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

Phylogenetic tree viewer ?
by Luobin Yang 16 May '11

16 May '11

Hi, Do you guys know any phylogenetics tree viewer that works well with Galaxy system? Thanks, Luobin

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SNP annotation
by Oliver, Gavin 12 May '11

12 May '11

Hi, I am new to Galaxy and am wondering what tools are available for annotation of SNPs? I know that snpEff is implemented in Galaxy and this enables annotation such as location and predicted effect, however I am wondering if there are any automated means of annotating a polymorphism as known/novel or determining its frequency in the population. Does Galaxy offer anything like this or would it be necessary to create scripts that would for exampole compare to dbSNP for uniqueness and the 1000 genomes project for frequency. Best, Gavin The contents of this message and any attachments to it are confidential and may be legally privileged. If you have received this message in error, you should delete it from your system immediately and advise the sender. Almac Group (UK) Limited, registered no. NI061368. Almac Sciences Limited, registered no. NI041550. Almac Discovery Limited, registered no. NI046249. Almac Pharma Services Limited, registered no. NI045055. Almac Clinical Services Limited, registered no. NI041905. Almac Clinical Technologies Limited, registered no. NI061202. Almac Diagnostics Limited, registered no. NI043067. All preceding companies are registered in Northern Ireland with a registered office address of Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK. Almac Sciences (Scotland) Limited, registered in Scotland no. SC154034. Almac Clinical Services LLC, Almac Clinical Technologies LLC, Almac Diagnostics LLC, Almac Pharma Services LLC and Almac Sciences LLC are Delaware limited liability companies and Almac Group Incorporated is a Delaware Corporation. More information on the Almac Group can be found on the Almac website: www.almacgroup.com

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Stastistics _q valu
by vasu punj 12 May '11

12 May '11

I am trying to use stat function of Galaxy, and compute q value from p values. it is giving following errors: An error occurred running this job: Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : scan() expected 'a real', got 'pvals' Execution halted Any suggestion

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Re: [galaxy-user] Galaxy Help: Extract sequences from [gtf file] + [genome FASTA file]
by Jeremy Goecks 12 May '11

12 May '11

Edge, Please send questions like this to the galaxy-user mailing list, where many people see your email and can help you and/or benefit from it. I've cc'd the list for this reply. The thread you linked to is out of date. To get sequences for the features in a GTF file, you can use the 'Extract Genomic DNA' tool and set the option 'Interpret features when possible' to Yes. To get sequences for Cufflinks transcripts, use the transcripts.gtf as input to the tool. Best, J. On May 12, 2011, at 3:08 AM, Edge Edge wrote: > > I just read through the post at the following link, http://lists.bx.psu.edu/pipermail/galaxy-user/2011-February/001934.html > I'm facing the same problem as well. > I'm desired to extract out the assembled transcript by Cufflink. > Can I know that how I link my output file from Tophat and Cufflink with the Galaxy? > I'm having the following output file right now: > junctions.bed > insertions.bed > deletions.bed > accepted_hits.bam > human_reference_genome.fasta > transcripts.gtf > isoforms.fpkm_tracking > genes.fpkm_tracking > > Sorry that I got a bit confusing about the explanation that you given to Karen, "in order to get the sequence data for transcripts in a Cuff* GTF file, you'll want to select for only exons (use Galaxy's 'Extract Features' tool) and then use the resultant dataset as input to Extract." > > Thanks a lot for your advice. > > best regards > edge > Master Student > UTAR Malaysia

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Re: [galaxy-user] Extract sequences from [gtf file] + [genome FASTA file]
by Edge Edge 12 May '11

12 May '11

Hi, I just read through the post at the following link, http://lists.bx.psu.edu/pipermail/galaxy-user/2011-February/001934.html I'm facing the same problem as well. I'm desired to extract out the assembled transcript by Cufflink. Can I know that how I link my output file from Tophat and Cufflink with the Galaxy? I'm having the following output file right now: junctions.bed insertions.bed deletions.bed accepted_hits.bam human_reference_genome.fasta transcripts.gtf isoforms.fpkm_tracking genes.fpkm_tracking I got a bit confusing about the explanation below: " in order to get the sequence data for transcripts in a Cuff* GTF file, you'll want to select for only exons (use Galaxy's 'Extract Features' tool) and then use the resultant dataset as input to Extract." Thanks a lot for advice. best regards edge

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Filter Tool
by Jeremy Goecks 11 May '11

11 May '11

(Starting new thread on galaxy-user.) Jagat, It depends what filter tool you're using and what dataset you're filtering. There is a generic filter tool that can be used to filter Cuffdiff tabular files for either FPKM values and differential expression tests. There is also a tool for filtering GTF files based on a Cuffdiff expr dataset. It sounds like you may be confusing either the tools or the inputs. If after double-checking you're still having problems with filtering, please put together a short list of your analysis steps and share your history with me, and I can take a look. Thanks, J. > Further to my question, It appear that there is some problem with the filter option: > When I use the isoform/gene exp file as such it work fine but when I filter these files with either parameter such as status if test was successful or on p value it return me empty file. The way am saving the file is - expr file filter save as txt file and upload back in Galaxy. > Any suggestion? > > Jagat > > > On Tue, May 3, 2011 at 3:08 AM, shamsher jagat <kanwarjag(a)gmail.com> wrote: > Jeremy, > > I have been trying to follow the steps in filtering Cufflink out put files you have described in one of the previous messages (http://gmod.827538.n3.nabble.com/Re-downstream-analysis-of-cuffdiff-out-put…) > > I have shared histroy with you, but in summary: > > File 35: when Filter GTF data by attributes value list on data 11 (combined GTF) and data 33 (which is gene expr file) . Will not this should have one gene per row. But it is not? > > File 39: Filter GTF file by attribute value list on data 11 and data 38 (Cuffdiff splicing expr) it failed. I would assume that it should filter on the basis of TSSid . The error message is > > Traceback (most recent call last): > File "/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py", line 67, in > filter( gff_file, attribute_name, ids_file, output_file ) > File "/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py", line 57, in filter > if attributes[ attribute_name ] in ids_dict: > KeyError: 'tss_id' > > 40 : Filter GTF data by attribute list on data 11 and 34 (tss group exp) failed and error message is: > > Traceback (most recent call last): > File "/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py", line 67, in > filter( gff_file, attribute_name, ids_file, output_file ) > File "/var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py", line 57, in filter > if attributes[ attribute_name ] in ids_dict: > KeyError: 'tss_id' > > I would consider that if one gene has different Id than there is splicing . > > However in contrast isoform file with transcript Id is working fine (File 20) > > On a different note can I convert GTF file to txt tab delaminated file I tried to convert file 11 in txt (following Edit attributes) but the file is not properly formatted especially col-pid and TSS id. Am I doing something wrong. > > Thanks. > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/

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Galaxy Community Conference Registration Closes May 17
by Dave Clements 09 May '11

09 May '11

Hello all, We are closing registrations for the Galaxy Community Conference at the end of May 17. However, the conference is likely to fill up before that date. So, if you are thinking about attending, *now* is the time to register for the meeting: http://galaxy.psu.edu/gcc2011/Register.html We have also secured some additional rooms on the night of May 24, in a hotel in Lunteren: http://galaxy.psu.edu/gcc2011/Logistics.html Again, it is not necessary to stay in Lunteren the night of May 24, as it is easy to get there from Amsterdam on May 25, before the meeting starts. Finally, a draft schedule is now available at: http://galaxy.psu.edu/gcc2011/Programme.html This is still subject to change, but we are hoping it won't change much. Just 15 days to go! Dave C. -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

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galaxy on the cloud - cannot select fastq files when trying to run workflow
by Amit Indap 09 May '11

09 May '11

Hi Galaxy, I am a newbie to Amazon EC2 and have been carefully following the steps in the screencast. I am able to upload two fastq files from the s3 bucket: http://s3.amazonaws.com/heteroplasmy/F4-bM4-1.fastq http://s3.amazonaws.com/heteroplasmy/F4-bM4-2.fastq I am also able import the published workflow http://s3.amazonaws.com/heteroplasmy/Galaxy-Workflow-mt_analysis_0.01_stran… But when it comes to running it, I cannot select the fastq file from the drop down menu. I am able to view them on my GC instance, since I imported them successfully, but am at a loss as to why I can't select them from the drop down menu in the workflow to begin their alignment. Is it something to do with my security group settings in setting up the EC2 instance? Any assistance you can provide would be great! Thanks, Amit -- Amit Indap

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Re: [galaxy-user] question about Filtering Cufflink files
by Jeremy Goecks 09 May '11

09 May '11

Jagat, First, a couple housekeeping issues: (a) the questions you're asking are better suited to the galaxy-user list (questions about using Galaxy and performing analyses) rather than galaxy-dev (questions about installing Galaxy locally and tool development), so I've moved this thread to galaxy-user; (b) please start new threads when appropriate rather than replying to older threads as this makes threads shorter and more focused. Onto your questions: > I have another question when I filter gene list In the filtered list there are multiple rows per gene. I should have one gene per row? I have attached the snap shot of out put, but not sure if galaxy server will take it or not. I did se the discussion on other forum: > http://seqanswers.com/forums/showthread.php?t=8830 GTF files have multiple lines per feature, so your output is reasonable. > which suggest that possible complications in getting one gene per row. My next question is in that scenario what should be the best way of representing one gene per FPKM value? should we take average of FPKM per gene? I think in the gene it is till giving the transcript FPKM value but these values are different from previous file filtered with transcript id. As Vasu noted, this is an ongoing area of research. For some experiments, it may be reasonable to group alternatively-spliced isoforms of the same gene and jointly estimate FPKM, and for others it may not. Fortunately, if you do want to group transcripts to get gene FPKM values, Cuffdiff does this for you: see its gene FPKM expression file. Best, J.

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RNA seq analysis
by puvan001＠umn.edu 07 May '11

07 May '11

Hi I have a couple of questions regarding RNA seq analysis. My questions are 1.I need to use a viral genome (very small, ~2kb ) as a reference genome and it is not available in Galaxy. I guess I can use this data from my history. I have a fasta file but I am not sure whether I have to do some kind of indexing or not. 2. In Tophat, default for "maximum number of alignments to be allowed" is 40. What my understanding is a single read can be aligned maximum 40 different places. I am wondering why this is 40. Is there any specific reason? If I need unique mapping, I have to use 1 instead of 40. Am I correct? Thanks SP

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Megblast GIs
by Douglas Rhoads 07 May '11

07 May '11

We have a local install of Galaxy and are using it for training grad and undergrad students (using the Windshield Splatter data). We have a relatively new install and the Megablast seems to be doing something funny with the output in that column 2 which is supposed to be the GI of the database hit is now two numbers joined with an underline (see below). I need to tell my IT people what is wrong so they can correct the problem. BL1-1-3 157649053_111750 91.30 46 4 0 10 55 58541 58496 2e- 06 60.0 BL1-1-5 161788633_175843 100.00 26 0 0 15 40 48812 48787 4e- 04 52.0 -- Douglas Rhoads, Professor of Biological Sciences Director of Graduate Program in Cell and Molecular Biology 601 SCEN, Dept. of Biological Sciences, 1 University of Arkansas, Fayetteville, AR 72701-1201 drhoads(at)uark.edu, http://www.uark.edu/ua/drhoads phone: 479-575-3251 FAX: 479-575-4010

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Text Manipulation: Filter out duplicates (uniq) from an plain text file ?
by Roman Valls 07 May '11

07 May '11

Hey galaxy users, Thats a fairly good question from one of my colleagues. I've looked through the menus (mainly "Text Manipulation" and "Filter and Sort"(Select)), googled (on the mailing list archives too), but couldn't find an answer: How should I remove duplicates on plain text files without resorting to: "echo file|sort|uniq" before uploading the file/text. or Putting a regexp together to replace the duplicate occurences as in: http://www.regular-expressions.info/duplicatelines.html I'm pretty sure I'm missing some really basic stuff here... is this basic operation something supposed to be done outside galaxy perhaps ? Thanks in advance !

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Galaxy's recent problems
by Dave Clements 06 May '11

06 May '11

Hello all, Galaxy has been ill recently due to disk space on the server filling up. In the short term we are working on freeing up space. In the longer term we are working on adding a quota system to limit how much space any one user can take, and we've also ordered a lot more disk. In the mean time, *please take a look at your saved histories and datasets and delete anything you no longer need*. This will greatly help us get through the current rough patch. In the longer term, you can also consider setting up your own local Galaxy instance, or running Galaxy on the cloud. See: http://getgalaxy.org/ https://bitbucket.org/galaxy/galaxy-central/wiki/cloud Thanks for your patience while we work this out, Dave C and the Galaxy Team -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

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Composite Datatypes Q.
by Todd Yilk 06 May '11

06 May '11

I have a program I'm trying to "galaxify" that emits a variable number of result files. I would like the output of my Galaxy tool to show up in Galaxy as an html file with links to the result files. So when you click on the eye, the html file should up in the middle pane ... sorry if I'm not describing this in an elegant way. Creating a composite datatype is the way to go in this situation, correct? I'm creating a class that inherits from Html. How do I get the result returned from my custom "generate_primary_file" function to show up as a tool's output ... if that's the right way to go about this? Thanks!

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Composite Datatypes Q.
by Todd Yilk 06 May '11

06 May '11

I have a program I'm trying to "galaxify" that emits a variable number of result files. I would like the output of my Galaxy tool to show up in Galaxy as an html file with links to the result files. So when you click on the eye, the html file should up in the middle pane ... sorry if I'm not describing this in an elegant way. Creating a composite datatype is the way to go in this situation, correct? I'm creating a class that inherits from Html. How do I get the result returned from my custom "generate_primary_file" function to show up as a tool's output ... if that's the right way to go about this? Thanks!

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Indel work flow questions
by Mike Dufault 03 May '11

03 May '11

Hi All, I have a question about the NGS: Indel analysis and SNP Calling. Assuming I have loaded my paired end reads, groomed, and got all the way through to alignment with BWA my question the becomes does the analysis for indel analysis and SNP analysis split in the work flow? For SNP analysis, It seems that I need to filter on SAM, convert SAM-to-BAM, etc... For Indel, It seem that I should use the BWA output that is in SAM format for indel analysis. Are these two above statments correct? I also have a question regarding the input for indel analysis. Should I use the BWA output directly (which is in SAM format) or should I first "filter on SAM" and use that output (which is also in SAM format). I have tried the indel analysis using both filtered and unfilterd and I get very similar results. It seems to me that should use the "filtered on SAM" output where I can indicate that the reads are paired=Yes, proper pairs=yes, unmapped=NO. Any thought, insight, etc. Thanks if advance, Mike

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RNA seq analysis
by puvan001＠umn.edu 03 May '11

03 May '11

I am new to Galaxy and I am not sure whether these topics were discussed earlier. I followed the steps up to cufflinks and I did not have any problems. Thanks for the RNA seq tutorial. My questions are 1. How do I know the number of reads mapped against the reference genome used after Top Hat mapping 2. I am aware that Cuffdiff is used to find the differences in expression. How do I combine replicates (3) of different treatments ? SP

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quality stat.
by Robin Mjelle 03 May '11

03 May '11

Dear User, I am trying to use the tool "Compute quality statistics<http://main.g2.bx.psu.edu/tool_runner?tool_id=cshl_fastx_quality_statistics>" in galaxy on Ilumina single reads. The file is 2.3 Gb, fastq format. I have performed Quality format converter on the data set and the format is now qualillumina. Despite of this, galaxy don't recognize any dataset in the workflow to use as input into quality statistics. Any idea why my dataset is not accepted as input? Best, Robin

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change queue with sge
by Sylvain Thomas 03 May '11

03 May '11

Hi I currently use a galaxy server with cluster. This cluster uses SGE. I'd like to specify a queue other than the default. I have tried many combinaisons with drmaa:/// without success. The queue used is always the default one. Does anyone has solved this problem? Thanks, Sylvain -- Sylvain Thomas tel : +33 (0)5 61 28 54 27 INRA - Unité de BIA Génopôle - plateforme Bio-informatique Chemin de Borde-Rouge - AUZEVILLE BP 52627 - 31326 CASTANET-TOLOSAN CEDEX

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uploading files from remote server
by camelia botez 02 May '11

02 May '11

How can we upload files from remote server running galaxy and using big storage for data ? Thank you

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Only first 5000 reads are displayed in this tile
by Jeremy Chien 02 May '11

02 May '11

Hi During the visualization of my mRNAseq data, some area have red line indicating that only the first 5000 reads are displayed. Within this region, some area have many reads. Some area, where exons exist, I don't see any reads. How do I interpret the data? If there are no reads shown in the visualization, although there is a read line saying only the first 5000 reads are displayed, does the absence of reads corresponding to a particular exon means it is not expressed? Thanks, Jeremy

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runtime warning with pysam egg
by Shantanu Pavgi 02 May '11

02 May '11

Hi, I am getting following warning when I start the galaxy server. I am using latest revision (50e249442c5a) of galaxy-dist. Am I missing anything in the configuration here? {{{ $ ./run.sh /home/galaxy/.python-eggs/pysam-0.4.1_kanwei_ae2bd50d9945-py2.6-linux-x86_64-ucs2.egg-tmp/csamtools.so:6: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility ###t#|}#######b###############S#5#####D###i)#######[####x,m ###<#=####L########B###########q##.:######$2###rDM###E3A#########j### python path is: /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/numpy-1.3.0-py2.6-linux-x86_64-ucs2.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/pysam-0.4.1_kanwei_ae2bd50d9945-py2.6-linux-x86_64-ucs2.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Whoosh-0.3.18-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs2.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs2.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/bx_python-0.7.0_14b6a6c95da6-py2.6-linux-x86_64-ucs2.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/amqplib-0.6.1-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/pexpect-2.4-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Babel-0.9.4-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Beaker-1.4-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Mako-0.2.5-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/WebHelpers-0.2-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/wchartype-0.1-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/elementtree-1.2.6_20050316-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/docutils-0.7-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/WebOb-0.8.5-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Routes-1.12.3-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs2.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/PasteDeploy-1.3.3-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/PasteScript-1.7.3-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Paste-1.6-py2.6.egg, /share/apps/galaxy/galaxy-dist-50e249442c5a/lib, /share/apps/galaxy/python/2.6.6/lib/python26.zip, /share/apps/galaxy/python/2.6.6/lib/python2.6, /share/apps/galaxy/python/2.6.6/lib/python2.6/plat-linux2, /share/apps/galaxy/python/2.6.6/lib/python2.6/lib-tk, /share/apps/galaxy/python/2.6.6/lib/python2.6/lib-old, /share/apps/galaxy/python/2.6.6/lib/python2.6/lib-dynload, /share/apps/galaxy/python/2.6.6/lib/python2.6/site-packages galaxy.datatypes.registry DEBUG 2011-04-25 12:37:54,637 Loading datatypes from datatypes_conf.xml galaxy.datatypes.registry DEBUG 2011-04-25 12:37:54,650 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False ... ... ... }}} -- Thanks, Shantanu.

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Removing deleted datasets
by Simon Lank 02 May '11

02 May '11

Hi. Our current galaxy database is ~ 600 gb, most of which are user deleted datasets. I followed the instructions here: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/PurgeHistoriesAndDa… and ran the shell scripts in recommended order. One of them in particular (I think it was purge_histories.sh) took amost 24 hours to complete. However, it doesn't appear any / most of the files were actually deleted, since we still have ~ 600 gb of dataset files. Is there something obvious I can try to get the files purged correctly? Thanks. Simon Simon Lank Research Specialist O'Connor Lab, WNPRC 555 Science Dr. Madison WI (608) 265-3389

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