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

Chip-Seq, Encode Peaks and Galaxy
by Radhouane Aniba 07 Sep '11

07 Sep '11

Hi everyone, I have a list of genomic regions with some variants and would like to study the correlation between theses variants and epigenomics marks such as histone modifications. >From Encode download page, i got some files corresponding to peaks of these hsitone modifications and would like to know if there is a way to create a pipeline using galaxy to map my variants, depending on genomic regions to the information I have from the histone modification peaks. Is there someone who can point me to a step by step to do things to start using Galaxy ? Thank you Rad

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suggestion for multithreading
by Louise-Amélie Schmitt 09 Aug '11

09 Aug '11

Hello everyone, I'm using TORQUE with Galaxy, and we noticed that if a tool is multithreaded, the number of needed cores is not communicated to pbs, leading to job crashes if the required resources are not available when the job is submitted. Therefore I modified a little the code as follows in lib/galaxy/jobs/runners/pbs.py 256 # define PBS job options 257 attrs.append( dict( name = pbs.ATTR_N, value = str( "%s_%s_% s" % ( job_wrapper.job_id, job_wrapper.tool.id, job_wrapper.user ) ) ) ) 258 mt_file = open('tool-data/multithreading.csv', 'r') 259 for l in mt_file: 260 l = string.split(l) 261 if ( l[0] == job_wrapper.tool.id ): 262 attrs.append( dict( name = pbs.ATTR_l, resource = 'nodes', value = '1:ppn='+str(l[1]) ) ) 263 attrs.append( dict( name = pbs.ATTR_l, resource = 'mem', value = str(l[2]) ) ) 264 break 265 mt_file.close() 266 job_attrs = pbs.new_attropl( len( attrs ) + len( pbs_options ) ) (sorry it didn't come out very well due to line breaking) The csv file contains a list of the multithreaded tools, each line containing: <tool id>\t<number of threads>\t<memory needed>\n And it works fine, the jobs wait for their turn properly, but information is duplicated. Perhaps there would be a way to include something similar in galaxy's original code (if it is not already the case, I may not be up-to-date) without duplicating data. I hope that helps :) Best regards, L-A

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Mosaik with Paired Reads
by John David Osborne 08 Aug '11

08 Aug '11

Hello, I'm trying to run Mosaik on our galaxy instance on Ilumina paired reads. However when I selected "paired reads" and Ilumina as an input option, I can still only select one of the two fastq files as input. No 2nd file selector appears like with bwa, bowtie, etc... Can anybody tell me what is going on - is this a known issue? -John

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keeping aditional data in the aaChanges tool
by Ximena Bonilla 08 Aug '11

08 Aug '11

Dear Galaxy staff, I have recently started using your tool and it has been really helpful, thank you! When using Human Genome Variation, aaChanges, I would like to keep some extra lines in the output file from either of the input files. In the tool description it says I should be able to keep them: "...chromosome, start, and end position as well as the SNP. The SNP can be given using ambiguous-nucleotide symbols or a list of two to four alleles separated by '/'. *Any other columns in the first input file will not be used but will be kept for the output*. The second input file contains..." However, I haven't found a way of actually have them in the output file. What am I missing/doing incorrectly? What I've been trying to keep by the way is rs IDs or Ensembl gene IDs. Thank you in advance for your answer. Kind regards, Ximena

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Fwd: Workflows with conditional statements
by Florent Angly 25 Jul '11

25 Jul '11

I filed an enhancement report since if the workflow conditional facility does not appear to exist in Galaxy: https://bitbucket.org/galaxy/galaxy-central/issue/547/conditional-workflow-… Best, Florent -------- Original Message -------- Subject: Workflows with conditional statements Date: Wed, 18 May 2011 10:31:21 +1000 From: Florent Angly <florent.angly(a)gmail.com> To: galaxy-user(a)lists.bx.psu.edu <galaxy-user(a)lists.bx.psu.edu> Hi all, I was wondering if there is a way to put conditional statements in a Galaxy workflow. This would be useful, for example, in the case of a workflow that has an optional advanced option that the user can click. This advanced option would add some extra steps to the data processing. Another example of how this could be useful is if inside a workflow, the data needs to be processed differently based on the results of previous workflow steps. Say, you have a worflow that takes some sequences, and calculate their average length. Using a conditional statement, the workflow would put the data through DeBruijn assembler if the reads are small, but through a traditional Overlap-Layout-Consensus assembler if the reads are long. Are conditional statements possible in Galaxy workflows and I just don't know how to use them? Best, Florent

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RNA-seq Galaxy workflow for PE barcoded samples?
by Whyte, Jeffrey 13 Jul '11

13 Jul '11

Hello, I posted to the seqanswers forum, but have not received any feedback. I am working with RNA-seq Illumina data files in Galaxy (http://main.g2.bx.psu.edu/) The two files are 100bp paired-end reads, multiplexed with barcoding to distinguish samples. The barcodes are the first four bases of the sequences in the s_7_1_sequence.txt file. Would the following Galaxy workflow be correct? 1. Upload both s_7_1_sequence.txt and s_7_2_sequence.txt to Galaxy with the reference genome selected 2. Run NGS: QC and manipulation --> FASTQ Groomer on each file to convert to Sanger FASTQ 3. Run NGS: QC and manipulation --> FASTQ joiner to combine the data from the two files 4. Run FASTX-TOOLKIT FOR FASTQ DATA --> Barcode Splitter to generate separate FASTQ files for each barcode group 5. Run NGS: RNA Analysis --> Tophat to map the reads from each group to the reference genome The problem I am having is that if I select paired-end for the library in Tophat, it requests two FASTQ files. Would I have to use FASTQ Splitter to separate the joined FASTQ files? If there is a more standard way to handle these types of barcoded files, I would appreciate hearing about this workflow. Thanks very much in advance, jjw P.S. Galaxy is an incredibly useful resource. Thanks!

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Workflow API
by Simon Lank 12 Jul '11

12 Jul '11

Hi Again Galaxy team. I'm attempting to use the new workflow API, which I understand is still in development. I created a test workflow with a single input, and was able to use 'example_watch_folder.py' to successfully execute it as a history and get the output to a specified location. My question is how I can modify the script to accept multiple inputs (i.e. how do I define which files in the input folder I want to be each input) and if there's a way to specify runtime parameters. For instance, the workflow I want to execute has a filter step on a tabular input item as one of the later steps which needs to be defined at runtime. How would I specify this in the 'watch_folder.py' parameters? or is this not possible yet? FYI, I know perl but not python, so ultimately I want to wrap the python scripts into a larger perl script to execute recursive workflows. Thanks for all your help. Galaxy is an amazing tool and the workflow API is a fantastic improvement. Simon Simon Lank Research Specialist O'Connor Lab, WNPRC 555 Science Dr. Madison WI (608) 265-3389

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Error running cufflinks on Galaxy
by David Robinson 06 Jul '11

06 Jul '11

Hello, When I attempt to run cufflinks based on .sam output from bowtie I get an error: An error occurred running this job: *cufflinks v1.0.1 cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 8 -b /galaxy/data/hg19/sam_index/hg19.fa Error running cufflinks. [Errno 2] No such file or directory: 'transcripts.gtf' *What can I do to get around this problem and run cufflinks? My workflow is on http://main.g2.bx.psu.edu and can be found here (I ran it using a .fastq file): http://main.g2.bx.psu.edu/u/dgrtwo/w/cufflinks-workflow-imported-from-uploa… Thanks in advance for your help! -David ************************************************ David Robinson Graduate Student Lewis-Sigler Institute for Integrative Genomics Carl Icahn Laboratory Princeton University 646-620-6630 ************************************************

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blastn: NameError: name 'cmd' is not defined
by Sergei Ryazansky 02 Jul '11

02 Jul '11

Hello all, First of all I would like to thank you guys for developing and mainting this so useful tool as Galaxy! I have our own installation fo Galaxy (galaxy-dist version) with ncbi-blast-plus. Calling blastn results to the following error message: An error occurred running this job:*Traceback (most recent call last): File "/home/galaxy/galaxy-dist/tools/ncbi_blast_plus/hide_stderr.py", line 29, in <module> sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err)) NameError: name 'cmd' is not defined* * * Could you please explain, what this error can mean? The link to the shared history is* * http://dmbcserv.dyndns.org:8080/u/hogart/h/test-of-blast* * * * Thank you in advance!

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Question regarding quality filtering of 454 amplicons
by Jackie Lighten 01 Jul '11

01 Jul '11

Hi, I have a question for you guys regarding quality filtering. I have a data set of double MID tagged 454 amplicons, from which I wish to select high quality sequences above Q20. The 454 quality filtering system seems to work differently from that given for the Illumina sequencing i.e. 454 filtering takes high quality segments, while Illumina (FASTQ) can select high quality full reads based on certain parameters. OK, so I know that the total length of my amplicon, including primers and barcodes is around 260bp. If I then set the 454 quality filtering tool to extract contiguous high quality sequence of >260, it gives me back around 45% of my raw data as hitting this criterion i.e. All 260bp are above Q20. I don¹t necessarily need this high stringency as most bases may not be informative. But if I convert my 454 data to FASTQ format and then run the Illumina filtering system which also allows me to set the number of bases allowed to deviate from the Q20 criteria, I get back over 90% of my data (allowing 10bp to deviate from Q20). I then need to go ahead and convert back to 454 format. Can you tell me if this is OK? Will I loose /confuse information somewhere along these conversions? It seems that if I do this, my barcodes are removed, as amplicons do not sort properly when I parse them through my barcode filtering program. Does anyone know of a program to filter 454 data based on average sequence quality score, which doesn¹t involve Linux and the Roche off instrument program (I have no experience in Linux! ) Thanks! -- Jack Lighten, Ph.D. Candidate, Bentzen Lab, Room 6078, Department of Biology, Dalhousie University, Halifax, NS, B3H 4J1 Canada Office:(902) 494-1398 Email: Jackie.Lighten(a)Dal.Ca Profile: www.marinebiodiversity.ca/CHONe/Members/lightenj/profile/bio

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