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• Galaxy Cloud @ AWS: how to use tophat2 multi-threaded?
  I'm trying to run tophat2 job on my cluster, having allocated 32 core worker node expecting some ...
• 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 ...
• Tophat can't see the build-in reference genome?
  I successfully fetch an hg19 and build an bowtie2 index with Data managers. Bowtie2 can see the r...
• Manage Jobs Tool Error
  Hello, We recently pulled the latest changes from the galaxy repository in to our new server Our...
• Job waiting to run
  I'm having a problem with "job waiting to run" and the job never running. I have my own cluster ...
• GALAXY_SLOTS and slashes
  Here is my experience with an exercise to make Galaxy utilize a multi-core / multi-processor envi...
• Having trouble passing outputs through a wrapper
  Hello,  I am trying to integrated a developed tool into Galaxy. I have to write a wrapper (I ch...
• FASTQ Groomer is taking a long time to process one file
  Hi,  I'm using the Main Galaxy instance to process RNA-seq FASTQ files. I used the batch mode to...
• Cufflink not running
  Dear galaxy admin and user, Cufflink is not running for two particular datasets. While cufflink ...
• Bowtie2 error on locally installed Galaxy : unable to finish job
  Hi, I've installed a local Galaxy. I used data_manager_fetch_genome_all_fasta to get a galGal4 ge...
• Failed in fetching reference genome in local instance
  Hi all, (This question is for Centos 6.5 server, python 2.7, November 2014 version of Galaxy) I...
• Job starts running then is resubmitted and queued
  Hi, I have submitted multiple jobs to both Bowtie2 and Bowtie for Illumina, and although 2 of th...
• Errors Trying to Fetch Reference Genome
  I am running Galaxy in AWS. I followed the instructions [here][1] to install it. I am trying to f...
• Galaxy crashing, running out of memory (database upload?)
  Hi,   For some reason my Galaxy process gets killed because it runs out of memory after a few s...
• Cloud Man - job triggering
  When I have jobs that have different memory and CPU requirements, is it possible to somehow speci...
• Encoding problem with return value from tool's custom dynamic_options function
  Dear Biostars community, I am having problems developing a python function to return some custom...