- galaxy-dev - lists.galaxyproject.org

Broad IGV
by Chorny, Ilya 24 Oct '11

24 Oct '11

I saw some posts and a commit which allows one to use broad IGV within galaxy but I do not see a tool, a link, or an option. Can someone explain how to set that up? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

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FTP UPLOAD
by alessandro albiero 24 Oct '11

24 Oct '11

Dear all, I've a question about FTP upload of data. The data uploaded via ftp are placed in the directory ftp_upload_dir defined in universe_wgsi.uni After the uploading, when a user select the data to import in its history, galaxy copy the file in the dir file_path (defined in universe_wgsi.uni). In this manner we have two copy of the same file, and with NGS data this not the best solution... I try to set the ftp_upload_dir and the file_path with the same path but galaxy copy the file in a dir called 000. In my ftp_upload_dir / file_path so I have: - user1(a)mail.com - user2(a)mail.com - 000 How can I avoid this duplication ? All the Best Alessandro -- ****************************** Alessandro Albiero Bioinformatics Lab CRIBI-Padua University Viale G. Colombo, 3 35121 Padova-Italy http://genomics.cribi.unipd.it http://genomics.cribi.unipd.it/index.php/User:Albiero Phone. +39. 049 827-6165 Fax. +39. 049 827-6159 ********************************

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Importing Historys in other Galaxy instances
by Stefanie Ververs 24 Oct '11

24 Oct '11

Hi everybody, I got another question concerning our own Galaxy instance. We are trying to import Histories from the public Galaxy server via "Export to file" (in the public-Galaxy-account), saving the export-Link and "Import from File" in the account on our local system. But the histories never show up there. As I read in some older mails, you need to be logged in the source account - I was, I checked that. Am I correct that it's possible to "copy" histories between different Galaxy instances at all? (I assume because it's the only case that makes sense to me..) We thought it might depend on some Apache configuration, but didn't figure it out yet. Maybe someone's got some ideas :-) Regards, Steffi

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Problem uploading sorted BAM files
by Stephen Eacker 24 Oct '11

24 Oct '11

Hello, I'm trying to upload a 600MB BAM file to my local instance of Galaxy but the upload fails. I tried to follow a thread on this topic archived on osdir.com but could not find if the issue was resolved. My BAM file has been previously been sorted and indexed which I think is the root of the problem. Advice? thanks, Steve Stephen Eacker, Ph.D. Postdoctoral Fellow Dawson Lab Institute for Cell Engineering Johns Hopkins Medical Institute (443) 287-5605 seacker1(a)jhmi.edu

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Database configuration
by Luciano Cosme 24 Oct '11

24 Oct '11

Hi, I am sorry about the trivial questions. I am following this guide http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP to set up a ftp server to upload data to my local instance of galaxy. I am getting a error when I am configuring the database server: postgres@aedes:~$ createuser -SDR galaxyftp postgres@aedes:~$ psql galaxydb psql (9.1.1) Type "help" for help. galaxydb=# ALTER ROLE galaxyftp PASSWORD 'dbpassword'; ALTER ROLE galaxydb=# GRANT SELECT ON galaxy_user TO galaxyftp; ERROR: relation "galaxy_user" does not exist galaxydb=# It might be something pretty simple, but I am new to it and any help will be appreciated. I create the user galaxy_user already. Thank you. Luciano

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Re: [galaxy-dev] FW: one error while installing galaxy
by Nate Coraor 24 Oct '11

24 Oct '11

Li, Jilong (MU-Student) wrote: > Hi, > > When I installed galaxy, one error message appeared, which said that > > ImportError: No module named distutils.util > Fetch failed. > > Could you tell me how to solve this problem? > Thank you very much! Hi Jilong, Since this is a question regarding a local installation, I've moved it over to the galaxy-dev list. Could you try the following: % unset PYTHONPATH % python ./scripts/fetch_eggs.py And then try to start Galaxy again? --nate > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/

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Re: [galaxy-dev] Few possible galaxy bugs ?
by Peter Cock 24 Oct '11

24 Oct '11

On Mon, Oct 24, 2011 at 3:55 PM, michael burrell (TOC) <michael.burrell(a)nbi.ac.uk> wrote: > Good afternoon Peter, > > Thank you for your rapid response, > > My understanding is that this tool was installed locally from the tool shed, unfortunately I do not know if it was working before the update was performed. > > Other tools installed from the tool shed do not seem to report errors, would you have any advice on resolving the small nlstradamus issue that is reported here? > > Thanks again for the information. > > Michael. I'm hoping Greg can give some clues. This part suggests Galaxy is trying to read the text readme file as if it were XML: galaxy.tools ERROR 2011-10-20 13:18:47,722 error reading tool from path: toolshed/nlstradamus/tools/protein_analysis/nlstradamus.txt ... ExpatError: syntax error: line 1, column 0 Peter

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upload error in the local instance of galaxy
by Amit Anand 24 Oct '11

24 Oct '11

Hi, I have just installed a local instance of galaxy. Though I am not too familiar with unix, I preferred a local instance because of large amount of data I have to process. However, I am unable to upload a file more that 2 GB in size, the error log is pased below 127.0.0.1 - - [19/Oct/2011:15:06:08 +0800] "POST /tool_runner/index HTTP/1.1" 500 - "http://127.0.0.1:8080/tool_runner?tool_id=upload1" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:6.0.2) Gecko/20100101 Firefox/6.0.2" Debug at: http://127.0.0.1:8080/_debug/view/1319007854 ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 61099) Traceback (most recent call last): File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread self.finish_request(request, client_address) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer.py", line 322, in finish_request self.RequestHandlerClass(request, client_address, self) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer.py", line 617, in __init__ self.handle() File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 432, in handle BaseHTTPRequestHandler.handle(self) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/BaseHTTPServer.py", line 329, in handle self.handle_one_request() File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 427, in handle_one_request self.wsgi_execute() File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 287, in wsgi_execute self.wsgi_start_response) File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/urlmap.py", line 202, in __call__ return app(environ, start_response) File "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/middleware/xforwardedhost.py", line 21, in __call__ return self.app( environ, start_response ) File "/Users/amit/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/config.py", line 164, in __call__ app_iter = self.application(environ, start_response) File "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/middleware/translogger.py", line 68, in __call__ return self.application(environ, replacement_start_response) File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py", line 226, in __call__ return self.respond(environ, start_response) File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py", line 399, in respond if self.xmlhttp_key in req.params: File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py", line 900, in params params = self.str_params File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py", line 892, in str_params return NestedMultiDict(self.str_GET, self.str_POST) File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py", line 818, in str_POST keep_blank_values=True) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 508, in __init__ self.read_multi(environ, keep_blank_values, strict_parsing) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 632, in read_multi environ, keep_blank_values, strict_parsing) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 510, in __init__ self.read_single() File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 647, in read_single self.read_lines() File "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/base.py", line 253, in read_lines self.read_lines_to_outerboundary() File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 697, in read_lines_to_outerboundary line = self.fp.readline(1<<16) File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 467, in readline data = self.file.readline(self.length - self._consumed) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/socket.py", line 409, in readline bline = buf.readline(size) OverflowError: long int too large to convert to int Please help me to fix this, the python version is 2.6.6. Thank you. Sincerely, Amit, Germline biology group Temasek Life Sciences Laboratory Singapore -- Amit Anand Germ Line Biology Group Temasek Life Sciences Laboratory 1, Research Link National University of Singapore Singapore, 117604 Information in this email is confidential and may also be privileged. It is intended solely for the person to whom it is addressed. If you are not the intended recipient, please notify the sender, and please delete the message and any other record of it from your system immediately.

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FW: how do I pass the URL of the input and output files to my tool wrapper?
by Chorny, Ilya 24 Oct '11

24 Oct '11

I thought I would add this to the list in case anyone in the galaxy :) knew the answer. I get a mapping error every time I invoke url_for. What variable stores the base url for the galaxy instance? Thanks, Ilya -----Original Message----- From: Chorny, Ilya Sent: Wednesday, October 19, 2011 4:21 PM To: 'James Taylor' Subject: RE: [galaxy-dev] how do I pass the URL of the input and output files to my tool wrapper? Hi James, I got the code working but I can't figure out how to set the URL. I have a hack right now (i.e. url = 'http://' + socket.getfqdn() + config_info.cookie_path + '/datasets/' + sec.encode_id(dataset.id) + '/display/?preview=True' ). I tried using url_for() but was unable to get that to work. Attached are the diff's for the files I made changes to. If you have any suggestions on how to properly set the url please let me know. Thanks, Ilya -----Original Message----- From: James Taylor [mailto:james@jamestaylor.org] Sent: Tuesday, October 18, 2011 11:38 AM To: Chorny, Ilya Subject: RE: [galaxy-dev] how do I pass the URL of the input and output files to my tool wrapper? Hi Ilya, I think any case where $__app__ is used should raise red flags, it is definitely breaking abstraction. In this case, you're passing a very specific implementation detail of the web layer all the way down to your tool. I think the right way to do what you want is to add a 'web_display_url' attribute to the class DatasetFilenameWrapper in tools/__init__.py. Every dataset gets wrapped by this when put into the namespace for building command lines. If you added an attribute it would them be available as ${input.web_display_url} in the command line template. Historically tool wrappers were designed so that they have no knowledge of the UI, allowing non-web UIs to be added on top. At this point it seems unlikely that this will ever happen, but it is still a good idea to avoid this kind of coupling. Otherwise we can't change how the web interface does security without changing individual tools. Excerpts from Chorny, Ilya's message of 2011-10-17 22:56:40 +0000: > So we came up with a work around and I wouldn't mind getting your opinion on it. Specifically with respect to passing cookie_path. I could not figure out how to get the proxy prefix from the universe_wsgi.ini file via the $__app__ call. Also you mention in the wiki the the $__app__ may get deprecated. > > Thanks, > > Ilya > > > We copied the encryption code (i.e) > > def encode_id(dataset_id,id_secret): > id_cipher = Blowfish.new(id_secret) > s = dataset_id > s = ( "!" * ( 8 - len(s) % 8 ) ) + s > encrypted_id = id_cipher.encrypt( s ).encode( 'hex' ) > return encrypted_id > > and we passed to the too wrapperl: > > -i input -i $input.dataset.id > > as well as > > --id_secret=$__app__.config.id_secret > --cookie_path=$__app__.config.cookie_path > > -----Original Message----- > From: Chorny, Ilya > Sent: Monday, October 17, 2011 11:10 AM > To: Chorny, Ilya; James Taylor > Cc: galaxy-dev > Subject: RE: [galaxy-dev] how do I pass the URL of the input and output files to my tool wrapper? > > Would it be difficult to add the url as an attribute of the input and output parameters ($param.url)? If you point me to where these values are set, I can try to make the changes to the code. > > Thanks, > > Ilya > > > -----Original Message----- > From: galaxy-dev-bounces(a)lists.bx.psu.edu > [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Chorny, Ilya > Sent: Sunday, October 16, 2011 7:36 AM > To: James Taylor > Cc: galaxy-dev > Subject: Re: [galaxy-dev] how do I pass the URL of the input and output files to my tool wrapper? > > PDF report. > > Sent from my iPhone > > On Oct 15, 2011, at 7:36 PM, "James Taylor" <james(a)jamestaylor.org> wrote: > > > Excerpts from Chorny, Ilya's message of 2011-10-14 23:46:25 +0000: > >> Anyone know if it possible to pass the url (shown in the eye ball) to a tool wrapper? > > > > Ilya, this isn't currently supported because it breaks the > > abstraction between the web interface and tools (tools shouldn't > > know they are being invoked by a web application). What are you trying to achieve with this? > > Is this for a tool generating an HTML report? > > -- > > James Taylor, Assistant Professor, Biology / Computer Science, Emory > > University > > ___________________________________________________________ > > 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: > > > > http://lists.bx.psu.edu/ > > ___________________________________________________________ > 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: > > http://lists.bx.psu.edu/ -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University

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Few possible galaxy bugs ?
by michael burrell (TOC) 24 Oct '11

24 Oct '11

Good Morning, I am just in the process of updating our development galaxy, the following issues are been reported and I am unable to resolved them, would anyone have any suggestions. Just a little more background info, galaxy@jic55666:~/software/galaxy-central$ hg tip changeset: 6143:6c8695c2a949 tag: tip user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Oct 19 16:47:25 2011 -0400 summary: Enhanced Galaxy instance <=> Galaxy tool shed integration: galaxy@jic55666:~/software/galaxy-central$ python --version Python 2.6.6 the errors reported.... ==== galaxy.tools DEBUG 2011-10-20 13:18:47,691 Loaded tool: hmmscan 1.0.0 docutils WARNING 2011-10-20 13:18:47,697 <string>:2: (WARNING/2) Inline strong start-string without end-string. docutils WARNING 2011-10-20 13:18:47,700 <string>:17: (ERROR/3) Unexpected indentation. ==== galaxy.tools ERROR 2011-10-20 13:18:47,722 error reading tool from path: toolshed/nlstradamus/tools/protein_analysis/nlstradamus.txt Traceback (most recent call last): File "/home/galaxy/software/galaxy-central/lib/galaxy/tools/__init__.py", line 106, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/home/galaxy/software/galaxy-central/lib/galaxy/tools/__init__.py", line 186, in load_tool tree = util.parse_xml( config_file ) File "/home/galaxy/software/galaxy-central/lib/galaxy/util/__init__.py", line 105, in parse_xml tree = ElementTree.parse(fname) File "/home/galaxy/software/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/galaxy/software/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 583, in parse parser.feed(data) File "/home/galaxy/software/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 1242, in feed self._parser.Parse(data, 0) ExpatError: syntax error: line 1, column 0 ==== galaxy.tools DEBUG 2011-10-20 13:18:50,172 Loaded tool: tophat 1.5.0 docutils WARNING 2011-10-20 13:18:50,208 <string>:50: (WARNING/2) Literal block expected; none found. galaxy.tools.test DEBUG 2011-10-20 13:18:50,221 Error in add_param for min_coverage_intron: Unable to determine parameter type of test input 'min_coverage_intron'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2011-10-20 13:18:50,222 Error in add_param for max_coverage_intron: Unable to determine parameter type of test input 'max_coverage_intron'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools DEBUG 2011-10-20 13:18:50,222 Loaded tool: tophat_color 1.0.0 galaxy.tools DEBUG 2011-10-20 13:18:50,255 Loaded tool: cufflinks 0.0.5 galaxy.tools DEBUG 2011-10-20 13:18:50,428 Loaded tool: cuffcompare 0.0.5 galaxy.tools DEBUG 2011-10-20 13:18:50,462 Loaded tool: cuffdiff 0.0.5 ==== galaxy.tools DEBUG 2011-10-20 13:18:51,301 Loaded tool: rgManQQ1 1.0.3 galaxy.tools.test DEBUG 2011-10-20 13:18:51,323 Error in add_param for force: Unable to determine parameter type of test input 'force'. Ensure that the parameter exists and that any container groups are defined first. ========= ----------------------------------------------------------------------------------------------------- Please note, that my email address is no longer givenname.surname(a)bbsrc.ac.uk. Please update your records to reflect my new email address of givenname.surname(a)nbi.ac.uk as shown on this email.

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