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• Setting clipping sequence as workflow parameter when running FASTX Clipper from BioBlend API
  I am using the BioBlend API to run a workflow on Galaxy, and I am having trouble setting the para...
• Need help with "MACS" tool
  Hi everyone, I don't quite understand the meaning of the parameters of this program.  1. What i...
• Need help with "FASTQ Quality Trimmer" tool
  I am not able to add my file to this tool.     Tool name: FASTQ Quality Trimmer Tool version:...
• How to configure genome in "Map with BWA" (existing tool) after adding it to my local section
  Hi. I have added the lines below to the section I made in config/tool_conf.xml file and "Map with...
• "Realigner Target Creator" tool on usegalaxy.org Locally cached reference unavailable
  HI  I have a bam file generated using a cached reference  (not a user custom one).  However if I...
• Need help with "Map with BWA for Illumina" tool
  Why can't I import my fastq file from my history? I am in the history with all files - gDNA reads...
• Need help with "Unified Genotyper" tool
  Hi there, I would like to add the file 'dbsnp_137.hg19.vcf' to my GATK unified-genotyper analysi...
• Need help with "Barcode Splitter" tool
  i uploaded a fastq file of the output from the sequencing but it is not recognized as a "library"...
• Need help with "Variant Annotator" tool
    What is the meaning of this error" History does not include a dataset of the required format /...
• Need help with "Filter by quality" tool
  which formet this tool gets?   Tool name: Filter by quality Tool version: 1.0.0 Tool ID: tools...
• Need help with "Mark Duplicate reads" tool
  What is the aim of this tool?   Tool name: Mark Duplicate reads Tool version: 1.56.0 Tool ID: ...
• Need help with "patmatdb" tool
  where to find the motif detail for plant membrane proteins   Tool name: patmatdb Tool version:...
• Need help with "Bowtie2" tool
  Hi, is there a way to upload our own reference genome?   Tool name: Bowtie2 Tool version: 0.2 ...
• Need help with "Map with BWA for Illumina" tool
  index   Tool name: Map with BWA for Illumina Tool version: 1.2.3 Tool ID: toolshed.g2.bx.psu.e...
• Need help with "ANNOVAR Annotate VCF" tool
  Hi!  I entered a vcf file into the annovar tool.  It looks like it ran and tells me then number o...
• Need help with "Map with BWA for Illumina" tool
  biuld index   Tool name: Map with BWA for Illumina Tool version: 1.2.3 Tool ID: toolshed.g2.bx...
• Need help with "FASTQ Quality Trimmer" tool
  I have uploaded my fastQ file but it is not showing in drop down list of fastQ-Quality Trimmer to...
• passing parameters to workflows via API
  Hello, I've two questions regarding passing input parameters through workflows API. I'm using th...
• Need help with "Fetch taxonomic representation" tool
  Hello, i need to fetch the HCV sequence from my data set how can i use the fetch-taxonomic-repre...
• Need help with "Filter sequences by length" tool
  How do I upload my fasta file? No options appear when I click the down arrow? Thanks! Jackie ...
• Need help with "Tophat2" tool
  Is there no yeast genome as a reference for using Tophat2 in Galaxy? I only found sc2 and sc3 it ...
• Need help with "Bowtie2" tool
  Although my fasq data is in loaded, why could I not see the fast file in the bowtie2 checkbox? T...
• Need help with "Map with Bowtie for Illumina" tool
  Hi, I would like to map RNA-seq reads to the genome of banana. Is it possible to include it in th...
• problem with "join" tool
  Dear All, I've got problem with "join" tool. When I'm trying to combine two datasets, I obtain ...