June 2015 - galaxy-dev - lists.galaxyproject.org

error return- PICRUSt
by Rebecca Prescott 05 Jun '15

05 Jun '15

Hello! I am a new user of Galaxy, I believe I am working on the MAIN (although I am not sure). I would like to use the PICRUSt tool on Galaxy through the web. I have created an account, but I did not download Galaxy. I uploaded two .biom files generated in QIIME (see attached). The Greengenes reference database that was used to generate these OTU tables is greengenes/gg_12_10 version. On the web-based PICRUSt tool in Galaxy, I selected the only other option than the current Greengenes database, which is listed as May18 2012. When I try to run normalize_by_copy_number.py I get the following error return for both files: Traceback (most recent call last): File "/net/rcstore02/ifs/rc_labs/galaxy/www/galaxy_hutlab14/galaxy-hutlab14-20150109/tools/picrust_galaxy/scripts/normalize_by_copy_number.py", line 146, in <module> main() File “/net/rcstore02/ifs/rc_labs/galax I am at a loss as to what this error term means. I suspect it is a format issue? But not sure what the issue is or how to fix it. Or that I am using the gg_12_10 version? Cheers Becks Rebecca Prescott, Ph.D University of Hawaii Manoa Department of Microbiology 2538 McCarthy Mall Honolulu, HI 96822

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How to access the api by jQuery ajax?
by Yanbo Ye 04 Jun '15

04 Jun '15

Hi, all I’m trying to access the api of my local galaxy instance from another site, under the remote user mode. At first, I sent request directly to the galaxy server. and it was OK when I test it using Postman (with ‘Remote-User’ in the header). But there’s CORS issue when I use it on my site. The preflight OPTIONS request gave me 403 error. So, I then tried to proxy the galaxy server to a location of the same domain of my site using apache. Now there’s no CORS issue. But it now ask me for authentication to use the api. Seems the ‘Remote-User’ value doesn’t work anymore. the request: [image: Inline image 1] error response: {"traceback": "No traceback available.", "err_msg": "API authentication required for this request", "err_code": 403001} Any one knows why? best, Yanbo -- *Yanbo Ye* *Guangzhou Institutes of Biomedicine and Health, * *Chinese Academy of Sciences* *190 Kaiyuan Avenue, Science Park, Guangzhou, China* *Email: ye_yanbo(a)gibh.ac.cn <ye_yanbo(a)gibh.ac.cn>* *Web: http://www.yeyanbo.com <http://www.yeyanbo.com>* *Phone: (86)-020-32093810*

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Re: [galaxy-dev] Sending tool output to input parameters of downstream tool(s)
by Alexander Vowinkel 04 Jun '15

04 Jun '15

Hi, I'd like to refer to an old post I found in the archive [1] and ask if there has been some progress in this? Best, Alexander [1] http://dev.list.galaxyproject.org/Sending-tool-output-to-input-parameters-o… > Hi all, > I was recently wondering how it might be possible for > an output from tool A to be used as a parameter when > calling tool B (without modifying tool B to take a data > configuration file or anything like that). > To clarify, I'm thinking about simple parameters like > a single integer/float/string like "median insert size" > or "average coverage" which map to a single input > parameter in a downstream tool. > Workflow parameters basic $variable support is > similar to what I'm thinking about here, see: > https://wiki.galaxyproject.org/DevNewsBriefs/2011_01_31 > Perhaps one day in addition to tool outputs being files, > they can include setting $variables (local to the history), > which could then be used within downstream tools? > I can see this has downsides with tracking the providence > of each variable though... thus: > Another idea would be extra filetypes for each parameter > type (Unix philosophy - make everything into a file), e.g. > integer_parameter, float_parameter, ... which "Tool A" > could define as an output, and write to. Galaxy would > then need to offer these history entries to the user when > a later tool (e.g. "Tool B") asked for a parameter of that > type (e.g. an integer, or a float). > (This idea could be extended further, with data files > using JSON or something to hold a structured set of > parameter values which Galaxy could then offer to > fill later tool's inputs.) > Crazy, or is there some mileage in this idea? > Peter

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Problem in Json datatype?
by Keith Suderman 04 Jun '15

04 Jun '15

Greetings, I was adding datatype classes to galaxy.datatype.text.py for our custom JSON formats and I noticed what I think is a problem with the Json datatype class, in particular the _looks_like_json method. The basic algorithm is (in pseudo code): if the_file_is_small_enough: try to load the the file as json return True on success, False otherwise else while True find first non-blank line if line starts with ‘{‘ or ‘[‘: return True else return False However, JSON is typically compressed by stripping whitespace (including newlines), particularly when it is fetched from a web service. This means that the first call to readLine is going to load the entire file, which defeats the purpose of checking the file size in the first place. I would submit a pull request with our fix, but since I am not a Python programmer I thought I would simply post the code here for review. class Json(Text): # Unchanged bits of the class have been omitted. # Add a function that reads a single character skipping over whitespace. def read(self, fileHandle): ch = fileHandle.read(1) while ch.isspace(): ch = fileHandle.read(1) return ch # Only the “else-part” has changed def _looks_like_json(self, filename): # Pattern used by SequenceSplitLocations if os.path.getsize(filename) < 50000: # If the file is small enough - don't guess just check. try: json.load(open(filename, "r")) return True except Exception: return False else: with open(filename, "r") as fh: ch = self.read(fh) return ch == '{' or ch == '[' We then use the read() method to sniff out our JSON formats. Once we can sniff a header subclasses only need to specify the header. class Lapps( Json ): header = ‘’’{“discriminator”:”http://vocab.lappsgrid.org''' def sniff(self, filename) with open(filename) as fh: for c in header: if c != self.read(fh) return False return True class Lif ( Lapps ): header = ‘’’{“discriminator”:”http://vocab.lappsgrid.org/ns/media/jsonld#lif”''' class Gate( Lapps ): header = ‘’’{“discriminator”:”http://vocab.lappsgrid.org/ns/media/gate”''' … Regardless of how the JSON is rendered (pretty printed or not) we can match the “magic” strings used to identify our formats. Being new to Python I don’t know how expensive it is to read a file one character at a time, but it has to be cheaper than potentially reading the entire file. Cheers, Keith ------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY

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Functional Test Failures with 15.05
by Ryan G 04 Jun '15

04 Jun '15

Hi - Are the functional tests for Galaxy supposed to run out of the box? I'm getting lots a failures with a fresh install in a virtual python environment.

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API access from Tool script
by Raffaele Montella 04 Jun '15

04 Jun '15

Dears, I’m working on a tool script (a Python script) that given a dataset id host and port, for example “http://web.uniparthenope.it:28080/api/datasets/3068f10db18abc2b” get the json dateset description in order to extract the file_name field as "file_name": "/home/0124000066/galaxy-python/galaxyTools/scratch/galaxy/files/001/dataset_1369.dat” The motivation is accessing to the actual filesystem path from the dataset id. There is any clean way to transfer the galaxysession cookie value to the tools script as an environment variable or any form of the authentication of the user that is running the tool? Bests, Raffaele****************************************************************************** IL MERITO DEGLI STUDENTI VIENE RICONOSCIUTO Il 5 per mille all'Universita' degli Studi di Napoli "Parthenope" incrementa le borse di studio agli studenti - codice fiscale 80018240632 http://www.uniparthenope.it/index.php/it/5-per-mille Questa informativa e' inserita in automatico dal sistema al fine esclusivo della realizzazione dei fini istituzionali dell'ente.

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LEfSe on local Galaxy instance
by Romain Maleysson 04 Jun '15

04 Jun '15

Hello, I recently installed Galaxy and among other tools I would like to have LEfSe on my local instance. I get the latest LEfSe's repository from the galaxy main tool shed, and I also install it's requirements packages and R libraries on the server (btw it's Debian based). I have a problem with the first tool, "A) Format Data for LEfSe", as you can see in the picture I attached "galaxy_lefse_error.png". In this step, I'm supposed to indicate which row Galaxy has to use to label the data. My issue is that the box "Select which row to use as class" remains saying "No options available", which blocks me to process the step. After checking the xml file of the tool, I found that a "dynamic option" is involved and normally have to generate the options list. I got helped by George Weingart (thanks to him and his patience) and I can say the following things : - My file is correct : I can run LEfSe on it with the public server Huttenhower-lab. I did the same manipulations with the example file provided by LEfSe's authors (found at this link http://www.huttenhower.org/webfm_send/73) and same result on my own Galaxy instance, while it's working on Huttenhower-lab; - This issue is not related to LEfSe : I installed the program outside of Galaxy (as stand alone) on the server and I get correct results. I tried to uninstall/reinstall LEfSe in Galaxy from the tool shed. I also replaced the LEfSe's scripts in the tool shed folder by the ones of my stand alone LEfSe. I checked the Galaxy log and didn't find any error possibly related to LEfSe. And finally, the other tools of LEfSe in my Galaxy instance are working well and give me correct results, only the "format data" tool has a problem; - With the same file (e.g. the example one), a difference occurs in the data loading between my Galaxy instance and Huttenhower-lab. After uploading, the datatype detected by my Galaxy instance is "axes", whereas it's "tabular" with Huttenhower-lab. Manually forcing the datatype to tabular (on upload or after upload) doesn't solve my issue. Does anyone have a clue to explain this difference in datatype detection? Many thanks in advance, Romain

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Multi-level datatype conversions
by David Kelly 03 Jun '15

03 Jun '15

Hello, Suppose I have three custom datatypes defined: a, b, and c I have a datatype converter that converts from a -> b I have a datatype converter that converts from b -> c Can I then send 'a' files as input into tools that accept type 'c'? This doesn't seem to work in my test case, but I thought it might be worth asking to see if anyone has tried this before. Thanks! Regards, David

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Migrating Galaxy 14.02 to 15.05 : error with tool migration
by Jean-Philippe Villemin 03 Jun '15

03 Jun '15

I'm trying to make an update ... I' have done the following commands hg pull hg update -C latest_15.05 ./run.sh "Exception: Your database has version '118' but this code expects version '129'. Please backup your database and then migrate the schema by running 'sh manage_db.sh -c ./universe_wsgi.ini upgrade'." sh manage_db.sh -c ./universe_wsgi.ini upgrade sh ./scripts/migrate_tools/0012_tools.sh -c universe_wsgi.ini install_dependencies I have the following error and i don't know what it means : No handlers could be found for logger "galaxy.tools.data" Traceback (most recent call last): File "./scripts/migrate_tools/migrate_tools.py", line 21, in <module> app = MigrateToolsApplication( sys.argv[ 1 ] ) File "/Users/galaxy_dev_user/galaxy-dist/lib/tool_shed/galaxy_install/migrate/common.py", line 41, in __init__ self._configure_toolbox() File "/Users/galaxy_dev_user/galaxy-dist/lib/galaxy/config.py", line 748, in _configure_toolbox self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self ) File "/Users/galaxy_dev_user/galaxy-dist/lib/galaxy/tools/__init__.py", line 106, in __init__ app=app, File "/Users/galaxy_dev_user/galaxy-dist/lib/galaxy/tools/toolbox/base.py", line 78, in __init__ self._load_tool_panel() File "/Users/galaxy_dev_user/galaxy-dist/lib/galaxy/tools/toolbox/base.py", line 312, in _load_tool_panel self.__add_tool_to_tool_panel( val, self._tool_panel, section=False ) File "/Users/galaxy_dev_user/galaxy-dist/lib/galaxy/tools/toolbox/base.py", line 251, in __add_tool_to_tool_panel tool = self._tools_by_id[ tool_id ] KeyError: 'tool_test' -- *Jean-Philippe Villemin *- Bioinformatics, Software Engineer - IURC (Institut Universitaire de Recherche Clinique) 641 avenue du Doyen Gaston Giraud 34093 Montpellier Cedex 5, France *Jean-Philippe.VILLEMIN(a)inserm.fr <Jean-Philippe.VILLEMIN(a)inserm.fr>*

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Problem sharing histories
by Poole, Richard 02 Jun '15

02 Jun '15

Hi Nate, Although it was working fine in the past (and older shared histories are still shared) we are currently experiencing an issue sharing histories on our local Galaxy server. I really don’t understand the error messages at all, other than it looking like its possible a proxy/webserver issue. After entering an email (which is a list for admin users but blank for non-admin users) I get the Internal Server Error page. Here is the log: 127.0.0.1 - - [02/Jun/2015:10:41:35 +0100] "GET /api/users?f_email=&_=1433238093664 HTTP/1.1" 200 - "http://****.****.ucl.ac.uk:8080/history/share?use_panels=False&id=93d12697461a7974" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_3) AppleWebKit/600.6.3 (KHTML, like Gecko) Version/8.0.6 Safari/600.6.3" 127.0.0.1 - - [02/Jun/2015:10:41:46 +0100] "GET /api/users?f_email=&_=1433238093665 HTTP/1.1" 200 - "http://****.****.ucl.ac.uk:8080/history/share?use_panels=False&id=93d12697461a7974" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_3) AppleWebKit/600.6.3 (KHTML, like Gecko) Version/8.0.6 Safari/600.6.3" 127.0.0.1 - - [02/Jun/2015:10:41:48 +0100] "POST /history/share HTTP/1.1" 500 - "http://****.****.ucl.ac.uk:8080/history/share?use_panels=False&id=93d12697461a7974" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_3) AppleWebKit/600.6.3 (KHTML, like Gecko) Version/8.0.6 Safari/600.6.3" Error - <type 'exceptions.TypeError'>: append() takes exactly one argument (0 given) URL: http://****.****.ucl.ac.uk:8080/history/share File '/Users/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/Library/Python/2.7/site-packages/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/Library/Python/2.7/site-packages/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/Users/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 133 in __call__ return self.handle_request( environ, start_response ) File '/Users/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 191 in handle_request body = method( trans, **kwargs ) File '/Users/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py', line 64 in decorator return func( self, trans, *args, **kwargs ) File '/Users/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/history.py', line 783 in share histories = self._get_histories( trans, id ) File '/Users/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/history.py', line 902 in _get_histories histories.append( ) TypeError: append() takes exactly one argument (0 given) CGI Variables ------------- CONTENT_LENGTH: '-1' CONTENT_TYPE: 'application/x-www-form-urlencoded' HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_ENCODING: 'gzip, deflate' HTTP_ACCEPT_LANGUAGE: 'en-us' HTTP_CONNECTION: 'close' HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603affb9e7f3db8ec24e38c21f8e92c63c0423b0bca935c4829106a35253947071a3; __utma=156947391.1608730577.1432903437.1432903437.1432903437.1; __utmz=156947391.1432903437.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none)' HTTP_DNT: '1' HTTP_HOST: '****.****.ucl.ac.uk<http://ucl.ac.uk>:8080' HTTP_ORIGIN: 'http://****.****.ucl.ac.uk:8080' HTTP_REFERER: 'http://****.****.ucl.ac.uk:8080/history/share?use_panels=False&id=93d12697461a7974' HTTP_USER_AGENT: 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_3) AppleWebKit/600.6.3 (KHTML, like Gecko) Version/8.0.6 Safari/600.6.3' HTTP_X_FORWARDED_FOR: '127.0.0.1' HTTP_X_FORWARDED_HOST: '****.****.ucl.ac.uk<http://ucl.ac.uk>:8080' HTTP_X_FORWARDED_SERVER: '****.****.ucl.ac.uk<http://ucl.ac.uk>' ORGINAL_HTTP_HOST: 'localhost:8081' ORGINAL_REMOTE_ADDR: '127.0.0.1' PATH_INFO: '/history/share' REMOTE_ADDR: '127.0.0.1' REQUEST_METHOD: 'POST' SERVER_NAME: '0.0.0.0' SERVER_PORT: '8081' SERVER_PROTOCOL: 'HTTP/1.1' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x10cc3e290> is_api_request: False paste.cookies: (<SimpleCookie: __utma='156947391.1608730577.1432903437.1432903437.1432903437.1' __utmz='156947391.1432903437.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none)' galaxysession='c6ca0ddb55be603affb9e7f3db8ec24e38c21f8e92c63c0423b0bca935c4829106a35253947071a3'>, 'galaxysession=c6ca0ddb55be603affb9e7f3db8ec24e38c21f8e92c63c0423b0bca935c4829106a35253947071a3; __utma=156947391.1608730577.1432903437.1432903437.1432903437.1; __utmz=156947391.1432903437.1.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none)') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x10cc3e1d0> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x10d21f690> paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True request_id: '96fdc0dc090b11e5aa28685b359a2712' webob._parsed_post_vars: (MultiDict([('id', '93d12697461a7974'), ('email', '33b43b4e7093c91f'), ('share_button', 'Submit')]), <FakeCGIBody at 10d4be2d0 viewing MultiDict([('id...t')])>) webob._parsed_query_vars: (MultiDict([]), '') wsgi process: 'Multithreaded' ------------------------------------------------------------ Any help with this greatly appreciated :) Richard Richard J Poole PhD Wellcome Trust Fellow Department of Cell and Developmental Biology University College London 21 University Street, London WC1E 6DE Office (518 Rockefeller): +44 20 7679 6577 (int. 46577) Lab (529 Rockefeller): +44 20 7679 6133 (int. 46133)

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