Question: Galaxy showing and hiding tools as refreshed?
gravatar for vebaev
3.3 years ago by
vebaev130 wrote:



I have installed some tools, but when I click on Galaxy logo and on Analyse data I see tools dissapearing and showing. In general I have to have 2 new groups of tools:
-NGS FASTQ manipulation 
-NGS mappers

but I see these 2 cases randomly when I refrech the page on Galaxy logo or on Analyse data top button:

Graph/Display Data
FASTQ Groomer convert between various FASTQ quality formats
FASTQ Summary Statistics by column
Clip adapter sequences
Compute quality statistics
Draw nucleotides distribution chart
Barcode Splitter
Rename sequences
Draw quality score boxplot
FASTQ to FASTA converter
FASTA Width formatter
Quality format converter (ASCII-Numeric)
Length Distribution chart
RNA/DNA converter
Remove sequencing artifacts
NGS mappers

On this one all FASTQ are appearing without group on the root menu, and mappers are missing (bowtie and tophat)

Graph/Display Data
NGS FASTQ manipulations
    FastQC Read Quality reports
    FASTQ to FASTA converter
    Filter by quality
    Trim sequences
    Collapse sequences
    Cutadapt Remove adapter sequences from Fastq/Fasta
Bowtie2 - map reads against reference genome
Tophat Gapped-read mapper for RNA-seq data​

Than I see FASTQ groupped but some missing, and mappers are again ungroupped.......

tools • 799 views
ADD COMMENTlink modified 3.3 years ago by Bjoern Gruening5.1k • written 3.3 years ago by vebaev130

I see also this behaviour in the data managers section - regreching it, it shows me randonly bowtie2 index manager or SAM FASTA index - builder manager but not all together?!....

ADD REPLYlink written 3.3 years ago by vebaev130
gravatar for Bjoern Gruening
3.3 years ago by
Bjoern Gruening5.1k
Bjoern Gruening5.1k wrote:

Answered here:

this is a general Galaxy problem. You need to restart all Galaxy workers to see your tools and data managers after install. Please restart Galaxy or your Docker container. This will solve your problem! :)
ADD COMMENTlink written 3.3 years ago by Bjoern Gruening5.1k
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