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

problem with build_chrom_db.py
by Curt Palm 22 Aug '11

22 Aug '11

I've been configuring my local instance of galaxy to use trackster according to the instructions on https://bitbucket.org/galaxy/galaxy-central/wiki/Visualization when I run the script: python ./cron/build_chrom_db.py ./tool-data/shared/ucsc/chrom/ I get files that begin with: <META http-equiv="Content-Script-Type" content="text/javascript"> chr1 247249719 chr1_random 166326 ... this causes an error in the browser: "Could not load chroms for this dbkey:" if i delete the first line " <META http-equiv="Content-Script-Type" content="text/javascript">" from the .len file, then trackster works fine. I'm thinking there is a new line the input to build_chrom_db.py that is not getting stripped by this script thanks, Curt Palm ******************************************************* Curtis J. Palm cpalm(a)stanford.edu Stanford Genome Technology Center MC: 8307 office: 650-812-1994 cell: 408 858-7849 *******************************************************

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Request for pulling the updated FASTQ (de-)interlacer tool
by Florent Angly 05 Aug '11

05 Aug '11

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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minor bug: double-quotes in dataset name
by Assaf Gordon 01 Aug '11

01 Aug '11

Hello, There's a small bug when entering a double-quote character in a dataset name: The double-quote confuses some later-on processing (templates and Display-Application XML), resulting in some problems. Example: This history has one BAM dataset with a name of: Hello "world" http://main.g2.bx.psu.edu/u/foobar/h/double-quotes-bug If you try to rename it (by clicking the "pencil" icon), you'll see only the "hello" part. If you try to load the BAM to the UCSC Genome browser, it will fail with this error message: Missing bigDataUrl setting from track of type=bam (Hello ) -gordon

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visual cue for <conditional> group parameters
by Assaf Gordon 01 Aug '11

01 Aug '11

Hi, The following tiny patch adds a light-gray visual cue in the html form, to give a better idea as to which parameters go together. It looks acceptable even with nested <conditional> parameters. See it in action here: http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_bowtie_pe1 http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_tophat_pe1 It might not be the prettiest thing, but it works nicely with minimal code changes. Patch is here: http://cancan.cshl.edu/labmembers/gordon/files/conditional-group-css2.patch Comments are welcomed, -gordon

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wrong static image URL when clicking re-run
by Assaf Gordon 01 Aug '11

01 Aug '11

Hi, A small bug: When clicking "re-run" to view a tool form, and the tool has embedded images, the URL of the images is not working. When viewing a tool that has embedded images, the relative <img> URL is "./static/images/histogram2.png". The tool's URL comes from: "http://main.g2.bx.psu.edu/tool_runner?tool_id=histogram_rpy" and so the absolute image URL becomes: "http://main.g2.bx.psu.edu/./static/images/histogram2.png" which works OK. But when viewing a tool by clicking "re-run", the tool's URL is: "http://main.g2.bx.psu.edu/galaxy/tool_runner/rerun?id=56" ("rerun" being a method in the "tool_runner" controller), which in turns makes the image absolute URL: "http://main.g2.bx.psu.edu/tool_runner/./static/images/XXXXX.png" - and it doesn't work. Note that the solution of changing all the images URLs in the XML files to start at the root (e.g. "/static/images/XXXX.png") is not optimal, because it will bypass the "prefix" URL that some people use (e.g. with "http://rave.cshl.edu/galaxy" instead of "http://rave.cshl.edu/"). a workaround (when using apache) is to add the following rewrite_rule: RewriteRule ^/tool_runner/static/(.*) /localdata1/galaxy/galaxy_prod/static/$1 [L] Or if using a "/galaxy" prefix: RewriteRule ^/galaxy/tool_runner/static/(.*) /localdata1/galaxy/galaxy_prod/static/$1 [L] -gordon

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removing "Select All" / "Unselect All" buttons from a set of check boxes
by Hans-Rudolf Hotz 13 Jul '11

13 Jul '11

Hi Is there a way to remove the "Select All" and "Unselect All" buttons from a set of check boxes? - crated with: <param name="samples" type="select" display="checkboxes" multiple="true" dynamic_options="ds_samplesFromServer()"/> I have a very long list, and I don't want to encourage people to tick all boxes. Thank you very much for your help, Hans

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Re: [galaxy-dev] LAJ Error
by Ellul Jason 13 Jul '11

13 Jul '11

Hi All, I have been able to workaround the problem I was having by modifying the LAJ_code.py to include 'and data != None' on each of the elif statements. i.e. if name == "maf_input": params["alignfile1"] = "display?id=%s" % data.id elif name == "seq_file1" and data != None and data.state == data.states.OK and data.has_data(): params["file1seq1"] = "display?id=%s" % data.id elif name == "seq_file2" and data != None and data.state == data.states.OK and data.has_data(): params["file1seq2"] = "display?id=%s" % data.id elif name == "exonfile" and data != None and data.state == data.states.OK and data.has_data(): params["exonfile"] = "display?id=%s" % data.id elif name == "repeatfile" and data != None and data.state == data.states.OK and data.has_data(): params["repeatfile"] = "display?id=%s" % data.id elif name == "annotationfile" and data != None and data.state == data.states.OK and data.has_data(): params["annotationfile"] = "display?id=%s" % data.id elif name == "underlayfile" and data != None and data.state == data.states.OK and data.has_data(): params["underlayfile"] = "display?id=%s" % data.id elif name == "highlightfile" and data != None and data.state == data.states.OK and data.has_data(): params["highlightfile"] = "display?id=%s" % data.id For some reason, even though repeatfile is optional the script always thinks that a file has been selected, even when one has not. Hence data is equal to None and it throws a 'nonetype has no attribute state' error when it checks data.state==data.states.OK. Could a developer please look into why it would think a file for the option repeatfile had been selected when one hasn't. Cheers, -- 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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how to purge histories/datasets not accessed/updated for a certain time
by Chaolin Zhang 13 Jul '11

13 Jul '11

Hi, We have a local mirror of the galaxy system and the disk is occupied really quickly. Is there a way to purge histories/datasets not accessed/updated for a certain period of time, no matter if they are deleted by the user? It looks like the current scripts for clean up only purges deleted histories/datasets. Thanks! Chaolin

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plotting/statistics tools suggestion
by Marshall Hampton 12 Jul '11

12 Jul '11

I've just started seriously looking at Galaxy, and I already have a suggestion (everyone's a critic...): switch from using rpy or even rpy2 to scipy/numpy/matplotlib for basic statistics and plots. I wrestled a bit with getting rpy to work on my local setup and decided it would be quicker to write my own plotting tool extensions, which indeed turned out to be the case. Since you already require python it seems much more natural to use python-native tools. To give some positive feedback, learning to write an extension was surprisingly easy and encourages me to work on more. I use currently use Sage (http://www.sagemath.org/) to both analyze next-generation sequence data (454 and Illumina) and create interactive tools for the biologists I collaborate with. The Sage project involves many of the same issues and challenges facing Galaxy. Sage is based on python, but includes R. I realize that there are many things you would want to do with R that aren't included in scipy/biopython, so it might be worthwhile to look at how Sage wraps R. Its far from perfect, but I prefer it to rpy2. In the Sage source tree the interface is at: $SAGE_ROOT/devel/sage/sage/interfaces/r.py. (Ugly online copy at: http://hg.sagemath.org/sage-main/file/361a4ad7d52c/sage/interfaces/r.py) -Marshall Hampton Department of Mathematics and Statistics and the Integrated Biosciences Program University of Minnesota Duluth

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suggestions for the SAM-to-BAM tool
by Assaf Gordon 06 Jul '11

06 Jul '11

Hi, Couple of things that can be slightly improved in the SAM-to-BAM tool: 1. "Reference list" is not informative (it's the technical way to say: "list of chromosomes and their sizes based on a FASTA file"). Users do not generally know what "reference list" is. 2. The "Locally Cached" option is not informative (I had to look in the source code to understand what it means). What it should say is something like: "Get list of chromosomes/sizes based on the dataset's organism/database" (could be shorter, but should be friendly enough). 3. There's no option of having the chromosome list in the SAM file header. Some SAM files will contain the header (can even be done in the standard bowtie tool wrapper) - saves the need to specify where to get the "reference list" from. 4. Autodetection in the "set-metadata" step will go a long way here: if the SAM file already have a header, then no need to even ask about it. If it doesn't have a header but have a DBKEY, then we're still OK. If no DBKEY and no header, then complain or ask for a FASTA file from current history. (I realize the implementing this feature is hard and annoying, I don't imply that it's easy to do, just that it's needed). 5. Inside the python script (sam_to_bam.py) there's a comment that says: "for some reason the samtools view command gzips the resulting bam file without warning" . Not sure why one cares about that, but "samtools view -u" will output an uncompressed BAM file. 6. samtools support piping, so a lot of I/O (and some time) can be spared by piping the two commands together: samtools view -u -b -S "INPUT.SAM" | samtools sort - OUTPUT Instead of running two commands and generating a temporary unsorted BAM file. -gordon

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