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• Using Data Managers for uploading new genome
  I just put in production a small CloudMan based Galaxy server for our institute and in addition t...
• Tophat in Cloudman: missing built-in genome
  Hell all, After several days of struggling, I finally managed to set up a Galaxy instance in Clo...
• SAM to BAM of samtools: It can't find built-in reference genome.
  as the title! I installed data manager of samtools index builder. What a strange affair! SAM_to_B...
• built-in genome for HISAT2 not available
  I am trying to map fastq to mm9 genome using HISAT2. But the drop-down list of built-in genomes i...
• Nucleotide Analysis - Gc Percentage
  Hi all, Are there any built in Galaxy tools that I have missed to do with GC percentage (or inde...
• Srma On A Local Galaxy Instance?
  Does anyone know how to get SRMA to work properly in galaxy? I've used the pre-built 0.1.15 jar ...
• HISAT2-reference genome not available in a local -- data must be installed first
  Hi everyone, When I'm trying to use in my local galaxy HISAT2 for mapping the reads I have an inf...
• Can't find the tool group "Operate on genomics interval" on the toolshed to add to server install
  We've just installed galaxy on our server. We would like to add the tool group, "Operate on geno...
• can't access data managers
  Hi, I'm trying to use Data Managers to add my own built-in reference genomes for Hisat on a loca...
• Integrating Pre-built Bowtie2 Indexes
  I have obtained the pre-built bowtie2 indexes from Ensemble and would like to integrate them into...
• How To Add A Built-In Index For Tophat2?
  TopHat2 needs built-in index/ reference genome in order for it to run. I need to add hg 16 index ...
• RNA-star: splice junction
  Hello, I am new to RNA-seq data. I am using the built-in index and using the reference genome 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 ...
• HISAT2 - no reference genome available
  HISAT2 does not have any options for a built-in reference genome. I need mm10. Source for the r...
• Papio Anubis 2.0 genome annotation
  Hello, I was wondering if there was a possibility of adding the papAnu_2.0 annotation as a built...
• Adding a reference genome to a local Galaxy
  Hoping to find some Galaxy Dev team experts. I am trying to add hg38 to the HiSat2 tool so that t...
• Cufflinks Returned 0 Value In All Rpkms
  Hi I have been trying to analyze a rat Solid SRA but I encountered a problem: cufflinks gave me ...
• Tools not installing in local galazy
  I'm trying to get galaxy running locally but when I try to install new tools the dependencies don...