I just started using the main galaxy instance. I uploaded via FTP and
imported several FASTQ files. They all appear in the list of my "saved
datasets" (see attached screenshot). However, when I click on any of the
tools in the left panel (e.g. "FASTQ Summary Statistics") I get in the
middle panel the info for the tool but the dropdown menu listing the
available FASTQ files is empty (see attached screenshot). What do I need to
do to be able to perform analysis on the FASTQ files that I uploaded?
I had an odd problem today, seems not a problem before:
I am trying to upload a simple tab-delimited text file into galaxy,
but it kept telling me:
format: txt, database: hg19
The uploaded binary file contains inappropriate content
Also, showed filesize as 0 bytes.
I tried Unix format, DOS format. It is a very small data, only 348 bytes.
4 rows, as attached.
What is WRONG?
I am new user to galaxy and I was wondering if there is a way to estimate the average delay before execution of currently submitted jobs in galaxy?
Benjamin Leblanc, Ph.D. - K. Helin group
BRIC - University of Copenhagen
Ole Maaløes Vej 5, building 4, 4th floor
DK-2200 Copenhagen N, Denmark
Office phone: +45 35 32 55 37
I am having problem with starting my query. For days it is showing "Job waiting to run". Is the system backed up and there is a long queue? or is there a problem with my query? Normally if there is any problem it shows an error message. I am within the usage limits. I am trying to map my SOLiD data set to custom reference genome (fasta format). I converted the SOLiD output to fastq. Then I am using Map with Bowtie for SOLiD. Everything went fine quickly except the last step, which waiting for over 6 days now. Any help or suggestions appreciated.
Redfield Building 3-04
Woods Hole Oceanographic Institution
45, Water Street
Woods Hole, MA
Dear Galaxy users,
We are happy to announce the release of version 1.6 of the Genomic HyperBrowser,
a analysis web server built on top of Galaxy. This release is a companion to an
article recently published in Nucleic Acids Research, to be included with the
2013 Webserver issue:
Sandve, Geir K., et al. "The Genomic HyperBrowser: an analysis web server
for genome-scale data." Nucleic acids research (2013)
To quote the abstract of the article:
"The Genomic HyperBrowser (http://hyperbrowser.uio.no) is an open-ended web
server for the analysis of genomic track data. Through the provision of
several highly customizable components for processing and statistical
analysis of genomic tracks, the HyperBrowser opens for a range of genomic
investigations, related to, e.g., gene regulation, disease association or
epigenetic modifications of the genome."
In this article, an overview of most of the 42 tools and 83 analyses included with the
Genomic HyperBrowser is presented (for the first time) in table form.
The Genomic HyperBrowser will also be presented in the 2013 Galaxy Community
Conference (http://wiki.galaxyproject.org/Events/GCC2013), in the Training day
workshop titled "Statistical Genome Analysis with Galaxy", and also in a regular
The focus of this release has been on new and revamped tools:
1. A set of new tools has been added:
- Visualize track elements relative to anchor regions
- Create high-resolution map of track distribution along genome
- Create high-resolution map of multiple track distributions along genome
- Extract segments where value is greater/less than threshold
2. A new hypothesis test for 3D-colocalization of genomic elements has been
added (along with a tool for easier access to the analysis). This hypothesis
tests checks whether the elements of a genomic track is positioned on the
DNA (in interphase) closer in 3D than expected by chance. The methodology
has been published in a separate article:
Paulsen, Jonas, et al. "Handling realistic assumptions in hypothesis testing
of 3D co-localization of genomic elements." Nucleic acids research (2013).
Included with this analysis are readily preprocessed Hi-C datasets for the
cell lines GM06990, GM12878, hESC, K562, and RWPE1 for human (hg19), in
addition to cell lines cortex and mEsc for mouse (mm9), all available in
3. The usability of tools has been improved:
- The structure of the HyperBrowser tools has been rearranged, and renamed
for easier understanding and use
- Help text and usage examples (using Galaxy Pages with embedded histories)
has been added to most tools
4. Numerous bug fixes and improvements have been made, including the
fixing of several memory leaks.
We hope you will find the Genomic HyperBrowser and new additions useful. Please
let us know if you experience any problems, need help with your analysis, or
have ideas for new functionality!
For the HyperBrowser team,
Sveinung Gundersen, PhD Student, Bioinformatics, Dept. of Tumor Biology, Inst.
for Cancer Research, The Norwegian Radium Hospital, Montebello, 0310 Oslo,
Hi, when we try using Map with BWA for Illumina on the public server, it never starts running and sits in a queued state forever. We have jobs that have been queued for more than 5 days. Any ideas on why these jobs never start?
Richard Casey, PhD
I am new at Galaxy. I need to define if a set loci ( about 700) is
transcribed, i.e. these loci overlap with those reported in the Encode
RNA-seq data. The track contains several tables, can you please suggest me
how to proceed? do I need to download all the tables from UCSC table
browser and then upload/send them to Galaxy? Is there a way to refer only
to the Encode RNA-seq track without downloading the whole table set?
I have the coordinates of each one of my loci, from those I can obtain the
sequences. I intended to use the Public Galaxy Main Instance.
Marco Santagostino, PhD
Laboratorio di Biologia Molecolare e Cellulare
Dipartimento di Biologia e Biotecnologie, University of Pavia
Ferrata street, 9 - 27100 Pavia, Italy
Tel.: +39 0382 985540
Fax: +39 0382 528496
I'm using Nebula and when I try to use the annotation tools (genomic
annotation and gene annotation in NGS annotation menu) I got always this
error despite of the bed file that I use:
An error occurred running this job:Unable to run this job due to a cluster
I also got this error message for everything that I try, even upload data
sets (which I can not upload anymore)
Could you indicate me how to solve this?
We have two Filter FASTQ jobs running on the Galaxy public server. Both jobs have been running for more than four days. This seems like an excessive amount of runtime. Do Filter FASTQ jobs normally take this long to run?