- galaxy-user - lists.galaxyproject.org

Data changes on usegalaxy.org
by Nate Coraor 29 Jun '11

29 Jun '11

Dear Galaxy Users: The usage of our public site is growing exponentially. As a result, we are starting to implement new functionality that will allow users to gauge the size of their datasets and histories. While most changes will be transparent, you may notice some slight change in history behavior stemming from this refactoring process. Here's what you might notice and how deal with it: - Some of the datasets you've previously deleted may be resurrected in your history. Simply re-delete them if you see this happening. - You may also find that necessary metadata files are missing when you use a dataset as a tool input. These metadata files can be regenerated using the "Auto-detect" button on the dataset's "Edit Attributes" page, accessible by clicking the dataset's pencil icon. Thank you for using Galaxy! --nate Galaxy Team http://usegalaxy.org/

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error occurred when converting the SOLID output to fastq
by Jia-Xing Yue 29 Jun '11

29 Jun '11

Hi, when I converted the solid output to fastq, the galaxy always complained the following error. Does anybody know why>> ------------- An error occurred running this job:Traceback (most recent call last): File "/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq.py", line 207, in <module> main() File "/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq.py", line 188, in main Traceback (most recent call last): File "/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq.py", line 207, in main() File "/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq.py", line 188, in main merge_reads_qual( fr, fq, con, trim_name=options.trim_name, out='db', double_encode=options.de, trim_first_base=options.trim_first_base, min_qual=options.min_qual, table_name="f3" ) File "/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq.py", line 83, in merge_reads_qual cursor.execute('insert into %s values("%s","%s","%s")' % (table_name, defline, lines[0], qual ) ) sqlite3.OperationalError: near "?3": syntax error ----------- Thanks! Jia-Xing -- Jia-Xing Yue Graduate Student Ecology & Evolutionary Bio. -MS 170 Rice University 6100 Main Street Houston TX 77005 Phone: 1-832-360-6228 E-mail: yjx(a)rice.edu Blog: http://bestrok.blogspot.com/

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downloading reference sequences and other questions
by Joanne Rampersad 29 Jun '11

29 Jun '11

Hi I have a few questions 1. I am trying to use Bowtie to map my data using a reference genome. the genome is available on Galaxy (Escherichia coli DH10B (20079)). Is there a way that I can download the file in fasta format to use as a reference in Tablet? I can import the SAM output into Tablet if I do not give it a reference, but I would like to see it with the reference 2. I have used the Sam to Bam converter and downloaded the file to my computer then tried to import it into Tablet, but it gives an error. Does anyone have any advice on doing this? 3. Does Galaxy have any tools for doing a blast search against a reference genome or database? Any help/instructions that you point me to is greatly appreciated. Jo

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pileup analysis
by Andrea Edwards 29 Jun '11

29 Jun '11

Hello I was wondering if there was anything available within galaxy that would let you do the following with pileup files: 1) filter for homozygous SNVs (i.e. that do not contain the reference genome allele in the genotype) 2) compare the pileup files for 2 (or more) individuals to find SNVs unique to each individual and to further limit this to homozygous SNPs unique to each individual 3) compare the pileup files for 2 (or more) individuals to find shared SNVs and to further limit to this to shared SNVs where the individuals have different alleles (rare as would assume triallelic snv) and then group the individuals according to the allele for each SNV. I could only see the filter pileup tool but nothing for comparing pileup files thanks

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SNP prioritization pipelines
by Radhouane Aniba 29 Jun '11

29 Jun '11

Hi Galaxy users, I am new to Galaxy, I am exploring the screencasts over your website, I would like to know if it is possible to deal with yet unseen example in your website. I downloaded NHGRI GWAS data table and I am interested in a given traits/complex diseases. Is it possible to build a workflow on SNPs prioritization using galaxy ? Does anyone already did this ? Thanks Rad

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Tophat error
by Simon Lank 29 Jun '11

29 Jun '11

Hi. Newbie here. I'm trying to setup tophat for our local install. I'm getting the following error when I try to run it. Has anyone seen this before or have any ideas what I can try to fix it. Thanks, Simon Error in tophat: [Wed Jun 29 11:54:09 2011] Beginning TopHat run (v1.3.1) ----------------------------------------------- [Wed Jun 29 11:54:09 2011] Preparing output location ./tophat_out/ [Wed Jun 29 11:54:09 2011] Checking for Bowtie index files [Wed Jun 29 11:54:09 2011] Checking for reference FASTA file Warning: Could not find FASTA file /var/folders/f1/f1aTv8DnERiCv5ic7O3rlk++-+6/-Tmp-/tmpe7Oa0l/dataset_127234.dat.fa [Wed Jun 29 11:54:09 2011] Reconstituting reference FASTA file from Bowtie index Executing: /Volumes/storagepool/oconnorlab/galaxy_dist/bin/bowtie-inspect /var/folders/f1/f1aTv8DnERiCv5ic7O3rlk++-+6/-Tmp-/tmpe7Oa0l/dataset_127234.dat > ./tophat_out/tmp/dataset_127234.dat.fa [Wed Jun 29 11:54:09 2011] Checking for Bowtie Bowtie version: 0.12.5.0 [Wed Jun 29 11:54:09 2011] Checking for Samtools Samtools Version: 0.1.7 [Wed Jun 29 11:54:09 2011] Generating SAM header for /var/folders/f1/f1aTv8DnERiCv5ic7O3rlk++-+6/-Tmp-/tmpe7Oa0l/dataset_127234.dat [Wed Jun 29 11:54:09 2011] Preparing reads format: fastq quality scale: phred33 (default) Left reads: min. length=17, count=2666051 Warning: short reads (<20bp) will make TopHat quite slow and take large amount of memory because they are likely to be mapped to too many places [Wed Jun 29 11:54:27 2011] Mapping left_kept_reads against dataset_127234.dat with Bowtie gzip: stdout: Broken pipe [Wed Jun 29 11:54:27 2011] Processing bowtie hits Traceback (most recent call last): File "/Volumes/storagepool/oconnorlab/galaxy_dist/bin/tophat", line 2607, in sys.exit(main()) File "/Volumes/storagepool/oconnorlab/galaxy_dist/bin/tophat", line 2566, in main user_supplied_deletions) File "/Volumes/storagepool/oconnorlab/galaxy_dist/bin/tophat", line 2256, in spliced_alignment ref_fasta) File "/Volumes/storagepool/oconnorlab/galaxy_dist/bin/tophat", line 2000, in junctions_from_segments if left_reads_map != left_seg_maps[0]: IndexError: list index out of range

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cloud instance drops settings on reboot
by Joseph Hargitai 29 Jun '11

29 Jun '11

Hi, setting the admin user in /mnt/galaxyTools/galaxy-central/universe_wsgi.ini did work after a simple restart of the galaxy service as user galaxy - ./runs.sh However, when I restarted the cloud instance (rebooted from Amazon console) the setting reverted to original. Is there perhaps another ini file that overrides this one on a reboot? Also, is there a proper/other way to restart the service? best, joe

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AXT and NIB files for AlignSeq.loc
by John David Osborne 29 Jun '11

29 Jun '11

I was wondering how to get a hold of the axt and/or nib files required by alignseq.loc. It's not mentioned on the local NGA Galaxy setup page. I was surprised to learn that: "Fetch Sequences -> Extract Genomic DNA" requires AXT or NIB alignment files in order to extract mouse genomic DNA from BED file co-ordinates?! I see some AXT files at UCSC (a lot for human) but the alignment file I am guessing I needed (for this mm9 genome extraction) is mouse self? I'm hoping I don't have to generate them all myself, but if I do, I would love to know how to do it (parameters, etc...). Any info appreciated, -John

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Re: [galaxy-user] Cuffdiff Question
by Jeremy Goecks 28 Jun '11

28 Jun '11

Hello Kurinji, > I was at your USC Galaxy seminar last week, which I found very helpful - thank you! Glad to hear that you found the workshop helpful. As a reminder, please email questions about using Galaxy and its tools to the galaxy-user mailing list (which I've cc'd). You may get quicker and different responses from community members, and everyone will benefit from the discussion. > I used my recently generated RNAseq data in Galaxy (which was pre-aligned using tophat and already had cufflinks run on it) - I ran cuffcompare with all the gtf files and then cuffdiff for the three pairs (there is 1 control and 3 different drug treatments - no replicates). I got several output files, as expected, but decided just to look at the gene differential expression as a start. Some questions I have are - > > 1. (very basic question!) which is sample 1 (and corresponding value 1) and sample 2 (and corresponding value 2)in my output file. This is what my output file is called - > > 90: Cuffdiff on data 37, data 38, and data 60: gene differential expression testing 33,969 lines > > Is 37 sample one or sample two? Given the data - I would expect sample 37 to correspond to "value 2" - but I could be wrong. Please let me know! The best way to figure out which dataset corresponds with Cuffdiff's labels is to click the rerun button in the dataset: sample names correspond directly to the reads datasets (i.e. BAM files) provided as input to Cuffdiff. > 2. How do I find the UCSC gene names corresponding with start/end sites - I did input the hg18 UCSC gtf file as a reference You'll need to use a reference annotation (GTF file) that has the gene_name attribute as input for Cufflinks/compare/difff. Typically Ensembl annotations have this attribute; however, you'll need to prepend 'chr' to each line--really, to each chromosome name--in order to bring Ensembl notation in line with UCSC/Galaxy notation. > Actually, I noticed that value 1 in this particular output file is all 0 - no idea why. It is not this way in the other files, making me wonder if there is an error somewhere. I am sure the bam file is okay as I viewed it on IGV and saw the patterns I would expect for some candidate genes I looked at. It's difficult for me to comment without seeing your analysis. Some output files depend on particular attributes being set correctly in the annotation file. You may want to search through our mailing list archives and see if your question has already been answered: http://gmod.827538.n3.nabble.com/Galaxy-Users-f815892.html Good luck, J.

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temporary files
by Christopher Schroeder 28 Jun '11

28 Jun '11

Dear all, we extended the galaxy functionality with a couple of smaller custom scripts. Now we are in the need of some tmpFiles, since our data is getting bigger. As far as I understand galaxy by now there might be several options: - job_working_directory (all "normal" files generated by the job, deleted upon completion of job - safe?) - tmp-folder within the database folder (custom path in universe_wsgi.ini?) - system-tmp-folder (e.g. samtools-wraper -> only very limited space on this harddisk) What is the best way to store temporary data in Galaxy (that can be deleted after job completion)? Thank you in advance for your help! Chris

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