May 2011 - galaxy-dev - lists.galaxyproject.org

LAJ Error
by Ellul Jason 04 May '11

04 May '11

Hi All, I am attempting to do a local install of Galaxy using the galaxy-dist source. While testing some of the the tools I have run into a problem with the laj Pairwise Alignment Viewer tool. I have also tested this on the test server http://test.g2.bx.psu.edu/ and I am getting a very similar error. I have used blastz to create a test lav file. On http://test.g2.bx.psu.edu/ the error is: Traceback (most recent call last): File "/var/opt/galaxy/g2test/galaxy_test/lib/galaxy/jobs/runners/pbs.py", line 514, in finish_job pbs_job_state.job_wrapper.finish( stdout, stderr ) File "/var/opt/galaxy/g2test/galaxy_test/lib/galaxy/jobs/__init__.py", line 630, in finish tool=self.tool, stdout=stdout, stderr=stderr ) File "/var/opt/galaxy/g2test/galaxy_test/lib/galaxy/tools/__init__.py", line 1664, in call_hook return code( *args, **kwargs ) File "./tools/visualization/LAJ_code.py", line 24, in exec_after_process elif name == "repeatfile" and data.state == data.states.OK and data.has_data(): AttributeError: ('E', 'r', 'r', 'o', 'r', ' ', 'i', 'n', ' ', "'", 'L', 'A', 'J', "'", ' ', 'h', 'o', 'o', 'k', ' ', "'", 'e', 'x', 'e', 'c', '_', 'a', 'f', 't', 'e', 'r', '_', 'p', 'r', 'o', 'c', 'e', 's', 's', "'", ',', ' ', 'o', 'r', 'i', 'g', 'i', 'n', 'a', 'l', ' ', 'm', 'e', 's', 's', 'a', 'g', 'e', ':', ' ', "'", 'N', 'o', 'n', 'e', 'T', 'y', 'p', 'e', "'", ' ', 'o', 'b', 'j', 'e', 'c', 't', ' ', 'h', 'a', 's', ' ', 'n', 'o', ' ', 'a', 't', 't', 'r', 'i', 'b', 'u', 't', 'e', ' ', "'", 's', 't', 'a', 't', 'e', "'") While on my local install it is : Traceback (most recent call last): File "/storage/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 125, in run_job job_wrapper.finish( stdout, stderr ) File "/storage/galaxy-dist/lib/galaxy/jobs/__init__.py", line 630, in finish tool=self.tool, stdout=stdout, stderr=stderr ) File "/storage/galaxy-dist/lib/galaxy/tools/__init__.py", line 1632, in call_hook return code( *args, **kwargs ) File "./tools/visualization/LAJ_code.py", line 24, in exec_after_process elif name == "repeatfile" and data.state == data.states.OK and data.has_data(): AttributeError: ('E', 'r', 'r', 'o', 'r', ' ', 'i', 'n', ' ', "'", 'L', 'A', 'J', "'", ' ', 'h', 'o', 'o', 'k', ' ', "'", 'e', 'x', 'e', 'c', '_', 'a', 'f', 't', 'e', 'r', '_', 'p', 'r', 'o', 'c', 'e', 's', 's', "'", ',', ' ', 'o', 'r', 'i', 'g', 'i', 'n', 'a', 'l', ' ', 'm', 'e', 's', 's', 'a', 'g', 'e', ':', ' ', "'", 'N', 'o', 'n', 'e', 'T', 'y', 'p', 'e', "'", ' ', 'o', 'b', 'j', 'e', 'c', 't', ' ', 'h', 'a', 's', ' ', 'n', 'o', ' ', 'a', 't', 't', 'r', 'i', 'b', 'u', 't', 'e', ' ', "'", 's', 't', 'a', 't', 'e', "'") Any help would be appreciated, Thanks, -- Jason Ellul Bioinformatician Cancer Research Division Peter MacCallum Cancer Centre TEL: +61 3 9656 1512 FAX: +61 3 9656 1411 EMAIL: jason.ellul(a)petermac.org Address: St Andrew's Place East Melbourne Victoria 3002 Australia Postal Address: Locked Bag No. 1 A'Beckett St., Victoria, 8006, Australia This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

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Version Error and Python 2.7
by John David Osborne 04 May '11

04 May '11

I have (or rather had) a functional galaxy installation on a CentOS box running python 2.4. I did an mecurial update for the first time and broke my installation. It looks like some eggs are getting out of date and when I run scramble.py I get an error (see below). I'm guessing this is because scramble expects python 2.5 or above for the import (import in 2.4 I don't believe takes arguments). My question is does galaxy really still support 2.4 and should I move to python 2.7 (the current stable version) because the wiki just mentions versions 2.4 to 2.6 as being supported. -John run_scramble_script(): Executing in /home/galaxy/galaxy_dist/scripts/scramble/build/py2.4/python_daemon: /usr/bin/python -ES scramble.py Traceback (most recent call last): File "scramble.py", line 29, in ? execfile( "setup.py", globals(), locals() ) File "setup.py", line 22, in ? main_module = __import__(main_module_name, fromlist=['version']) TypeError: __import__() takes no keyword arguments scramble(): Egg already exists, remove to force rebuild: /home/galaxy/galaxy_dist/eggs/nose-0.11.1-py2.4.egg scramble(): Egg already exists, remove to force rebuild: /home/galaxy/galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.4.egg scramble(): Egg already exists, remove to force rebuild: /home/galaxy/galaxy_dist/eggs/WebOb-0.8.5-py2.4.egg scramble(): Egg already exists, remove to force rebuild: /home/galaxy/galaxy_dist/eggs/PasteScript-1.7.3-py2.4.egg Traceback (most recent call last): File "scripts/scramble.py", line 23, in ? eggs = c.scramble() File "/home/galaxy/galaxy_dist/lib/galaxy/eggs/scramble.py", line 243, in scramble raise last_exc # only 1 failure out of the crate, be more informative galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for python_daemon 1.5.5

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Basic HTML markup in loc files (e.g. italics in descriptions)
by Peter Cock 03 May '11

03 May '11

Hi all, In biology we often want to use italics, the key examples that come to mind are species and gene names. I think it is natural therefore to want to be able to use italics in the description of data resources in Galaxy's loc files. For example, in our local Galaxy for the BLAST databases listed in blastdb.loc and blastdb_p.loc, I currently have some <i>Species name</i> entries (using the HTML i tag for italics). [I originally compiled our BLASTDB loc files from our existing configuration files for wwwblast, where the HTML italics tags worked.] In the Galaxy BLAST+ tools, the select database parameter field shows these entries in plain text (with no italics styling, and without the HTML tags). I'm not confident about this looking back, but would this ever have shown the italics? It would be nice if it did... Is this sanitation (removing the tags) deliberate? This brings me to my next question - I'm working on a wrapper for the NCBI BLAST+ tool blastdbcmd, and setup the output file as follows in the tool XML: <outputs> <data name="seq" format="fasta" label="Sequences from ${db_opts.database.fields.name}" /> </outputs> This works, but in the right hand history panel, the dataset name is shown with the raw HTML tags from the loc file (in this case when I have a species specific BLAST database, the user sees the < i > and < /i > tags around the species name). So, there is an inconsistency: The select parameter seems to sanitize the tags, the output label does not. Ideally I would like both to support italics and bold, but would settle on both being sanitised. If this is not intended to work, I'll just remove the italics tags from our BLAST loc files. If this is intended to work, should I file an issue on bitbucket? Thanks, Peter

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Question Regarding Local Galaxy Installation Uploading Files Error
by George Yianni Michopoulos 03 May '11

03 May '11

To any wonderful person that can help me: I recently uploaded a local instance of Galaxy on a new computer at the Fernald Lab at Stanford. I am not too familiar with Unix, but needed to install the local instance due to the high volume of genomic data we will be processing, and so that we could install/use the FastX toolkit. I managed to successfully install the toolkit, but now I just realized that I can't seem to upload any of my correctly formatted data files. The error I get is pasted below: "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_4; en-us) AppleWebKit/533.18.1 (KHTML, like Gecko) Version/5.0.2 Safari/533.18.5" Debug at: http://localhost:8080/_debug/view/1303859435 ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 61553) Traceback (most recent call last): File "/Users/***/bin/fastx_bin/galaxy_test/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/***/bin/fastx_bin/galaxy_test/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/***/bin/fastx_bin/galaxy_test/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 427, in handle_one_request self.wsgi_execute() File "/Users/***/bin/fastx_bin/galaxy_test/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 287, in wsgi_execute self.wsgi_start_response) File "/Users/***/bin/fastx_bin/galaxy_test/eggs/Paste-1.6-py2.6.egg/paste/urlmap.py", line 202, in __call__ return app(environ, start_response) File "/Users/***/bin/fastx_bin/galaxy_test/lib/galaxy/web/framework/middleware/xforwardedhost.py", line 21, in __call__ return self.app( environ, start_response ) File "/Users/***/bin/fastx_bin/galaxy_test/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/***/bin/fastx_bin/galaxy_test/lib/galaxy/web/framework/middleware/translogger.py", line 68, in __call__ return self.application(environ, replacement_start_response) File "/Users/***/bin/fastx_bin/galaxy_test/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py", line 226, in __call__ return self.respond(environ, start_response) File "/Users/***/bin/fastx_bin/galaxy_test/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py", line 399, in respond if self.xmlhttp_key in req.params: File "/Users/***/bin/fastx_bin/galaxy_test/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py", line 900, in params params = self.str_params File "/Users/***/bin/fastx_bin/galaxy_test/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/***/bin/fastx_bin/galaxy_test/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/***/bin/fastx_bin/galaxy_test/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/***/bin/fastx_bin/galaxy_test/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" (I replaced irrelevant components of the file path with *** for confidentiality purposes) Do you have any idea what the problem is and how I can fix it? I feel like it has something to do with my python, but I downloaded 2.6.6, which I thought should work according to the Install Readme. Thanks so much for your help! Sincerely, George Michopoulos Stanford University '13 on behalf of the Fernald Lab

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Re: [galaxy-dev] [galaxy-user] Removing deleted datasets
by Nate Coraor 03 May '11

03 May '11

Simon Lank wrote: > Hi. > > Our current galaxy database is ~ 600 gb, most of which are user deleted > datasets. > > I followed the instructions here: > https://bitbucket.org/galaxy/galaxy-central/wiki/Config/PurgeHistoriesAndDa… > > and ran the shell scripts in recommended order. One of them in particular (I > think it was purge_histories.sh) took amost 24 hours to complete. However, > it doesn't appear any / most of the files were actually deleted, since we > still have ~ 600 gb of dataset files. Is there something obvious I can try > to get the files purged correctly? Hi Simon, I've moved this conversation to the -dev list since it involves a local installation. Datasets are not removed until the number of days specified with the -d to cleanup_datasets.py has elapsed. To remove all deleted data immediately, rerun the scripts outside of the provided wrappers and set -d to 0. --nate > > Thanks. > > Simon > > Simon Lank > Research Specialist > O'Connor Lab, WNPRC > 555 Science Dr. Madison WI > (608) 265-3389 > ___________________________________________________________ > 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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tool parameter attribute for option display value (not passed value)?
by Leandro Hermida 02 May '11

02 May '11

Hi, For a tool select input parameter: <param name="input1" type="select"> <option value="hs33">Homo sapiens</option> <option value="mm19">Mus musculus</option> <option value="rn43">Rattus norvegicus</option> </param> Is there an attribute for the variable $input1 that will give me the displayed value (e.g. Homo sapiens, not hs33)? thank you, Leandro

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