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• How to fix SNPeff`s error "WARNING: All frames are zero! "?
  After execution of the job for processing of the normalized with VT Tools Pilon`s VCF file we h...
• What Galaxy tools can preprocess VCF file before running the SNPEff annotation process?
  What Galaxy tools can preprocess VCF file before running the SNPEff annotation process? We have t...
• No Output Produced.....
  Hi, I have my own image registration tool that I've created on my own local instance of galax...
• Markduplicates won't run
  hi there, This is what happened when I try to run Markduplicates the tool. Anyone knows how fix ...
• Cuffcompare Error In Galaxy
  Dear galaxy team: I was testing local galaxy of our lab by analyzing RNA-seq data in JeremyĄŚs...
• Help W Sam To Bam
  Hi, We're loving Galaxy. This is an excellent interface and set of tools. The issue we're havi...
• Data manager failure to create index(s) in 17.05 local
  Been having a devil of a time getting Galaxy going on a brand new 17_05 installation. I have use...
• FastQC Fatal Error: Exit code 1 ()
  Hi, I'm new to Galaxy and have minimal experience with Linux. I have installed Galaxy on a local...
• Bowtie2 error on locally installed Galaxy : unable to finish job
  Hi, I've installed a local Galaxy. I used data_manager_fetch_genome_all_fasta to get a galGal4 ge...
• Help local tool wrapper not seeing BWA getting error: sh: bwa: command not found
  Help I have created a tool with a local wrapper that uses BWA when I specify the absolute path t...
• Premature End-Of-File Error in Fastx_Clipper
  Hi all. I'm having trouble running fastx_clipper, which always returns an error like the followin...
• Tool cant find datasets even though they exist correctly
  Hi, I just imported a workflow from another Galaxy instance and when running it, the tool pindel...
• 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...
• Varscan on multiple samples generates error
  Hello, I am using "samtools mpileup" to generate a pileup file from my .bam dataset and then pas...
• MUMmer dot plot error
  Dear all, I have installed into my local Galaxy the tool Mummer dot plot, I have an error that  ...
• Custom galaxy tool: multiple output files
  This is my first attempt to install a custom tool on galaxy and I'm having some trouble getting *...
• Updating a local ToolShed repo failed because it don't find index data
  Hi, I try to put a tool which use index data in a local toolshed. Planemo test and planemo serve...