User: vladimir.gritsenko

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Tel Aviv University
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2 years, 9 months ago
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Posts by vladimir.gritsenko

<prev • 22 results • page 1 of 3 • next >
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Comment: C: Queueing issues on usegalaxy.org
... I'm seeing the same thing. Also Workflows don't seem to enter the history at all. ...
written 16 months ago by vladimir.gritsenko90
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Answer: A: HaplotypeCaller tool on galaxy
... Seems that GATK's license is too restrictive for Galaxy, so HaplotypeCaller won't be added in the foreseeable future. See Jennifer Jackson's answer and advice regarding alternative SNP callers here: https://biostar.usegalaxy.org/p/21564/#21616 ...
written 16 months ago by vladimir.gritsenko90
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Comment: C: Variable doesn't work in Workflow editor for certain tools?
... Thanks for the reply! Is there a particular reason why you're phasing out these Broad tools? Aren't they considered best-of-breed for SNP calling? Does that mean you're recommending FreeBayes and VarScan for that purpose? ...
written 16 months ago by vladimir.gritsenko90
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Variable doesn't work in Workflow editor for certain tools?
... Hello, I've started using variables in the workflow editor to make tracking the datasets easier, and so far its been working OK. One tool has given me trouble, though - UnifiedGenotyper. The BAM input name seems to be stored in the `input_bam` variable, but when I set the new dataset's name to `#{i ...
workflow written 16 months ago by vladimir.gritsenko90 • updated 16 months ago by Jennifer Hillman Jackson25k
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Comment: C: Bowtie2 not working
... It seems that BWA doesn't work, either, though FastQC and the Groomer do work. This is true both for uploaded fastq.gz files and for the Groomer output. ...
written 16 months ago by vladimir.gritsenko90
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Comment: C: Requirements
... Hi Jennifer, there seems to be no (public) mailing for Galaxy admins - where should such questions go? The public dev mailing list? We're also looking into setting up Galaxy at our institution, but my questions revolve mostly around manpower. ...
written 20 months ago by vladimir.gritsenko90
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Comment: C: Is it possible to upload SnpEff databases to Galaxy?
... Thank you for the reply! It's a pity this functionality is missing. Can you consider adding it? ...
written 23 months ago by vladimir.gritsenko90
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Answer: C: Re: Reference Genome
... You can upload a custom reference as a FASTA file, and most (all?) tools should accept it (you can instruct them to use a reference from the history, as opposed to the local cache). ...
written 23 months ago by vladimir.gritsenko90
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Is it possible to upload SnpEff databases to Galaxy?
... I have created a database with SnpEff 4.0, which should be compatible with Galaxy. Is it possible to upload this database to Galaxy for use with SnpEff? If yes, how? EDIT: as a corollary, it seems relatively easy to add a database-installing tool, though I haven't found it. Thanks! ...
variant-annotation data-managers toolshed snpeff written 23 months ago by vladimir.gritsenko90 • updated 23 months ago by Jennifer Hillman Jackson25k
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Comment: C: problem in grooming
... What exactly is failing, and what error message does it give? ...
written 2.1 years ago by vladimir.gritsenko90

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