I’m struggling to figure out how to visualise a SAM file in Trackster as a normal user (i.e. without admin privileges). I’ve tried both my local install and use galaxy.org.
This is what I’ve done on usegalaxy.org:
Uploaded paired-end fastq sequences and a reference fasta file.
Mapped with BWA.
Clicked on SAM output – Visualize > Trackster
Chose 'View in new visualisation’, then ‘Add a Custom Build’.
In the ‘Add a Custom Build’ I give my build the name ‘solanum_reference’ and the key ‘solanum_reference_1’. I select the fasta mapping reference from my history under the ‘FASTA’ tab and under the Len File entry I upload a .len file (tab-delimited) called ‘solanum_reference_1.len’.
I navigate back to my SAM history item, associate the Database/Build with my new build (via the Edit attributes icon) and then again Visualize > Trackster > View in New Visualization. I name the Browser, select my ‘solanum_reference’ as the 'Reference genome build' and hit ‘Create’.
The view changes to the Trackster Browser and at the top I reads: "Preparing data, This can take a while for a large dataset…..etc., etc. "
After a few minutes, this changes too: “Cannot display dataset due to an error.” If I click on ‘View error’ I get:
Couldn't open /galaxy/data/chrom/solanum_reference_1.len , No such file or directory
Is it possible to create a custom build and use it to view a SAM file without adding the .len and .2bit files in to the Galaxy file system as an administrator?
If so, what am I doing wrong?
Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
Tel: +44 (0)1603 450601
I've been trying to use the cufflinks-cuffmerge-cuffdiff flow to analyze my
RNAseq data. However, cuffmerge lost my p_id. My p_id was originally from
changing the protein_id to p_id by myself in the gtf file. The current p_id
showed up in the same attributes column as gene_id in the gtf file. Does
anyone know how to make it reachable by cuff? I'm using galaxy public
platform. Apparently in the history people say solving the problem by
writing an extra code. But I cannot find anywhere to input codes in galaxy.
Do I have to run everything on my own computer?
Thanks a lot!!!!!
I am trying to upload files on galaxy main since yesterday and I can't
get it work.
The files I want to upload are RNAseq fastq files from ENCODE (about 8
Go in size). So I first tried to use the http address of the files. The
job is running forever but without finishing and without error message.
I also tried using FTP but in that case, I could not connect to the
main.g2.bx.psu.edu server (I get the message "ECONNREFUSED - Connection
refused by server"). I am using my email address as login (the same as
for galaxy login) and the same password.
Do I do something wrong or is there a global problem?
Thank you in advance for your help.
Dr. Emmanuelle LERAT, CR1 CNRS, HDR
Laboratoire Biometrie et Biologie Evolutive
Universite Claude Bernard - Lyon 1
UMR-CNRS 5558 - Bat. Mendel
43 bd du 11 novembre 1918
69622 Villeurbanne cedex
Phone: 33+ 220.127.116.11.18
Fax: 33+ 18.104.22.168.88
Hello, galaxy users and developers, I wrote a perl script conducting saturation analysis which called macs several times.The tool's output was right but ,errorAn error occurred with this dataset:INFO @ Sat, 18 Jan 2014 21:46:33: # ARGUMENTS LIST: # name = /usr/local/galaxy-dist/database/job_working_directory/000/0.output # format = BED # ChIP-seq file = 0.test.bed # control file = 0.control.bed # effective genome size = 2.70e+09 # tag size = 2
Tool execution generated the following error message: INFO @ Sat, 18 Jan 2014 21:46:33:
# ARGUMENTS LIST:
# name = /usr/local/galaxy-dist/database/job_working_directory/000/0.output
# format = BED
# ChIP-seq file = 0.test.bed
# control file = 0.control.bed
# effective genome size = 2.70e+09
# tag size = 28
# band width = 300
# model fold = 16
# pvalue cutoff = 1.00e-05
# Ranges for calculating regional lambda are : peak_region,1000,5000,10000
INFO @ Sat, 18 Jan 2014 21:46:33: #1 read tag files...
INFO @ Sat, 18 Jan 2014 21:46:33: #1 read treatment tags...
INFO @ Sat, 18 Jan 2014 21:46:37: #1.2 read input tags...
INFO @ Sat, 18 Jan 2014 21:46:39: #1 Background Redundant rate: 0.04
INFO @ Sat, 18 Jan 2014 21:46:39: #1 finished!
INFO @ Sat, 18 Jan 2014 21:46:39: #2 Build Peak Model...
INFO @ Sat, 18 Jan 2014 21:46:47: #2 number of paired peaks: 11875
INFO @ Sat, 18 Jan 2014 21:46:47: #2 finished!
INFO @ Sat, 18 Jan 2014 21:46:47: #2.2 Generate R script for model : /usr/local/galaxy-dist/database/job_working_directory/000/0.output_model.r
INFO @ Sat, 18 Jan 2014 21:46:47: #3 Call peaks...
INFO @ Sat, 18 Jan 2014 21:46:47: #3 shift treatment data
INFO @ Sat, 18 Jan 2014 21:46:47: #3 merge +/- strand of treatment data
INFO @ Sat, 18 Jan 2014 21:46:47: #3 call peak candidates
INFO @ Sat, 18 Jan 2014 21:46:48: #3 shift control data
INFO @ Sat, 18 Jan 2014 21:46:48: #3 merge +/- strand of control data
INFO @ Sat, 18 Jan 2014 21:46:48: #3 call negative peak candidates
INFO @ Sat, 18 Jan 2014 21:46:48: #3 use control data to filter peak candidates...
INFO @ Sat, 18 Jan 2014 21:46:48: #3 Finally, 2003 peaks are called!
INFO @ Sat, 18 Jan 2014 21:46:48: #3 find negative peaks by reversing treat and control
INFO @ Sat, 18 Jan 2014 21:46:49: #3 Finally, 120 peaks are called!
INFO @ Sat, 18 Jan 2014 21:46:49: #4 Write output xls file... /usr/local/galaxy-dist/database/job_working_directory/000/0.output_peaks.xls
INFO @ Sat, 18 Jan 2014 21:46:49: #4 Write output bed file... /usr/local/galaxy-dist/database/job_working_directory/000/0.output_peaks.bed
INFO @ Sat, 18 Jan 2014 21:46:49: #4 Write output xls file for negative peaks... /usr/local/galaxy-dist/database/job_working_directory/000/0.output_negative_peaks.xls
INFO @ Sat, 18 Jan 2014 21:46:49: #5 Done! Check the output files!
Just ordinary macs output, we see it in galaxy-macs report. The only problem is that they're in stderr. With this error I cannot do other works with the output of this tool.How can I deal with it?Thanks!
I have a question about the use of BedTools in Galaxy. I am trying to
obtain a graph or table of the number of RNA reads mapped to different
locations on my custom genome. When I try running "Create a Bedgraph of
Genome Coverage" it requires selection of the "Genome Build" from a
dropdown list. Is it possible for the program to utilize a custom genome
not in this list?
over the last month we developed a new version of GATK2 wrappers and are
now seeking for testers, users and overall feedback.
We are currently targeting GATK 2.8. One of the big issues with GATK2 is
the new licence. Because of that we can't install GATK2 with the
wrappers, but we hope we have done it as easy as possible to plugin your
local installed version. Furthermore, we made it easy to disable the
'call home feature' of GATK2 (if you have a GATK keyfile). Read more
The code is stored here:
The ToolShed wrappers can be found here:
I would like to thank Jim Johnson, Nicola Soranzo, Dan Blankenberg and
the Galaxy Team. If you like the wrappers you know what to do during the
If you have feedback or patches please let us know.
*We are pleased to announce the 1st Galaxy Australasia Workshop 2014 (GAW
2014) <https://wiki.galaxyproject.org/Events/GAW2014> will be held in
Melbourne, Australia on 24 and 25th March 2014.*
The Galaxy Australasia
a great opportunity for you to participate in two full days of
presentations, discussions, poster sessions, keynotes and lightning talks,
all about ways of using Galaxy for high-throughput biology, imaging and
other scientific applications. The workshop will also include Training
Sessions taught by Galaxy developers and master users. GAW 2014 will run 24
and 25th March, immediately preceding Computational and Simulation Sciences
and eResearch <http://wp.csiro.au/css/> in Melbourne.
GAW 2014 will also include poster session, keynote speakers.
*You should attend to:*
- Present your work!
- Learn best practices for deploying Galaxy, defining and installing
resources, and managing and moving large datasets.
- Network with others in the Galaxy community who are facing similar
challenges and using Galaxy and other tools to address them.
- Learn what the Galaxy Project's plans are, and contribute to Galaxy's
- how to visualize your data in Galaxy and use visualization to guide
your analysis (visual analytics)
- how to share, publish, and reuse your analyses with Galaxy
- how to perform and enable your users to perform common, yet
complex, analyses using Galaxy
- when and how to use Galaxy on the Cloud
*Topics will potentially include:*
- Image analysis and processing using Galaxy.
- RNAseq/ChIPseq/Variant Calling/RNA Quality Control.
- Galaxy on the Research Cloud.
- CSIRO galaxy service - partnership between science and IT.
- Identifying proteins from mass spec data with Galaxy.
*Call For Abstracts*
Participants who wish to give presentations or present posters (potentially
with technical demonstrations) that showcase use of Galaxy should submit a
brief one-page abstract and brief one-paragraph bio to the GAW2014
Organisers <gaw2014-org(a)groups.galaxyproject.org> *by February 15th,
will be notified by February 28th. Speakers, panelists, and poster
presenters will be selected by the program committee based on relevance to
symposium objectives and workshop balance.
Submissions should clearly state whether they are for: poster or oral
Looking forward to seeing you all in Melbourne!
GAW 2014 Organising
I shared a history with another user and I am now trying to delete said history. When I go to delete it I am told to unshare it first. I found one message in the [dev] list which says to click the "shared" link when viewing Saved Histories and choose "unshare". When I do this nothing happens. When I had the other user (who has a button which says "unshare" for this history) click "unshare" that user is told they can't unshare it. How to go about this?
Jen, maybe you can add deleting shared histories to your deleting/disk space video?