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• This tool was disabled before the job completed
  Hello everyone, I am working on a local instance of galaxy. I am using uswgi and 2 handlers, wit...
• Trimmomatic and Trim Galore are not working.
  I am performing an RNA-seq and am trying to trim adapter sequences with Trim Galore. When I made ...
• My Tophat Jobs Are Stuck In The Queue
  Hi, I've been running small tophat jobs as part of a student exercise, but since yesterday morni...
• Cufflinks not working for a week
  Hi There, I am trying to run cufflinks for about a week by now but job remains on the cue (grey) ...
• This job is waiting to run for almost 12 hours
  Hi, I'm a newbie using Galaxy. I am trying to create assemblies with Unicycler, but the job is n...
• FastQC doesn't work after Splitter
  Hello, I am working with paired-end reads, in separate files, and as far as I understood these s...
• Galaxy slurm cluster empty files
  I have connected galaxy to our slurm cluster, but am having an issue with running jobs. Galaxy sh...
• Trim Galore run time issue
  Hello, I am following the tutorial for NGS Quolity Control. I reached the step where the Trim Gal...
• Error with "Trim leading or trailing characters" tool
  Hi all, I have been trying to trim my fastq files, and I am running into problems. I used the "T...
• Question: Trim Galore in Galaxy cannot work
  Hi, everyone, I have a problem about Galaxy trim galore tools. When I download data from SRA, Ga...
• splitting and rejoining datasets
  I am working with large fastq files which are too big to use on galaxy (about 120 gb, so even aft...
• unable to run tophat on trim galore processed reads
  dear sir i have run tophat on reads trimmed by trim galore with reference to hg19. i am getting r...
• Personalised tool not running in local galaxy (always yellow but not sending command)
  Hi, I am creating a wrapper to run a personalised tool in my local galaxy installation. I tested...
• Prolonged - Job Waiting To Run
  Dear Galaxy team,   I am running short read alignments with Bowtie for illumina using some data g...
• Usegalaxy main server down? (Queue not working) - PROBLEM FIXED
  Hi all, Is the main usegalaxy server running, or is it just under a high work load? I've run cuf...
• wig to bigwig
  Hi Galaxy, I am trying to convert 12 Wig files to bigWigs since 7PM on Saturday. Conversion work...
• TopHat running since Saturday night
  Hi, A TopHat job keeps running since Saturday night. Similar jobs worked in 3 hours before this ...
• Trimming And Thinning Of Paired-End Reads
  Hi galaxy users, I've been experiencing some problems trimming the adapters and filtering by qua...
• Trinity with multiple datasets
  Hello, I am running trinity on 4 data sets (2 left reads, 2 right reads) and I want it to be com...
• Problem Reimporting Histories
  Dear galaxy users, here at European Institute of Oncology we're deploying a brand new ga...
• RNA genes count using HTseq
  Hello: I am new to Galaxy, but based on my understanding of how things work, I mapped some RNA-s...
• Adapter and quality trimming using Trim Galore integrated Galaxy
  Hello. I need to make adapter trimming and quality trimming for my FASTQ paired files. I work in ...
• Job Status - Waiting to run since yesterday and not changing
  Hello, I am a new user. I have been trying to get a job that uses MACS tool (Model-based Analys...