- galaxy-user - lists.galaxyproject.org

[patch] much more efficient fasta tools
by James Casbon 14 Jan '09

14 Jan '09

Hi everyone, I got bored waiting around for the fasta tools to finish so I improved the length filter and fasta to tabular scripts. On a reasonable data set these were taking over ten minutes with the old version. With this version its a few seconds. The improvement comes from not reformatting the data, caching it in memory or building a hash. All of these are unnecessary for these tasks IMO. cheers, James

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debian init scripts
by James Casbon 14 Jan '09

14 Jan '09

Hi All, Attached a debian/ubuntu init script for galaxy if your interested. You could cook up a red hat equivalent from here: http://wiki.pylonshq.com/display/pylonscookbook/Red+Hat+friendly+init.d+scr… cheers, James PS you should really bundle these with your app ;)

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displaying ucsc tracks when using external auth
by James Casbon 12 Jan '09

12 Jan '09

Hi All, When attempting to display a custom track on the UCSC genome browser, galaxy generates a URL such as... http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr1:1-1000&hgt.cu… The first problem I have is that the base url is wrong for the customText - I am using https - is there a way to set that? The customText parameter is the bit that allows UCSC to pick up the data - but it is not going to get past the external auth. Is there a reasonable way to fix this? I suppose there must be a way to bypass the auth if the request comes from UCSC and looks like a certain URL, but is there a better way? thanks, James

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Local Mirror *away* from server root
by Suraj Mukatira 08 Jan '09

08 Jan '09

Hi, I modified the universe_wsgi.ini file as below, based on the FAQ input # ---- HTTP Server ---------------------------------------------------------- [server:main] use = egg:Paste#http port = 8080 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 # ---- Galaxy Web Interface ------------------------------------------------- #[app:main] [composite:main] use=egg:Paste#urlmap[[BR]] /galaxy/=galaxy [app:galaxy] # Specifies the factory for the universe WSGI application paste.app_factory = galaxy.web.buildapp:app_factory log_level = DEBUG ...rest same However I get the following error: LookupError: Entry point 'urlmap[[BR]] /galaxy/=galaxy' not found in egg 'Paste' (dir: /var/www/html/galaxy_dist/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg; protocols: paste.app_factory, paste.composite_factory, paste.composit_factory; entry_points: ) What is wrong with my modification of universe_wsgi.ini Thanks in anticiaption Sm

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bitset problem
by Jose Jorge Galan 02 Jan '09

02 Jan '09

Dear all, I am trying to intersect overlapping pieces of intervals from two queries. When the process finishes I get the following message: "Info: Skipped 2 invalid lines of 1st dataset, 1st line #39: "chrX 153771797 154493114 ", problem: 536870912 is larger than the size of this BitSet (536870912)." How can I solve this problem? I have tried to do the same intersect with the two queries in BED and in interval format, but the results are the same. Thanks in advance, Yours, Jose Jorge Galan, PhD _________________________________________________________________ Invite your mail contacts to join your friends list with Windows Live Spaces. It's easy! http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/friends.aspx…

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Workflows with Tools that use DBKEY
by Assaf Gordon 19 Dec '08

19 Dec '08

Hello, Is there a way to add a tool that needs a 'dbkey' information (that is - a genome metadata information) in an <option> tag to a workflow ? For example: the Lift-Over tool ? Thanks, Gordon.

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Tool XML Question - using option/from_file name in 'label'
by Assaf Gordon 19 Dec '08

19 Dec '08

Hello, I have a tool which has an <option> with 'from_file' attribute: ... <param name="database" type="select" label="Mapping Database"> <options from_file="mapping_filter_databases.txt"> <column name="name" index="1"/> <column name="value" index="0"/> </options> </param> ... I want to use the database name in the label of the output dataset: <outputs> <data format="fasta" name="output_mapped" label="Mappers of $input.name to $database" /> </outputs> The '$database' variables is replaced with the database's filename (the 'value' column). I'd like it to be the 'name' column, but using "$database.name" throws an runtime exception: NotFound: cannot find 'name' while searching for 'database.name' (full backtrace is listed below). Is there a way to display the name instead of the value in an <option> clause ? Thanks! Gordon. URL: http://tango/tool_runner/index File 'build/bdist.solaris-2.11-i86pc/egg/weberror/evalexception/middleware.py', line 364 in respond File 'build/bdist.solaris-2.11-i86pc/egg/paste/debug/prints.py', line 98 in __call__ File 'build/bdist.solaris-2.11-i86pc/egg/paste/wsgilib.py', line 539 in intercept_output File 'build/bdist.solaris-2.11-i86pc/egg/beaker/session.py', line 103 in __call__ File 'build/bdist.solaris-2.11-i86pc/egg/paste/recursive.py', line 80 in __call__ File 'build/bdist.solaris-2.11-i86pc/egg/paste/httpexceptions.py', line 632 in __call__ File '/media/sdb1/galaxy/galaxy_devel/lib/galaxy/web/framework/base.py', line 126 in __call__ body = method( trans, **kwargs ) File '/media/sdb1/galaxy/galaxy_devel/lib/galaxy/web/controllers/tool_runner.py', line 45 in index template, vars = tool.handle_input( trans, params.__dict__ ) File '/media/sdb1/galaxy/galaxy_devel/lib/galaxy/tools/__init__.py', line 708 in handle_input out_data = self.execute( trans, incoming=params ) File '/media/sdb1/galaxy/galaxy_devel/lib/galaxy/tools/__init__.py', line 915 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid ) File '/media/sdb1/galaxy/galaxy_devel/lib/galaxy/tools/actions/__init__.py', line 159 in execute data.name = fill_template( output.label, context=params ) File '/media/sdb1/galaxy/galaxy_devel/lib/galaxy/util/template.py', line 9 in fill_template return str( Template( source=template_text, searchList=[context] ) ) File '<string>', line 28 in respond NotFound: cannot find 'name' while searching for 'database.name'

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MAF alignments
by Stewart Stevens 18 Dec '08

18 Dec '08

Hi, I have a local Galaxy instance. (http://bioanalysis.otago.ac.nz/ galaxy) A problem I'm having is when I try to extract a multiple alignment I get an error, "The MAF source specified (28_WAY_MULTIZ_hg18) appears to be invalid.," The background is that I have downloaded the alignment from http://hgdownload.cse.ucsc.edu/goldenPath and modified the maf_index.loc file according to the commented example. I'm new to python but I did have a look in the debugger and it seems to be missing an index file. The parameters it has loaded from maf_index.loc appear to be as expected. I'm guessing with more looking at the code it will become clear that a script to produce these indexes from mafs needs to be run. Or should these indexes be being built on the fly? Maybe someone can save me a load more digging? Thanks if you can! Cheers, Stewart -- Stewart Stevens Software Developer - Integrated Genomics University of Otago Department of Biochemistry Tel: +64(0)3 479 7863 Fax: +64(0)3 479 7866

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ask a question about MAF alignment file
by Anyuan Guo 11 Dec '08

11 Dec '08

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Suggestion: new tag in tool's XML file (long)
by Assaf Gordon 09 Dec '08

09 Dec '08

Hello, As recently discussed on this mailing list, With long workflows it becomes somewhat difficult to make sense of the datasets names. The 'label' option in the <output> tag is good start, but there's still room for improvement. I propose a new 'tag' element which might help a little bit. Here's an example: I have five tools in a simple workflow: Starting with a FASTQ file, FASTQ-to-FASTA FASTA-clipper, FASTA-collapser, FASTA-filter-by-length, FASTA-low-complexity-repeats-remover. Each tool has an <output> option with a label. The label takes the description of the tool, and the name of the input. Example from the low-complexity-repeats-remove tool: <output> <data format="input" name="output" label="$input.name (without low-complexity repeats)" metadata_source="input" /> </output> Similarly, most of the other tools have a 'label' option in the XML file. The problem is that after running the workflow, the name of each dataset becomes longer and longer, and more cumbersome. Even if I start with a very short name for the initial FASTQ file (e.g. 'AG14'), The other datasets are named like: AG14 (Fasta), AG14 (Fasta) clipped, AG14 (Fasta) clipped collapsed, Filter sequences by length on data 5 Filter sequences by length on data 5 (without low complexity repeats) (The filter-sequences-by-length tool doesn't have a 'label' option with makes the output even worse.) My suggestion: I would like each data set to have a 'tag' - a short name which is carried over from one dataset to the next, without taking the entire dataset's name. This 'tag' is usually just the name of the initial dataset. going back to the previous example, if I use the initial library name as the tag (=AG14), the output of the workflow would look like: AG14 AG14 (Fasta) AG14 (Clipped) AG14 (Collapsed) AG14 (Filtered Sequences) AG14 (without low complexity repeats) I tried to add this functionality to the galaxy source code. I'm aware that the Right Thing to do is probably to add a new column to the relevant database table, and setup the tools to automatically take the tag from one dataset to the next. However, as an intermediate solution, my hack works nicely (I'm attaching pictures of 'before' and 'after :-) ). With this hack, one can use the following 'label' in the XML <output> tag: <outputs> <data format="input" name="output" label="$input.tag clipped" metadata_source="input" /> </outputs> The "$input.tag" extract the tag from the input's name, and puts in the square brackets, so that the next tool will also be able to extract the tag. Here's the added code ( ./lib/galaxy/model/__init__.py ): ... class HistoryDatasetAssociation( object ): ... @property def tag ( self ): #Hack by gordon: #add a '.tag' attribute tag_match = re.search( '\[([^[]+)\]', self.name); if tag_match: tag = "[" + tag_match.group(1) + "]" ; else: tag = "[" + self.name + "]" ; return tag Thanks for reading so far, Any comments and welcomed, Gordon.

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