User: galaxyNewbie

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galaxyNewbie30
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Posts by galaxyNewbie

<prev • 23 results • page 1 of 3 • next >
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Galaxy package(s) for gene expression
... Hello, We have RNA-Seq sequences in bam format and would like to perform gene expression analysis for specific genes. The most important step for us is to prepare count matrices. Are there any packages available via galaxy that could perform this analysis? ...
htseq gene expression de featurecounts rna-seq written 4 weeks ago by galaxyNewbie30 • updated 4 weeks ago by Jennifer Hillman Jackson25k
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hgvs_vcf input format?
... For the HGVS_VCF package it appears the input format is simply a tabular file. I uploaded a .txt file with validated HGVS formatted entries. Could anyone provide information about the input formatting to the HGVS_VCF galaxy package? Are there any galaxy package alternatives which would convert h ...
vcf hgvs galaxy written 3 months ago by galaxyNewbie30 • updated 3 months ago by Jennifer Hillman Jackson25k
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Comment: C: import data from filesystem into the library without copying it
... RESOLVED... 1). Added myself to the approved role 2). Modified "user_library_import_dir = xxx" in the configuration file. ...
written 3 months ago by galaxyNewbie30
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(Closed) import data from filesystem into the library without copying it
... Under Admin I created a linked dataset for file > 2GB. The Galaxy message says "This job is running" but I do not see any linked dataset in my current histories tab. Am I supposed to be able to view the linked dataset (link instead of copying) from my local galaxy histories? FYI...I have a ...
link instead of copying written 3 months ago by galaxyNewbie30
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best galaxy app for viewing plink .bed files
... Hello, What is the best galaxy package to view a plink .bed file? Since it is a binary file I know the contents cannot be viewed directly, but I was wondering whether there is a galaxy package for viewing the binary file. Thank you. ...
galaxy plink written 3 months ago by galaxyNewbie30 • updated 3 months ago by Jennifer Hillman Jackson25k
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Comment: C: Link to dataset (rather than copying)
... Thank you for your quick reply! I found the options under admin...Data Libraries. But I may still have some configuration questions. ...
written 4 months ago by galaxyNewbie30
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Admin: Link to dataset inside Data Library rather than copying or importing
... According to the Data Libraries documentation you can link to datasets as opposed to importing them. through a copy. I have a local galaxy installation. My primary goal is to not be required to import, since I have a datasets > 2GB. I am an admin., but do not see any "add datasets to curr ...
dataset copy libraries galaxy link written 4 months ago by galaxyNewbie30 • updated 4 months ago by Jennifer Hillman Jackson25k
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Installation of new tools gets stuck on "cloning"
... Installation of new tools does not proceed past "cloning." I'm using galaxy version 18.09. There is no entry for this when I select "view error log." Thank you. ...
18.09 galaxy local install admin written 4 months ago by galaxyNewbie30 • updated 4 months ago by Jennifer Hillman Jackson25k
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administrator e-mail designation through galaxy.yml.sample
... Hello. I just re-installed galaxy after purchasing a new laptop. As I have done in the past I added my e-mail address in the admin_user section of the config file. However, it appears this time the config file = galaxy.yml.sample. Last time the config file = galaxy.ini, I believe. After adding ...
config admin written 4 months ago by galaxyNewbie30 • updated 4 months ago by Martin Čech ♦♦ 4.9k
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"Upload" of files > 2GB into Galaxy
... I have a local instance of Galaxy installed and would like to use .bam files > 2GB in samtools and other galaxy packages. Without having to FTP them into Galaxy, is there a way to simply provide a link inside galaxy to these >2 GB files? Thank you. ...
galaxy upload written 4 months ago by galaxyNewbie30 • updated 4 months ago by Hotz, Hans-Rudolf1.8k

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