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 • 6,598 results • page 1 of 660 • next >
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Comment: C: Unicycler jobs - "This job is waiting to run" for 2 days
... The ticket has been updated, both **Trinity** and **Unicycler** were impacted, and this is what it states: Update - the jobs should be successful now but we are still running a few more tests before closing this out. If your original job failed with an error like: > Remote job ...
written 1 hour ago by Jennifer Hillman Jackson25k
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Answer: A: Interpreting detected "duplicates" between different tools
... Hello, The tools count up duplicated reads based on different criteria. Also, FastQC only analyzes the first 100-200k reads (depending on the module), where the Picard mark duplicate step only considers mapped reads. It may help to review the tools to better understand how they function. Links to ...
written 4 hours ago by Jennifer Hillman Jackson25k
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Comment: C: Unicycler jobs - "This job is waiting to run" for 2 days
... It does look like there is a cluster problem. Our admin is out today so it may be until Monday before this is fixed. Tracking ticket with details: https://github.com/galaxyproject/usegalaxy-playbook/issues/152 That ticket will update once things are fixed and I'll also post back here and close thi ...
written 4 hours ago by Jennifer Hillman Jackson25k
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Comment: C: Workflows don't execute after successfully being invoked at https://usegalaxy.or
... Update: I can confirm the problem, this is the issue ticket with details: https://github.com/galaxyproject/usegalaxy-playbook/issues/151 I'll also post back once confirmed to be fixed. Thanks again for reporting this, it is new. ...
written 5 hours ago by Jennifer Hillman Jackson25k
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Comment: C: Workflows don't execute after successfully being invoked at https://usegalaxy.or
... I ran into some other problems with workfow tests, too. Our admin is out today, so it may not be until Monday when we get back to you with more (noting a fix or a link to an issue ticket). Thanks for reporting the problem and sorry for the current inconvenience! Jen ...
written 6 hours ago by Jennifer Hillman Jackson25k
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Comment: C: Workflows don't execute after successfully being invoked
... Could you share links to the workflows? There can be multiple version of these on the server and I want to make sure I am looking at the exact version you are using. I can probably find your originating histories, so you don't need to share them publically. Will write back for more info if needed ...
written 7 hours ago by Jennifer Hillman Jackson25k
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Answer: A: Excel file to gff file
... Hello, There isn't a Galaxy tool that does this. I would suggest searching for line command utilities online, or asking at https://www.biostars.org/ if someone knows of an existing reliable script - I didn't find any prior posts with this info. Alternatively, you could create your own script. Th ...
written 9 hours ago by Jennifer Hillman Jackson25k
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Comment: C: Unicycler jobs - "This job is waiting to run" for 2 days
... Thanks for reporting the issue - we'll check the cluster status and get back to you. Thanks, Jen, Galaxy team ...
written 10 hours ago by Jennifer Hillman Jackson25k
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Comment: C: Cufflinks dependency problem error - Solution: use version 2.2.1.2 or later
... The difference is most likely due to using different parameters between the two runs. Many wrapped tools, including Cufflinks, have default parameters plus advanced parameters. These can all be adjusted on the tool forms. Galaxy provides a web interface but jobs are still submitted line-command for ...
written 22 hours ago by Jennifer Hillman Jackson25k
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Comment: C: How to solve DESeq2 error
... Hi - I am unable to reproduce this at Galaxy Main https://usegalaxy.org. If working at that server or can reproduce the problem there, would one of you please send in a bug report? Be sure to leave all inputs/outputs undeleted and include a link to this post so we can connect the two. https://galaxy ...
written 1 day ago by Jennifer Hillman Jackson25k

Latest awards to Jennifer Hillman Jackson

Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Mapping paired reads to reference genome, variant calling
Scholar 4 days ago, created an answer that has been accepted. For A: Need help with "Stitch MAF blocks" tool
Scholar 22 days ago, created an answer that has been accepted. For A: Configure file path for storing datasets
Scholar 4 weeks ago, created an answer that has been accepted. For A: Two instances on different server with only one postgres database ?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Mapping paired reads to reference genome, variant calling
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Mean Inner Distance
Scholar 6 weeks ago, created an answer that has been accepted. For A: Jobs starting to run and then stopping
Scholar 7 weeks ago, created an answer that has been accepted. For A: Multi-Join shows Error
Scholar 9 weeks ago, created an answer that has been accepted. For A: Star-Fusion last-matching gene pairs file
Scholar 10 weeks ago, created an answer that has been accepted. For A: Upload to the Galaxy ftp server
Scholar 11 weeks ago, created an answer that has been accepted. For A: How to know if mapping to reference genome was succesful?
Scholar 11 weeks ago, created an answer that has been accepted. For A: Trinity- error setting metadata
Scholar 12 weeks ago, created an answer that has been accepted. For A: Need help with "Reorder SAM/BAM" tool
Popular Question 3 months ago, created a question with more than 1,000 views. For Re: Mitochondrial Transcripts
Scholar 3 months ago, created an answer that has been accepted. For C: Error using DataManager to fetch a reference genome
Scholar 3 months ago, created an answer that has been accepted. For A: Star-Fusion last-matching gene pairs file
Scholar 3 months ago, created an answer that has been accepted. For A: How to delete workflow from list of published workflows
Popular Question 3 months ago, created a question with more than 1,000 views. For Load Data From Galaxy To Igv
Scholar 3 months ago, created an answer that has been accepted. For A: Error in Galaxy - ''Fatal error: The HTSeq python package is not properly instal
Great Question 3 months ago, created a question with more than 5,000 views. For Get Galaxy! Your own Local Server
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Mapping paired reads to reference genome, variant calling
Scholar 3 months ago, created an answer that has been accepted. For A: Jobs starting to run and then stopping
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: bowtie2 out of memory
Scholar 4 months ago, created an answer that has been accepted. For A: How to know if mapping to reference genome was succesful?
Scholar 4 months ago, created an answer that has been accepted. For A: 'Hidden' Galaxy features which are really useful /

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