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• Extending workflow from single file input to collection input
  So I've made a work flow with various tools on the toolshed. These tools can only take in a singl...
• cummeRbund SQLite database error from Galaxy main CuffDiff tool
  I'm trying to create an SQLite database to download and use with cummeRbund by using the "Create ...
• SnpEff database build tool for C.elegans
  I am trying to use the SnpEff build database tool to build reference genome for C.elegans and use...
• mixing collections and "multiple" input tools
  I'm trying to modify a workflow to work on list collections. Most tools work as expected without ...
• Filename Extension In New Tool
  I have a tool that takes a pdb file as input. The authors of the *compiled* code require that th...
• 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...
• sam to bam - Galaxy version 17.01
  Hi All First of all I am not a bioinformatician, I'm looking at someone else's test workflow. I ...
• Database Error When Bootstrapping Tool Shed
  I'm attempting to host a local instance of the Galaxy Tool Shed for development purposes. I've al...
• How many input BAM files for Cuffquant?
  I'm trying to use the Cufflinks v. >2.2.0 workflow, which uses Cuffquant. The Cufflinks docume...
• How to align sequences with MAFFT
  I want to align two FASTA sequences. I am trying to use MAFFT , Multialign tool in Galaxy. Doe...
• How do I process multiple pileup files at once with Varscan to get the vcf files?
  I have a list of 100 SRA IDs for which I need to get the VCF files using VARSCAN. VARSCAN takes...
• Setting Dbkey In A Workflow
  I'm working on making my first workflow in Galaxy, using a local server. A high level overview of...
• Varscan on multiple samples generates error
  Hello, I am using "samtools mpileup" to generate a pileup file from my .bam dataset and then pas...
• No Output Produced.....
  Hi, I have my own image registration tool that I've created on my own local instance of galax...
• Automatic BAM Index creation but tool is unsuccessful in identifying index
  Hello Everyone, I am currently working on a few tools in galaxy which require both a bam and bam...