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 • 5,456 results • page 1 of 546 • next >
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Answer: A: RNAseq data to be processed in two ways: (i) mapping to de novo Trinity-based tr
... Hi, The RNA-seq tutorials here cover the current best-practices for the analysis you describe. Perhaps compare and decide the optimal workflow for your purposes using that information as a guide? https://galaxyproject.org/learn/ Tutorials cover QA/QC of reads (including interpreting and acting on ...
written 20 minutes ago by Jennifer Hillman Jackson23k
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Answer: A: Is it possible to tune a standard Galaxy instance on the Amazon cloud or we have
... Hello, You can add tools/data to Galaxy Cloudman the same way as you would for other Galaxy flavors (using [Admin functions][1]). [Cloudman][2] itself can also be upgraded if a new ami is available. For Globus integration with Galaxy in a cloud environment (GridFTP), please see this post: https:/ ...
written 38 minutes ago by Jennifer Hillman Jackson23k
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Answer: A: How to transfer files from Globus to usegalaxy.org
... Hello, GridFTP looks to still be a work-in-progress (https://github.com/galaxyproject/ansible-galaxy-extras/issues/86) but I've asked the developers for some feedback. You can follow along here at the IUC gitter channel: https://gitter.im/galaxy-iuc/iuc Some feedback came already. Just match the t ...
written 54 minutes ago by Jennifer Hillman Jackson23k
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Comment: C: HAMMOCK local installation
... Hi - I just checked and when logged into the Tool Shed, the option to contact the author is available. This graphic shows and explains how: https://imgur.com/JlX5hu4 The linked publication also includes a contact: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681989/ Another option when troublesho ...
written 3 hours ago by Jennifer Hillman Jackson23k
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Answer: A: Renaming Galaxy Output
... Hello, The output format for this tool can be inherited from the input's datatype (for example `bed`) or assigned by the tool as `interval`. I suspect that the dataset's current content/assigned datatype does not include the required data columns or have the required metadata attributes assigned th ...
written 7 hours ago by Jennifer Hillman Jackson23k
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Answer: A: Disk quota exceed - history quota higher than expected
... Hello, There are two active histories in your account and the total combined size is ~ 270 GB. The account quota size at https://usegalaxy.org is 250 GB. Go to the **History menu (gear icon) > Saved Histories** view to see all of your account's data. If your project is academic researched base ...
written 8 hours ago by Jennifer Hillman Jackson23k
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Answer: A: HAMMOCK local installation
... Hello, You could try installing these dependencies directly. The tool was recently updated but still uses packages. Packages are considered a deprecated method of installing dependencies but can still work. But if doing that does not resolve the problems, you should contact the repository owner fo ...
written 1 day ago by Jennifer Hillman Jackson23k
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Comment: C: awk ... fatal: print to "standard output" failed
... The output does not have any tabs, is just a single row of data with spaces leading and in between the two values. Commands I used: $ awk '{if(NR%4==1) {print $0}}' test.fastqsanger | head -n 1 | awk -F ":" '{print $1}' | cut -c 2- | awk '{print length;}' | sort | uniq -c > out_no_escaping ...
written 1 day ago by Jennifer Hillman Jackson23k
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Answer: A: awk ... fatal: print to "standard output" failed
... Hello, Try changing this `\$0` to be just `$0`. Do the same for `\$1` to be instead `$1`. The escaping looked odd to me so I tested it out just to be sure. It triggers an error on MAC OSX (line-command) and when using the Galaxy Awk tool in the Text Manipulation group. Leaving it out allows portion ...
written 1 day ago by Jennifer Hillman Jackson23k
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Answer: A: I have a VCF.gz and 26 BAM files... no idea how to use them. please help
... Hello, This public Galaxy instance hosts specific tools and tutorials that cover what I think you are trying to do: - https://galaxyproject.org/public-galaxy-servers/dintor/ Other public servers can be reviewed here, many are also domain specific: - General list: https://galaxyproject.org/pu ...
written 1 day ago by Jennifer Hillman Jackson23k

Latest awards to Jennifer Hillman Jackson

Scholar 8 days ago, created an answer that has been accepted. For A: how to Installing Tools into Galaxy from Tool Shed
Scholar 6 weeks ago, created an answer that has been accepted. For A: Extract Genomic DNA error with custom genome
Scholar 12 weeks ago, created an answer that has been accepted. For A: Illumina DNA sequence upload problem
Popular Question 3 months ago, created a question with more than 1,000 views. For Welcome to Galaxy Biostar
Scholar 3 months ago, created an answer that has been accepted. For A: filter by fasta ids
Scholar 3 months ago, created an answer that has been accepted. For A: CuffDiff Replicates - which files do replicates 0, 1, 2 point to?
Scholar 3 months ago, created an answer that has been accepted. For A: Illumina DNA sequence upload problem
Popular Question 3 months ago, created a question with more than 1,000 views. For April 8, 2011 Galaxy Development News Brief
Popular Question 3 months ago, created a question with more than 1,000 views. For Text Editing
Scholar 4 months ago, created an answer that has been accepted. For A: How get Cancer WGS for analysis in Galaxy
Scholar 4 months ago, created an answer that has been accepted. For A: 'Sampling' Bam or BigWig files?
Scholar 4 months ago, created an answer that has been accepted. For A: Aligning more than 2 sequences
Scholar 4 months ago, created an answer that has been accepted. For A: Trinity- error setting metadata
Scholar 4 months ago, created an answer that has been accepted. For A: Help with intersect -BedTools, WindowBed
Scholar 4 months ago, created an answer that has been accepted. For A: Trinity unusual error
Scholar 5 months ago, created an answer that has been accepted. For A: filter by fasta ids
Scholar 5 months ago, created an answer that has been accepted. For A: Extract Genomic DNA error with custom genome
Popular Question 5 months ago, created a question with more than 1,000 views. For Get Galaxy! Your own Local Server
Popular Question 5 months ago, created a question with more than 1,000 views. For About Galaxy !
Scholar 5 months ago, created an answer that has been accepted. For A: bowtie2 out of memory
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: bowtie2 out of memory
Scholar 6 months ago, created an answer that has been accepted. For C: Error using DataManager to fetch a reference genome
Scholar 6 months ago, created an answer that has been accepted. For A: Each sample as a condition? - cuffdiff
Scholar 7 months ago, created an answer that has been accepted. For A: Can I get back "Operate on Genomic Interval" on local Galaxy instance?
Scholar 7 months ago, created an answer that has been accepted. For A: DEPRECATED tools in Galaxy

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