locally\cloud Galaxy that downloads to AMADEUS the relevant sequences (~3000 sequences) according to the peaks locations from a BED file supplied by the user. As I see it - the galaxy installation will have to follow the objectives: 1. Work on windows OS. 2. Can be installed in the user computer by a script in AMADEUS 3. downloading time of the relevant sequences (~3000) won't take above 1-2 minutes I will appreciate if someone of you will guide me with the procedure and advise me with the best way to work with Galaxy-AMADEUS interface. Thanks, Tom hait

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