Admin: Jennifer Hillman Jackson

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Location:
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Last seen:
2 days, 17 hours ago
Joined:
8 years, 1 month ago
Email:
j**@galaxyproject.org

Jennifer Hillman-Jackson

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

Posts by Jennifer Hillman Jackson

<prev • 6,688 results • page 2 of 669 • next >
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Comment: C: The jobs are permanently on hold
... Hello - I went through the inputs again and dataset 787 (hidden) has metadata problems. This causes downstream jobs to stay "on hold" until the input issues are resolved. Choose to display hidden datasets in the history and you'll find the warning within the 787 dataset displayed in a yellow box. ...
written 11 days ago by Jennifer Hillman Jackson25k
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Answer: A: RNA-seq without a reference genome
... Hello, Galaxy tutorials for de novo RNA-seq analysis are included here: https://galaxyproject.org/learn/ Thanks! Jen, Galaxy team ...
written 11 days ago by Jennifer Hillman Jackson25k
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Comment: C: Problem with the tool: Extract Genomic DNA
... There does seem to be a tool problem. This happens even when the input is assigned to a database and that database is indexed on the server (or at least at Galaxy Main https://usegalaxy.org). The genome mm10 should be fine. For genomes not indexed on the server, a custom genome can be used. More ...
written 12 days ago by Jennifer Hillman Jackson25k
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Answer: A: Workflow Failure Issue with .dat Compressed Files on a Local Galaxy Instance
... Hello, That post is much older (7.5 years ago) and the Galaxy architecture has matured since then. Galaxy tool wrappers do not rely on file names (as displayed in the web GUI or as stored on disk) but the assigned `datatype` metadata attribute to determine file formats. The starting fastq inputs ...
written 12 days ago by Jennifer Hillman Jackson25k
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Answer: A: Galaxy Start it up error: .venv/bin/activate: No such file or directory
... Hello, Running Galaxy on Windows is not recommended. You could try using the Docker version instead. - Galaxy Ecosystem: https://galaxyproject.github.io/ - Base Galaxy Docker image (version 18.05): https://hub.docker.com/r/bgruening/galaxy-stable/ - Other Docker Flavours: https://githu ...
written 12 days ago by Jennifer Hillman Jackson25k
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Answer: A: Upload at usegalaxy.org producing Internal Server Error (500) directly or failin
... **Update 7-31-2018 Evening** * The issues with Upload and FTP are resolved. * The issues with https://depot.galaxyproject.org are also now resolved. Please try any failed jobs again now. Thanks! Jen & Galaxy team ...
written 13 days ago by Jennifer Hillman Jackson25k
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Answer: A: Extract identifiers from collection in tool XML
... Hello, The developers recognized the issue and replied at Gitter. Quoted reply from https://github.com/mvdbeek at https://gitter.im/galaxyproject/Lobby?at=5b60dd4ffe0be93f3b242d6a ---- `.element_identifier` instead of `.name` There's a section on that in the planemo docs: https://planemo.readth ...
written 13 days ago by Jennifer Hillman Jackson25k
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Answer: A: How to align sequences with MFFFT
... Hello, The two sequences should be stacked one on top of each other (tool: Concatenate), in strict fasta format (tool: NormalizeFasta), and have unique identifiers. **FAQs for Custom genomes/fasta** -- the formatting rules also apply to most other tools that accept fasta format inputs (for any inp ...
written 13 days ago by Jennifer Hillman Jackson25k
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Comment: C: Extract identifiers from collection in tool XML
... Hello, I asked the developers for some feedback at the Galaxy Gitter channel: https://gitter.im/galaxyproject/Lobby?at=5b60dd0dac380e3f3a10f30c Please feel free to join in on the conversation and/or add more details. Planemo is the recommended way to troubleshoot tool development issues, but th ...
written 13 days ago by Jennifer Hillman Jackson25k
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Answer: A: Help for pathway image: draw a KEGG pathway
... Hello, Include the pathway to graph on the tool form under the option **Pathway** (in addition to selecting the correct **Column with KEGG gene ID/pathways**). This will extract all entries that include that pathway in the output. **From the tool form help:** Pathway Image : Draw a KEGG pathway, h ...
written 13 days ago by Jennifer Hillman Jackson25k

Latest awards to Jennifer Hillman Jackson

Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Mapping paired reads to reference genome, variant calling
Scholar 13 days ago, created an answer that has been accepted. For A: CuffDiff Replicates - which files do replicates 0, 1, 2 point to?
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Mapping paired reads to reference genome, variant calling
Scholar 14 days ago, created an answer that has been accepted. For A: Star-Fusion last-matching gene pairs file
Scholar 17 days ago, created an answer that has been accepted. For A: Checking coverage of yeast whole genome sequencing data
Scholar 17 days ago, created an answer that has been accepted. For A: DEPRECATED tools in Galaxy
Popular Question 19 days ago, created a question with more than 1,000 views. For Installing Galaxy On My Computer
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: Mapping paired reads to reference genome, variant calling
Scholar 28 days ago, created an answer that has been accepted. For A: Need help with "Stitch MAF blocks" tool
Scholar 6 weeks ago, created an answer that has been accepted. For A: Configure file path for storing datasets
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Mapping paired reads to reference genome, variant calling
Scholar 8 weeks ago, created an answer that has been accepted. For A: Two instances on different server with only one postgres database ?
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Mean Inner Distance
Scholar 9 weeks ago, created an answer that has been accepted. For A: Jobs starting to run and then stopping
Scholar 10 weeks ago, created an answer that has been accepted. For A: Multi-Join shows Error
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: Upload to the Galaxy ftp server
Scholar 3 months ago, created an answer that has been accepted. For A: How to know if mapping to reference genome was succesful?
Scholar 3 months ago, created an answer that has been accepted. For A: Trinity- error setting metadata
Scholar 3 months 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 4 months ago, created an answer that has been accepted. For A: How to delete workflow from list of published workflows
Popular Question 4 months ago, created a question with more than 1,000 views. For Load Data From Galaxy To Igv

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