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• Need help with mpileup tool on Galaxy
  Hey, I'm new to bioinformatics and I'm having some trouble creating an mpileup. Trying to create ...
• Tool error "Remote job server indicated a problem running or monitoring this job"
  Hello Galaxy team, I'm trying to align some fastq files to mm10 and the job crashes with this de...
• Multiple cores on galaxy?
  Hi I'm a complete Galaxy newbie, and am trying to configure a 16-core workstation to run, with a...
• extract reads with fastq-dump tool
  I'm trying to extract reads from sra files but it says that one of the files is a new dataset and...
• Running TopHat locally
  Hi, I'm trying to run Tophat2 on a local instance of galaxy. Tophat2 and Bowtie 2 have been inst...
• using SAF gene annotation file in featurecounts
  Hello! I'm new to Galaxy and was wondering if I could get some help with using the featurecounts...
• Population Genetics analysis help
  Hello, I'm trying to do a bioinformatics analysis for my senior undergrad project. I have 3GB wo...
• Admin privileges on local Galaxy
  I'm trying to use a local instance of Galaxy that is installed on my BioLinux machine. To add som...
• Why won't Galaxy recognise uploaded hg19 .fasta.gz file?
  Hi. I'm doing RNA-seq analysis for the first time and want to upload the hg19 genome from 1000 Ge...
• Wrapping Weka tools in Galaxy
  i'm new in galaxy ,and i tried to write  weka command line in XML file but it is not work ,Is the...
• homer installaton from tool shed
  Hello, I'm running a galaxy local instance in my computer. I'm trying to install homer from tool...
• Which Tools Can A File Be Used With?
  I'm starting to poke around wtih Galaxy. Suppose I have a file that I've uploaded, or pulled in ...
• add custom tools to local galaxy
  hi, I'm installing tools to galaxy, but some tools are not existed in tool shed, such as fqt...
• Custom JavaScript file in Galaxy
  Hi all! I want to add some custom features to my own Galaxy instance and I need to load a new Ja...
• Interactive (web page-based) tools
  I have several cases where it would be useful to be able to have an interactive webpage as part o...
• Limitations of DAVID pathways
  Hi all, Sorry for posting what is probably a dumb question but I'm a masters student writing up ...
• Error Handling In Galaxy Workflows ?
  Hi All- Is there any plumbing in place for handling errors that occur in component tools of work...
• Tool Installation from Tool Shed
  Hi all, I recently downloaded and installed a local version of Galaxy and am following some basi...
• input file types to DESeq on the cloud
  Hi there, I've had a go at using the Ratsch lab DESeq tool but it seems to require your input fi...
• RNA-Seq High Expression Genes Lost
  Hi I'm noticing that after running my BAM files through CuffDiff and CuffNorm that some genes th...
• Stitch Maf Blocks
  Hi, I don't undestand how to use the tool "Stitch MAF blocks". I update a small bed file and now ...
• Lading SRA files into Galaxy
  I have been trying to load SRA files into Galaxy. I have tried using SRA tools, EBI download and...
• can't get any VCF tools to work
  Hi, I can't seem to get any of the VCF tools to work on my combined VCF file, can't sort it, can'...
• How to start job on dynamically started openstack hosted pulsar server?
  I'm trying to set up a cloud based tool execution function where a job is started on a local gala...