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• DiffBind issues on Galaxy
  Hi, I'm trying to use DiffBind on Galaxy, and i got always the same error, and my output files a...
• DiffBind problem on Galaxy
  Hi, I am using Diffbind and get the following message: [1] "en_US.UTF-8" Fatal error: An undefin...
• DiffBind on Galaxy
  Hi, I am trying to perform Diff Bind on Galaxy using output from MACS and bam files for Read and...
• Diffbind and repmatch fatal error
  Hi! I have 3 chip replicates and I want to find common peaks within them. I used diffbind to do s...
• Custom tool error, results have been output, but galaxy error.
  Hi, I have a custom tool, WGCNA, an R package to construct co-expression network. and in galaxy...
• Help with using the multiBam Summary tool - error message
  Hello, I have just aligned some reads using Bowtie2 and am wanting to look at correlation betwe...
• Diffbind ignores R_HOME and searches diffbind.R in wrong path
  Dear all, I ran into a problem, when trying to use diffbind. I am running a local server of Gala...
• Problem with running TopHat and MARKDuplicates on Galaxy
  To galaxy experts, I would like to ask your advice on some problems I've been encountering with r...
• Error: package "GenomeInfoDb" could not be loaded
  I have a local instance of galaxy (release 18.05) and am trying to use a custom R script that use...
• DeepTools plotCorrelation Error "IOError: [Errno 22] Invalid argument"
  Dear all, I used a matrix generated from multiBamSummary to run plotCorrelation but the error m...
• Galaxy: Genomic Intervals to strict BED Conversion
  Hello: I'm new to the forum and Galaxy/bioinformatics. In the last two months I've been followi...
• Not able to queue jobs via PBS
  Hello, I've been trying hard for past week or so to queue jobs via PBS to run our ATAC sequence ...
• Job's red even if the outputs are correct
  Hey So i've added a new tool to my galaxy and when i run it the job is red (failed) in the error...
• Cuffdiff 2.2.1.5 error with cummeRbund SQlite. "Fatal error: Exit code 1 () -- use version 2.2.1.3 instead
  Hi, so as a disclaimer, I am very new to RNA seq analysis. I received the following error while r...
• Error of installing local Galaxy
  I am trying to install my own local galaxy in my computer. It is OK to run git clone -b release_1...
• Error installing Galaxy locally with Conda environment
  Hi everyone, I'm trying to install a local instance of Galaxy in my Ubuntu using Conda as the de...
• Error with DESeq2 with Kallisto abundance.tsv input
  Hello everyone, I'm trying to run DESeq2 (Galaxy Version 2.11.40.2) on Kallisto abundance.tsv dat...
• Install-tools via yaml file error
  dear all, I want to install a bunch of tools using the install-tools function. In my yaml file to...
• Genome file for Bam to Bed or Genome Coverage
  I generated BAM (mm9) files in Tophat and tried to convert them to Bedgraphs using the BedTools p...
• Error while running cuffdiff "Fatal error: Exit Code 1()"
  Hello, I recently posted about having problems with cuffdiff (https://biostar.usegalaxy.org/p/18...
• Error while trying to filter files
  Hi, I am using the Galaxy Main server to try and filter an interval file by one of the columns, ...
• Problem in FastuniFrac
  Hello, I have been using FastUniFrac but recently facing troubles. I was trying to perform clust...