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• Getting (Or Setting) Physical File Name
  So one of my colleagues has a script he wants to turn into a Galaxy tool. The twist is that scri...
• discover_dataset rename dataset in history
  Hi, I am using discover_dataset to retrieve multiple output files created. The xml works fine, bu...
• Job Output Not Returned From Cluster
  Hi, I came across the following error message sometime ago while launching some jobs on our SGE...
• Tool Installation from Tool Shed
  Hi all, I recently downloaded and installed a local version of Galaxy and am following some basi...
• Options For History Description Using Tool Config
  If you configure your tool using the xml config file it displays by default the tool action on da...
• Galaxy crash messed up NGINX AND workflow editing tool ?
  Hi everyone. I have a big issue on a local instance of Galaxy for diagnosis purpose. Here is wha...
• November 24, 2010 Galaxy Development News Brief
  November 24, 2010 Galaxy Development News Brief Here are the highlights of the following upgrade...
• Cuffdiff analysis output
  Hi there, I tried to run cuffdiff with the annotation of iGenome but still no sucess to have a o...
• Upload Custom Tool
  Hello everyone, I have been struggling with a custom tool I have been trying to create for a bit ...
• Samtools error assoicated with multiple mapping tools
  Hoping for some help here. I am having issues with several mapping tools that utilize samtools a...
• LiftOver no id column
  I have a question related to LiftOver. LiftOver output does not allow any id columns in the out...
• Mutliple UCSC gene names in RStudio Data Table
  Hi there, I am using the cummeRbund package in R Studio on my personal computer to analyze diffe...
• Help with interpreting RNA-seq output
  I am new to galaxy and have been trying to figure out how to align RNA-seq reads to a genome in o...
• Questions Regarding Galaxy Tool Xml File
  Hi, I am working on a project to automate workflow generation and its execution and I found the ...
• Fetch taxonomic representation tool error - missing lines
  Hello, I have been using the Fetch taxonomic representation tool from Galaxy online to retrieve ...
• Is there a way to fetch taxonomic information for a list of GI numbers in Galaxy?
  Hello, I performed a MEGABLAST analysis a few days ago, but I am now unable to automatically ret...
• Known Name Outputs Shown In /Database/Files But Not In Galaxy Windows
  I have made a wrapper that has a tool that giving it an input file, gives you two output files wi...
• bedtools, changing output attributes
  Hi, I'm using the bedtools "Intersect intervals find overlapping intervals in various ways" tool....
• Workflow import bug: import from link missing metadata
  Hello, I believe I've identified a bug affecting the importing of Galaxy workflows. Depending on ...
• 'error loading field data' when using tools in workflow interface
    Hi  I am trying to set up a galaxy instance at our institute, our IT person made a 'standard ...
• Problems with MACS peak calling--FDRs of 100%
  Hello, I am having some issues with MACS peak calling. I have 5 files in my ChIP-Seq dataset (in...
• Need help with changing galaxy.ini to fix freezing Pilon in Cloning stage
  Need help with changing galaxy.ini to fix freezing Pilon in Cloning stage. How to contact Pilon, ...
• Tools integrated into a pipeline not working on a galaxy instance
  Hi, I am trying to integrate my own tool into galaxy on a remote server (LSF). I have made mysel...