- galaxy-user - lists.galaxyproject.org

Multiple sample runs using workflow
by Praveen Raj Somarajan 04 Apr '12

04 Apr '12

Hello All, I'm seeking help on how do we run a workflow (say bwa mapping on PE data) on multiple samples (eg: 10 samples, PE data) together. I assume "multiple input files selection" option does not work here as the workflow accepts two fastq input files (PE data). Do you have any experience on this? Best, Raj ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD

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Re: [galaxy-user] Galaxy Server running error in fetching sequences
by Jennifer Jackson 04 Apr '12

04 Apr '12

Hello Hong, To let you know, the Extract tool will work with any fasta dataset in your history as a "Custom reference genome". Instructions are here: http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome Take care, Jen Galaxy team On 4/4/12 10:37 AM, hongxu wrote: > Hi Jen, > > Thank you for the reply. I'll try BED6 and see in Galaxy. > I would also want to try ENSEMBL API, because one of our publication is based on ENSEMBL database. > > Best, > Hong Xu >> From: Jennifer Jackson<jen(a)bx.psu.edu> >> Reply-To: >> To: hongxu<hongxu(a)zju.edu.cn> >> Subject: Re: [galaxy-user] Galaxy Server running error in fetching sequences >> Date: Wed, 04 Apr 2012 07:14:27 -0700 >> >> Hello Hong, >> >> There is likely a problem with the formatting of your input file. BED >> and GFF format are very different, and this may be the problem. You will >> want to input a strict "BED6" file to this tool: >> >> http://wiki.g2.bx.psu.edu/Learn/Datatypes#Bed >> >> http://wiki.g2.bx.psu.edu/Learn/Datatypes#GFF >> >> If you continue to have problems, please submit a bug report by clicking >> on the green bug icon for the red error dataset. This allows us to >> access your data/job privately and provide help/feedback. >> >> Best, >> >> Jen >> Galaxy team >> >>> On Apr 3, 2012, at 4:37 PM, xu hong wrote: >>> >>>> Hi Anton, >>>> >>>> I'm a biological student using Galaxy sever to fetch sequences in >>>> fasta format for our bioinformatics data analysis. First, I uploaded >>>> our BED file(I think there is no significant difference from the GFF >>>> format defined in Galaxy/UCSC), and then use "Fetch Sequences" >>>> function in Galaxy Server. >>>> However, I got the following error: >>>> >>>> "2: Extract Genomic DNA on data 1 >>>> 0 bytes >>>> An error occurred running this job: Traceback (most recent call last): >>>> File "/galaxy/home/g2main/galaxy_main/tools/extract/extract_genomic_dna.py", >>>> line 288, in > >>>> f __name__ == "__main__": __main__() >>>> File "/galaxy/home/g2main/galaxy_main/tools/extract/extract_genomic_dna.py" >>>> " >>>> >>>> Could you help me configure out what's wrong with my analysis or could >>>> you get the fasta file I want for me? >>>> >>>> Attached is the BED file(based on hg18) I uploaded to Galaxy server in psu. >>>> >>>> Thanks. >>>> >>>> Beg your reply. >>>> >>>> Best >>>> Hong Xu >>>> Zhejiang University,China >>>> > >>> >>> >>> ___________________________________________________________ >>> The Galaxy User list should be used for the discussion of >>> Galaxy analysis and other features on the public server >>> at usegalaxy.org. Please keep all replies on the list by >>> using "reply all" in your mail client. For discussion of >>> local Galaxy instances and the Galaxy source code, please >>> use the Galaxy Development list: >>> >>> http://lists.bx.psu.edu/listinfo/galaxy-dev >>> >>> To manage your subscriptions to this and other Galaxy lists, >>> please use the interface at: >>> >>> http://lists.bx.psu.edu/ >> >> >

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Re: [galaxy-user] Generating gff file
by Jennifer Jackson 04 Apr '12

04 Apr '12

Hello again, The general path will be: - "Convert Formats -> GFF-to-BED" - click on pencil icon to assign format as "interval", double checking the assignment of the columns, including strand. From there you have different analysis choices, including: * Find out which UCSC tracks have annotation for the gene regions themselves: - "Operate on Genomic Intervals -> Profile Annotations" * Find out which UCSC tracks have annotation for the upstream/downstream regions: - "Operate on Genomic Intervals -> Get flanks" - "Operate on Genomic Intervals -> Profile Annotations" * Extract sequence for the upstream/downstream regions: - "Operate on Genomic Intervals -> Get flanks" - "Fetch Sequences -> Extract Genomic DNA" * Extract complete annotation track from UCSC and find overlapping regions with your regions (any: genes or flanks) - "Get Data -> UCSC Main" select your genome, track of interest (perhaps from profile annotations results, could limit by regions (UCSC accepts up to 1000 regions), etc. - "Operate on Genomic Intervals -> Coverage" this is one suggestion. See our wiki for other choices: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations Hopefully this helps to get you started, Jen Galaxy team On 4/4/12 9:01 AM, Abdullah Al Mahmud wrote: > Hi Jen, > > Thank you for your reply. > I uploaded a gff file to my galaxy. which contains almost 250 gene > annotation. It is for D. melanogaster. I want to know using galaxy and > UCSC genome browser is there a way to collect sequence information > about 1000pb upstream and down stream of all the gene? > > With best regards, > > Abdullah > > On Wed, Apr 4, 2012 at 10:59 AM, Jennifer Jackson<jen(a)bx.psu.edu> wrote: >> Hello Abdullah, >> >> Galaxy can convert BED data to GFF data (type in "GFF" in tool search, top >> of right tool panel). So, any BED file created (MACS, etc.) or imported >> ("Get Data" or other) could be converted and exported as GFF. Please note >> this is "GFF", not "GFF3". >> >> SeqMonk also accepts BED format, so converting may not be necessary. GTF and >> BAM/SAM are also accepted. >> >> Is this what you wanted to know? Did you have a specific data in mind that >> you wanted to create/obtain for visualization? >> >> Please let us know if we can help more, >> >> Jen >> Galaxy team >> >> >> On 4/2/12 12:18 PM, Abdullah Al Mahmud wrote: >>> >>> Hi, >>> >>> Is it possible to generate gff file in galaxy which I can use in Seqmonk? >>> >>> Abdullah >>> >> > > >

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BWA in Galaxy
by shamsher jagat 04 Apr '12

04 Apr '12

Is it possible to align FASTq reads from Illumina Hi-seq reads to human genome in Galaxy? I see only Bowtie/ I guess next question will be how different is Bowtie from BWA? I want to find out sequence variations. Thanks

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Generating gff file
by Abdullah Al Mahmud 04 Apr '12

04 Apr '12

Hi, Is it possible to generate gff file in galaxy which I can use in Seqmonk? Abdullah -- Abdullah Al Mahmud, PhD Postdoctoral fellow University of Montreal Lab of Dr. Jacques Michaud CHU Sainte-Justine Research Center, 3175, Cote-Sainte-Catherine, A-709 Montreal, Quebec, H3T 1C5, Canada. abdullah.al.mahmud(a)umontreal.ca

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Re: [galaxy-user] Galaxy Server running error in fetching sequences
by Anton Nekrutenko 04 Apr '12

04 Apr '12

Hong: I'm forwarding this to our official user mailing list. Please, use it in the future for your inquiries. Thanks! anton Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org On Apr 3, 2012, at 4:37 PM, xu hong wrote: > Hi Anton, > > I'm a biological student using Galaxy sever to fetch sequences in > fasta format for our bioinformatics data analysis. First, I uploaded > our BED file(I think there is no significant difference from the GFF > format defined in Galaxy/UCSC), and then use "Fetch Sequences" > function in Galaxy Server. > However, I got the following error: > > "2: Extract Genomic DNA on data 1 > 0 bytes > An error occurred running this job: Traceback (most recent call last): > File "/galaxy/home/g2main/galaxy_main/tools/extract/extract_genomic_dna.py", > line 288, in <module> > f __name__ == "__main__": __main__() > File "/galaxy/home/g2main/galaxy_main/tools/extract/extract_genomic_dna.py" > " > > Could you help me configure out what's wrong with my analysis or could > you get the fasta file I want for me? > > Attached is the BED file(based on hg18) I uploaded to Galaxy server in psu. > > Thanks. > > Beg your reply. > > Best > Hong Xu > Zhejiang University,China > <IGGPart2.rar>

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Cloudman - Problem starting shared cluster
by mailing list 03 Apr '12

03 Apr '12

Hi guys, After launching Cloudman on the Initial Cluster Configuration dialog I selected the "Share-an-Instance Cluster" option and put in this share string: cm-31bf91279e41769ff78af22c1a276ece/shared/2012-01-12--18-03 But after that I see this message in the log: 12:52:19 - Problem copying shared cluster configuration files. Cannot continue with shared cluster initialization. And nothing else happens after that. The "applications" status stays yellow, and disk status says "0/0". Here is some more information about the run: That sharestring is from a share I made in January. It worked when I last tested it in January. I launched via the BioCloudCentral wep app. Other run information: Instance ID i-8523cee2 Image ID (AMI) ami-500cd139 Security group CloudMan Key pair cloudman_key_pair Placement (zone) us-east-1b Let me know what other information would be helpful. Thanks, Greg

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input for GATK DepthOfCoverage
by Lilach Friedman 03 Apr '12

03 Apr '12

Hi Galaxy Team, I'm trying to use GATK DepthOfCoverage, and to give a BAM file of alined results as input. My steps were: 1. BWA alignment 2. SAM-to-BAM 3. rmdup. when I'm trying to give 3 (rmdup results) as an input to GATK DepthOfCoverage, an error appears: " Sequences are not currently available for the specified build." What did I do wrong? Many thanks! Lilach

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Blast2GO local instance Re: Table with gene count reads
by Luciano Cosme 03 Apr '12

03 Apr '12

Howdy, Thanks Jen, I will try it tomorrow. I installed Blast2Go from the Toolshed in my local instance of Galaxy and when I try to run it I get the following error: Index file named 'blast2go.loc' is required by tool but not available. I logged as admin and the installation did not gave me any error. From the terminal: galaxy.util.shed_util DEBUG 2012-03-23 17:23:37,088 Installing repository 'blast2go' galaxy.util.shed_util DEBUG 2012-03-23 17:23:37,088 Cloning http://testtoolshed.g2.bx.psu.edu/repos/peterjc/blast2go destination directory: blast2go requesting all changes adding changesets adding manifests adding file changes added 2 changesets with 6 changes to 3 files updating to branch default 3 files updated, 0 files merged, 0 files removed, 0 files unresolved galaxy.util.shed_util DEBUG 2012-03-23 17:23:42,798 Updating cloned repository to revision "7b53cc52e7ed" Anyway, I was thinking to use it because most of my differentially expressed genes are unknown. I was thinking to use Blast2GO to get them at least clustered in functional groups. I am not sure if that would be the best approach to find what might be the function of these genes. I also checked the list of public services that might have this tool, and Berkeley BOP is listed, but it seems that they no longer have the server or it was down when I checked (or the link is broken http://galaxy.berkeleybop.org/) Thank you. Luciano On Fri, Mar 23, 2012 at 8:43 AM, Jennifer Jackson <jen(a)bx.psu.edu> wrote: > Hello Luciano, > > There is no single tool do to this operation (although there has been some > discussion about including one in the Tool Shed), but the same information > can be obtained by using a combination of existing tools. > > First, start by converting both starting datasets to interval format. > > mapped reads: > - for TopHat output, "NGS: SAM Tools -> Convert SAM to interval" > features: > - for GFF file (convert to tabular if necessary), subtract "1" > from the start position's value using tool "Text Manipulation -> > Compute" > - cut columns chrom, new start, stop, strand, name, and score from > this result file using "Text Manipulation -> Cut" > - set the data type to "interval" using the 'Edit attributes form > (pencil icon) > > Next, use a tool in the group "Operate on Genomic Intervals" to compare > these intervals for overlap. The tool "Cluster" with the option "Find" is > mostly likely the one you will want to use. > > As a final step, summarize the data by feature using the tool "Join, > Subtract and Group -> Group". > > Hopefully this helps, > > Best, > > Jen > Galaxy team > > > On 3/19/12 4:36 PM, Luciano Cosme wrote: > >> Hi, >> I was wondering if there is any tool on Galaxy were I can obtain a >> table with how many reads have been mapped to a given sample and to a >> given gene (for example, use a Tophat output and use a GFF file to >> obtain the table). I am using HTSeq to get it (htseq-count). There is >> also GenomicRanges and easyRNASeq packages in bioconductor. >> Thank you. >> >> Luciano >> >> >> >> ______________________________**_____________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> http://lists.bx.psu.edu/**listinfo/galaxy-dev<http://lists.bx.psu.edu/listinfo/galaxy-dev> >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ >> >

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Training on NGS data analysis
by Aarti Desai 02 Apr '12

02 Apr '12

Hi Jennifer, We are working on developing NGS data analysis pipeline. Does your institution have a training program where one or two people from my team can be trained on NGS data analysis, particularly de novo genome assembly? Regards, Aarti Dr. Aarti Desai | Domain Specialist - Life Sciences Domain aarti_desai(a)persistent.co.in<mailto:aarti_desai@persistent.co.in> | Cell: +91-9673009492 | Tel: +91-20-30236348 Persistent Systems Ltd. | Partners in Innovation | www.persistentsys.com<http://www.persistentsys.com/> DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.

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