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

importing annotation with dataset
by Davide Cittaro 01 Jul '11

01 Jul '11

Hi, is it just me or when I try to import a dataset from a library to a history, annotation is not retained (whereas "info" is)? d /* Davide Cittaro, PhD Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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importing into history from library
by Glen Beane 01 Jul '11

01 Jul '11

We're running the latest galaxy-dist and noticed a problem importing files from libraries into our history. If we click the down arrow to the right of a dataset and choose "Import this dataset into selected histories" it works fine, however if our datasets are in folders within the library and we select multiple datasets and then do "Import selected datasets into histories" nothing happens. If I go to a library with datasets that are not in a folder then selecting multiple works. Has anyone else seen this? -- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153

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bwa failure preparing job
by Branden Timm 29 Jun '11

29 Jun '11

Hi All, I'm having issues running BWA for Illumina with the latest version of Galaxy (5433:c1aeb2f33b4a). It seems that the error is a python list error while preparing the job: Traceback (most recent call last): File "/home/galaxy/galaxy-central/lib/galaxy/jobs/runners/local.py", line 58, in run_job job_wrapper.prepare() File "/home/galaxy/galaxy-central/lib/galaxy/jobs/__init__.py", line 371, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/home/galaxy/galaxy-central/lib/galaxy/tools/__init__.py", line 1575, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/home/galaxy/galaxy-central/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/home/galaxy/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 106, in respond IndexError: list index out of range I checked the bwa_index.loc file for errors, it seems that the line for the reference genome I'm trying to map against is correct (all whitespace is tab characters): synpcc7002 synpcc7002 Synechococcus /home/galaxy/galaxy-central/bwa_ indices/SYNPCC7002 I'm not sure what the next troubleshooting step is, any ideas? -- Branden Timm btimm(a)glbrc.wisc.edu

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galaxy with SGE cluster
by Shantanu Pavgi 17 Jun '11

17 Jun '11

I need some help in configuring galaxy with SGE scheduler using unified method. The galaxy is running on a system distinct from SGE scheduler install. The cluster nodes can access galaxy install, galaxy-tools and dataset files using NFS. I am not sure how drmaa works and how galaxy submits jobs to the cluster/scheduler. Do we need specify some type of connection string or ssh-config to connect with the cluster/scheduler? Does it need any configuration changes on the SGE scheduler side? Any explanation regarding this will be really helpful. -- Thanks, Shantanu.

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API
by Frederick van Staden 16 Jun '11

16 Jun '11

Anyone know where i can get the galaxy API? Regards Fred

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Fwd: Request for pulling the updated FASTQ (de-)interlacer tool
by Florent Angly 10 Jun '11

10 Jun '11

Let me know if you have any questions about this. Thanks, Florent -------- Original Message -------- Subject: Request for pulling the updated FASTQ (de-)interlacer tool Date: Tue, 17 May 2011 17:47:13 +1000 From: Florent Angly <florent.angly(a)gmail.com> To: galaxy-dev(a)lists.bx.psu.edu <galaxy-dev(a)lists.bx.psu.edu> Dear Galaxy team, Please consider pulling these changes I made to the interlacer/de-interlacer tools into the main Galaxy repository: https://bitbucket.org/fangly/galaxy-central/changeset/7f7ec8f05d36 While the tools were handling mate pairs fine, I now added the ability to also keep single reads (reads that miss their mate) in a separate file. The functional tests were updated and pass. Thanks, Florent

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select menu in conditional tag cannot be set at runtime in workflow editor
by Leandro Hermida 09 Jun '11

09 Jun '11

Hi all, In a tool XML I have a select menu param within/driving a conditional tag and in the workflow editor it doesn't let me choose to allow the user to set this select menu at runtime? Is this a bug? best, leandro

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AttributeError: 'list' object has no attribute 'missing_meta' when doing multiple="true" input datasets
by Leandro Hermida 09 Jun '11

09 Jun '11

Hi, I have a tool where the input is multi-select of datasets, e.g.: <param type="data" multiple="true" name="input1" /> I tested it to see what it would pass to my command and I get the following debug page and error in Galaxy: AttributeError: 'list' object has no attribute 'missing_meta' The last part of the stack trace looks like: >> validator.validate( value, history ) Module galaxy.tools.parameters.validation:185 in validate history <galaxy.model.History object at 0xb8ea190> self <galaxy.tools.parameters.validation.MetadataValidator object at 0xb8e6250> value [<galaxy.model.HistoryDatasetAssociation object at 0xa255550>, <galaxy.model.HistoryDataset ... Association object at 0xb8ea210>] >> if value and value.missing_meta( check = self.check, skip = self.skip ): AttributeError: 'list' object has no attribute 'missing_meta' What am I doing wrong? regards, Leandro

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Update of cufflinks
by Sarah Diehl 06 Jun '11

06 Jun '11

Hello everybody, I just found out that there was a major update to cufflinks on 5/5/2011. At least for us it now makes no sense anymore to use the old version, besides the fact that the cufflinks team highly recommends upgrading. Does anybody already have new wrappers for all the cuff... tools ready? Do you know if/when the Galaxy codebase will be updated to the new cufflinks version? Best regards, Sarah

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Blast2GO in Galaxy
by Peter Cock 03 Jun '11

03 Jun '11

Hi all, As I mentioned on Twitter, at the end of last week I wrapped Blast2GO for Galaxy, using the b2g4pipe program (Blast2GO for pipelines). See http://blast2go.org/ Currently current code is on bitbucket under my tools branch, https://bitbucket.org/peterjc/galaxy-central/src/tools/ Specifically files tools/ncbi_blast_plus/blast2go.* viewable here: https://bitbucket.org/peterjc/galaxy-central/src/tools/tools/ncbi_blast_plu… I've using a Galaxy location file, tool-data/blast2go.loc, to offer one or more Blast2GO configurations (properties files), mapping this to the -prop argument. This way you could have for example the Spanish Blast2GO server with its current database (May 2010), and a local Blast2GO database. I want to setup a local database and try this before submitting the wrapper to the Tool Shed. The input to the tool is a BLAST XML file, specifically blasting against a protein database like NR (so blastp or blastx, not blastn etc). I want to try some very large BLAST XML files to confirm b2g4pipe copes with the current BLAST+ output files - I gather there were some problems in this area in the past, so having the wrapper script fragment the XML might be a workaround. Currently the only real function of the wrapper script is to rename the output file - b2g4pipe insists on using the *.annot extension. Right now the only output is a tabular three column *.annot file, which can be loaded into the Blast2GO GUI. For analysis within Galaxy, I'm wondering about an option to split the first column (which holds the original FASTA query's identifier and any description) in two. i.e. Split at the first white space to give the FASTA identifier, and any optional description as a separate column. That would make linking/joining/filtering on the ID much easier. If anyone has any comments or feedback now, that would be welcome. Yesterday Alex Bossers indicated on Twitter that Gerrit had also been looking at this (CC'd). Regards, Peter

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