Admin: Jennifer Hillman Jackson

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Jennifer Hillman-Jackson

Galaxy Application Support
http://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org

Posts by Jennifer Hillman Jackson

<prev • 5,956 results • page 1 of 596 • next >
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Answer: A: GATK Runtime error - Avoid using deprecated tools or risk unexpected errors/resu
... Hello, All GATK tools wrapped for Galaxy, whether found on a public server, including Galaxy Main https://usegalaxy.org, or still available in the Main ToolShed http://usegalaxy.org/toolshed) are deprecated and should not be used. There is no active development planned for these older tool versions ...
written 46 minutes ago by Jennifer Hillman Jackson24k
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Comment: C: RNA Seq workflow with dataset collections
... Hi Steve - There are a few issues. The most important is that you have encountered a known issue with workflows (tool version conflicts in workflows: https://github.com/galaxyproject/galaxy/issues/4041). Trimmomatic is impacted and possibly HISAT2. The workaround is to disconnect all of the inputs/ ...
written 16 hours ago by Jennifer Hillman Jackson24k
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Answer: A: Salmon human GTF or tabular annotation reference input dataset
... Hello, Annotation GTF datasets can be extracted from the UCSC Table browser directly into Galaxy (Get Data > UCSC main). The problem will be that the gene_id and transcript_id attributes will have same content from this source (both will be the transcript_id value). This is true for all GTF data ...
written 21 hours ago by Jennifer Hillman Jackson24k
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Answer: A: history not showing
... Hello, Go to **User > Saved Histories** to review all of your active histories. Use the Advanced search function to review all or deleted/permanently deleted (purged) histories. Details in this FAQ: https://galaxyproject.org/support/ - [My history is missing! Good news, it probably isn't.][1] ...
written 1 day ago by Jennifer Hillman Jackson24k
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Answer: A: Trinity + Unicycler assembly failures at https://usegalaxy.org
... Update: The issues have been resolved. Please rerun any jobs that failed. Prior queued jobs will also need to be rerun (will appear as grey queued jobs in the history). Thanks! Jen & the Galaxy team ...
written 1 day ago by Jennifer Hillman Jackson24k
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Comment: C: Job errors at https://usegalaxy.org Galaxy version 17.09 18.01
... Did you still need help? If so, could you post back more details? Capturing what is available in the UI might be enough. Or you can try to reproduce at Galaxy main and send in a bug report. **Alternative1:** 1 - The exact tool name and version. This is at the top of the tool form or you can captu ...
written 1 day ago by Jennifer Hillman Jackson24k
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Comment: C: Tophat Error for SRA accessions
... From chandrugcg_77 in a duplicated post: > tool error An error occurred with this dataset: Remote job server > indicated a problem running or monitoring this job. > > [2018-02-22 05:14:53] Reporting output tracks [FAILED] Error running > /cvmfs/main.galaxyproject.org/deps/tophat/2. ...
written 1 day ago by Jennifer Hillman Jackson24k
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Comment: C: RNA Seq workflow with dataset collections
... Hi Steve - Strange but glad you reported this. We've seen workflow invocation issues recently but it should be cleared up. The pre-release on Main may have a bug. I'll review/do some testing and get back to you. Thanks! Jen ...
written 1 day ago by Jennifer Hillman Jackson24k
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Comment: C: Trinity assembly failed at https://usegalaxy.org
... The service is undergoing corrections. We have disabled the tool until fixed. Our team will post back when ready to use again. ...
written 1 day ago by Jennifer Hillman Jackson24k
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Comment: C: Tophat Error for SRA accessions
... If you still need help, please comment back with the error details. I was able to download all four using the tool Download and Extract Reads in FASTA/Q format from NCBI SRA. That outputs `fastqsanger` formatted data ready to QA and use with tools. Galaxy tutorials: https://galaxyproject.org/lear ...
written 1 day ago by Jennifer Hillman Jackson24k

Latest awards to Jennifer Hillman Jackson

Scholar 8 days ago, created an answer that has been accepted. For A: Multiple input for samtools mpileup (-b option) for GBS pipeline
Scholar 15 days ago, created an answer that has been accepted. For A: TopHat error (An error occurred setting the metadata for this dataset Set it man
Scholar 15 days ago, created an answer that has been accepted. For C: Error using DataManager to fetch a reference genome
Scholar 16 days ago, created an answer that has been accepted. For A: How to know if mapping to reference genome was succesful?
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: bowtie2 out of memory
Scholar 20 days ago, created an answer that has been accepted. For A: SAM-to-BAM 'Failed runtime validation of Using reference genome' Error - Local G
Scholar 29 days ago, created an answer that has been accepted. For A: bowtie2 out of memory
Scholar 4 weeks ago, created an answer that has been accepted. For A: how to Installing Tools into Galaxy from Tool Shed
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Getting Started with Galaxy Biostar
Scholar 5 weeks ago, created an answer that has been accepted. For C: AddOrReplaceReadGroups Fatal error
Scholar 5 weeks ago, created an answer that has been accepted. For A: Fasta Files from FTP sites
Scholar 5 weeks ago, created an answer that has been accepted. For A: Statistics - Count Tool
Scholar 5 weeks ago, created an answer that has been accepted. For A: Error and job completion notification via email
Appreciated 7 weeks ago, created a post with more than 5 votes. For Welcome to Galaxy Biostar
Scholar 9 weeks ago, created an answer that has been accepted. For A: location of tool after installed from toolshed
Scholar 9 weeks ago, created an answer that has been accepted. For A: Reference genome download - a step-by-step please?
Scholar 10 weeks ago, created an answer that has been accepted. For A: Reference genome download - a step-by-step please?
Scholar 12 weeks ago, created an answer that has been accepted. For A: CummerRbund sqlite input file doesnt correspond to Cuffdiff output
Scholar 12 weeks ago, created an answer that has been accepted. For A: FASTA QC ON GROOMER DATA :
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: bowtie2 out of memory
Scholar 12 weeks ago, created an answer that has been accepted. For A: Trinity- error setting metadata
Popular Question 3 months ago, created a question with more than 1,000 views. For Getting Started with Galaxy Biostar
Popular Question 3 months ago, created a question with more than 1,000 views. For February 18, 2011 Galaxy Development News Brief
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: bowtie2 out of memory

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