October 2010 - galaxy-dev - lists.galaxyproject.org

megablast installation in Galaxy
by Eric Enns 05 Oct '10

05 Oct '10

Hi I am implementing a local installation of galaxy and am stuck on the megablast portion. I installed blast 2.2.24 which includes formatdb and megablast. The installation guide says to use BLAST+, but that does not have megablast or formatdb in it. The megablast installation I have does not output in the correct format. How do I install BLAST+ so that it will work in galaxy. -Eric

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Setting default entry in select parameter
by Peter 05 Oct '10

05 Oct '10

Hi all, I'm trying to setup a select parameter where I want to pre-select an entry as the default (rather than just the first entry). To that end, I have set the value attribute as implied by the wiki documentation: http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax e.g. <param name="matrix" type="select" value="BLOSUM62" label="Scoring matrix"> <option value="BLOSUM80">BLOSUM80</option> <option value="BLOSUM62">BLOSUM62 (default)</option> <option value="BLOSUM50">BLOSUM50</option> <option value="BLOSUM45">BLOSUM45</option> <option value="PAM250">PAM250</option> <option value="BLOSUM90">BLOSUM90</option> <option value="PAM30">PAM30</option> <option value="PAM70">PAM70</option> </param> This does not work - Galaxy (in Firefox at least) always defaults to the first entry as the default. This also happens if I set display="radio". Is this a bug, is setting a default for select parameters done in another way, or is this a missing feature? For now I have just put the default at the top, breaking the alphabetic order: <param name="matrix" type="select" label="Scoring matrix"> <option value="BLOSUM62">BLOSUM62 (default)</option> <option value="BLOSUM80">BLOSUM80</option> <option value="BLOSUM50">BLOSUM50</option> <option value="BLOSUM45">BLOSUM45</option> <option value="PAM250">PAM250</option> <option value="BLOSUM90">BLOSUM90</option> <option value="PAM30">PAM30</option> <option value="PAM70">PAM70</option> </param> Regards, Peter

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Managing galaxy-central in a local svn repo
by Branden Timm 05 Oct '10

05 Oct '10

Hello, I am trying to figure out the best way to use subversion to track both galaxy-central and our local tool integration work. We are standardized on subversion, so I'd like to use it if possible. What I've done so far: Downloaded the latest galaxy-central 'hg clone https://bitbucket.org/galaxy/galaxy-central' Copied galaxy-central, including mercurial info, into the /trunk subdirectory of my repo. My plan is that when future revisions to galaxy-central are available, I can create a new branch, use hg pull to update the codebase, test, and finally merge that branch back into /trunk. I noticed that just the size of the galaxy-central mercurial repo is about 230M. Is this because back-versions are being included? If so, should I just do a clone to the most recent revision and then use 'hg pull' to apply future revisions? Cheers -- Branden Timm University of Wisconsin Great Lakes Bioenergy Research Center btimm(a)glbrc.wisc.edu

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Implementation of data connection protocol
by Zhe Chen 05 Oct '10

05 Oct '10

Hi, Can u tell me how to implement the "send query to galaxy" button on page http://genome.ucsc.edu/cgi-bin/hgTables ? which is the tool in (Get Data)->(UCSC Main tool), on page 2. Do you have any sample code beside http://bitbucket.org/galaxy/galaxy-central/wiki/DataSources? Thanks

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Using rsyslog for logging from Galaxy
by Peter 05 Oct '10

05 Oct '10

Hi all, For our production server we are using rsyslog for centralised logging, http://www.rsyslog.com/ Galaxy is using "import logging" which can output to rsyslog, using SysLogHandler rather than StreamHandler or FileHandler. Based on grep'ing the source code Galaxy doesn't support this yet. I could probably add it but it isn't clear to me where this would be done... functions configure_logging() in lib/galaxy/config.py and in lib/galaxy/webapps/community/config.py look like strong possibilities but both allow for some global_conf_parser override (and I'm not sure what that does). Has anyone looked at modifying this area before, or could offer some tips? Thanks, Peter

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Re: [galaxy-dev] [galaxy-user] Undocumented tags for tool configuration
by Kelly Vincent 04 Oct '10

04 Oct '10

Jelle, (I've copied this to galaxy-dev since it's more appropriate to that one) The data table approach is fairly new, so there aren't too many examples yet, although more tools are being converted and will be available soon in the distribution. Basically, there are 3 steps to using it: 1. Modify tool_data_table_conf.xml to specify: - the bowtie data table - the column types in the loc file - It should look something like this: <table name="bowtie_indexes"> <columns>name, value</columns> <file path="tool-data/bowtie_indices.loc" /> </table> 2. Create/modify the loc file to correspond with the column types specified in tool_data_table_conf.xml (in this example, the loc file doesn't have to be changed), though we are going to be changing the specification to <columns>value, dbkey, name, path</columns> 3. Modify the Bowtie wrapper to use the data table instead of the loc file directly, replacing this: <options from_file="bowtie_indices.loc"> <column name="value" index="1" /> <column name="name" index="0" /> </options> - with this: <options from_data_table="bowtie_indexes"/> The <actions> in the Bowtie wrapper is used in lieu of the deprecated <code> tag to set the dbkey of the output dataset. In bowtie_wrapper.xml, according to the first action block, if the refGenomeSource.genomeSource is "indexed" (not "history"), then it will assign the dbkey of the output file to be the same as that of the reference file. It does this by looking at through the loc file and finding the line that has the value that's been selected in the index dropdown box as column 1 of the loc file entry and using the dbkey, in column 0 (ignoring comment lines (starting with #) along the way). If refGenomeSource.genomeSource is "history", it resorts to default behavior for Galaxy, which is that the output is assigned the same value as the first input that has a dbkey specified. The second block would not be needed for most cases--it is required here to handle the specific case of a small reference file we use for functional testing. It says that if the dbkey has been set to "equCab2chrM" (that's what the <filter type="metadata_value"... column="1" /> tag) does then it should be changed to "equCab2" (the <option type="from_param" ... column="0" ...> tag does). If you need more information than this, let us know. Regards, Kelly On Oct 1, 2010, at 4:22 AM, Jelle Scholtalbers wrote: > Hey, > > I was looking through the bowtie_wrapper.xml to get some information > about how to use the tool_data_table_conf.xml. There I also noticed > in the output section the tag <actions>. > Is there any information on this tag as is does seem to be used a lot? > > Cheers, > Jelle > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user

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Update .hgignore for typical Unix editor backup files
by Peter 01 Oct '10

01 Oct '10

Hi all, Would it make sense to add the following to the official .hgignore file to ignore backup files from common Unix editors, *~ *.swp *.bak Thanks, Peter

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target in links
by Belinda M. Giardine 01 Oct '10

01 Oct '10

Am I missing something or is it not possible to set the target in the links from reStructuredText? It would be nice to be able to open help links in a separate window. Belinda

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Error running workflow
by Branden Timm 01 Oct '10

01 Oct '10

Hello, I seem to be having database-related issues when running my workflow. galaxy.jobs DEBUG 2010-09-09 21:14:48,967 dispatching job 180 to local runner galaxy.jobs INFO 2010-09-09 21:14:49,058 job 180 dispatched galaxy.jobs.runners.local DEBUG 2010-09-09 21:14:49,697 executing: soap -a /home/galaxy/galaxy_dist/database/files/000/dataset_400.dat -D /home/galaxy/galaxy_dist/soap_indices/ecoli_U00096.fasta.index -o /home/galaxy/galaxy_dist/database/files/000/dataset_431.dat -u None -r 1 -n 5 -v 2 -M 4 2>&1 galaxy.jobs ERROR 2010-09-09 21:14:50,209 failure running job 181 Traceback (most recent call last): File "/home/galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py", line 185, in __monitor_step self.sa_session.refresh( job ) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/scoping.py", line 127, in do return getattr(self.registry(), name)(*args, **kwargs) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py", line 926, in refresh self._validate_persistent(state) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py", line 1234, in _validate_persistent raise sa_exc.InvalidRequestError( InvalidRequestError: Instance '<Job at 0x1a4074d0>' is not persistent within this Session 146.151.211.150 - - [09/Sep/2010:21:14:48 -0500] "POST /workflow/run?id=f597429621d6eb2b HTTP/1.1" 200 - "http://galaxy.glbrc.wisc.edu/workflow/run?id=f597429621d6eb2b" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_4; en-us) AppleWebKit/533.17.8 (KHTML, like Gecko) Version/5.0.1 Safari/533.17.8" galaxy.jobs ERROR 2010-09-09 21:14:51,219 failure running job 182 Traceback (most recent call last): File "/home/galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py", line 185, in __monitor_step self.sa_session.refresh( job ) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/scoping.py", line 127, in do return getattr(self.registry(), name)(*args, **kwargs) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py", line 926, in refresh self._validate_persistent(state) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/orm/session.py", line 1234, in _validate_persistent raise sa_exc.InvalidRequestError( InvalidRequestError: Instance '<Job at 0x2aaab001acd0>' is not persistent within this Session galaxy.jobs.runners.local DEBUG 2010-09-09 21:14:52,460 execution finished: soap -a /home/galaxy/galaxy_dist/database/files/000/dataset_400.dat -D /home/galaxy/galaxy_dist/soap_indices/ecoli_U00096.fasta.index -o /home/galaxy/galaxy_dist/database/files/000/dataset_431.dat -u None -r 1 -n 5 -v 2 -M 4 2>&1 In Galaxy itself, the SOAP tool returns its results and the rest of the jobs just wait to run. Why am I having these errors? Cheers -- Branden Timm btimm(a)glbrc.wisc.edu

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user interface aspects don't show up right or look right in IE 7
by Leandro Hermida 01 Oct '10

01 Oct '10

Hello, I just had a look and see initially that certain aspects of the Galaxy UI don't show up or don't look right in IE 7, e.g. in the history pane the underlying link on the name of each data object to expand it isn't there. Is IE 7 supported? I dislike IE and don't use it otherwise but am forced to use it in my environment as it's part of there standard client image and it is almost impossible to get another browser like Firefox installed for every user that will use Galaxy. best, Leandro

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