In the admin panel > Manage data libraries section I have an issue with
When I click on each dataset's triangle menu and ask for deletion,
everything is fine. But whenever I select datasets and ask for deletion
with the drop down menu at the bottom of the page, Galaxy tells me I
don't have the rights to delete them.
I get the following message:
"You are not authorized to delete any of the selected datasets."
Did I miss anything?
Dear Galaxy Team,
I was recently pointed to your website to analyse my NGS data, my
primary interest is in mapping small RNA reads to microRNA.
After following the tutorials (which are excellent) I am able to
upload and map with Bowtie by small RNA data set produced from the
From this point I am completely lost with what to do next to obtain
small RNA/microRNA mapped to the genome and a count of the tags etc as
the RNA Analysis seams to be dedicated to transcript assembly and
quantitation rather than microRNA from mirBase.
I have been also looking at the DARIO websever http://dario.bioinf.uni-leipzig.de/index.py
for doing the mapping, but I need to convert my BOWTIE SAM output to
either BED or BAM file format and remain under 60MB in size.
They suggest that the converting the mapping results to BED file be
done with map2bed.pl (does Galaxy have a tool for this).
For conversion of the mapping to BAM, I can use SAM to BAM with
SAMTOOLS with header file intact as this is required for DARIO
This also seems a problem as I dont think I have the header
Any help or suggestions would be appreciated.
Shayne A. Bellingham
Department of Biochemistry and Molecular Biology
Bio21 Molecular Science and Biotechnology Institute
The University of Melbourne
30 Flemington Road
Parkville VICTORIA 3010
I was looking through your Galaxy Wiki, but could not find an answer to my
question. I would most appreciate any help regarding the following issue:
I'm conducting a GWAS study in horses. Up until now I've been using PLINK
for my association analysis, and now I wish to generate a Manhattan plot.
I've been looking through your online version of Galaxy-Tool under SNP/WGA:
QC; LD; Plots <http://main.g2.bx.psu.edu/root/tool_menu#> -->
and I've read all the instructions. I think I have an appropriate file ready
to run this on your online version, but I was hoping you can send me an
example file of how exactly the data should look like (and not just brief
explanations about the syntax), and in what format exactly should I upload
it? If you have a tutorial about this, even better.
Molecular Evolution Lab
Koret School of Veterinary Medicine
The Hebrew University of Jerusalem
I am only recently beginning to discover Galaxy, so please bear with me...
I am trying to convert a bed to bigbed file, but the job remains
'grey', it does not start. I repeated the same conversion with the
UCSC sample file
(http://genome.ucsc.edu/goldenPath/help/examples/bedExample.txt) , but
it still does not work. I simply uploaded the file directly from the
link and then used the bed-to-bigbed conversion tool.
So either I am doing something wrong or could there be an issue with
this conversion on the server?
Thanks for your insights,
We uploaded 12 samples to Galaxy last night via FTP. This morning, I went to "Get Data" and clicked on all 12 that were under the FTP location, chose the type of file they were and reference genome and then clicked "Excecute." The 12 moved over to the History panel and after a couple of minutes went from gray to yellow. As of this moment, all 12 are still in the yellow stage (still spinning). Is this normal for that many samples (each sample is about 8GB in size) or should they already have turned green? Any info would be greatly appreciated.
There will be two Galaxy workshops at the University of Southern California
(USC) next week. Both are presented by Jeremy Goecks of Emory University and
the Galaxy team. *Both workshops are open to the public:*
*Galaxy: A web‐based workbench for interactive and reproducible analysis of
high‐throughput sequencing data, Thursday, June 23, 2011*
At Aresty Auditorium, Harylene J Norris Cancer Research Tower, USC Health
Science Campus, 1450 Biggy Street Registration is free, but required.
Register at https://uschsl.qualtrics.com/SE/?SID=SV_bDaxnZwEfrfk1BG
9:15am-Noon Introduction to Galaxy including 30 min. Q&A Session
2:00pm-5:00pm High‐throughput sequencing data analysis including 45 min.
*Progress and Challenges in Developing a Web-based Platform for
Computational Biomedical Research, Friday, June 24, 2011
See USC ISI AI Seminar Page (
http://ai.isi.edu/index.php?module=seminars/index) for details on time and
The recent reliance on computation in biology has created an informatics
crisis for biomedical researchers: computational resources are often
difficult to use, communicating techniques and experiments is challenging,
and reproducibility is very limited. Galaxy is one approach for addressing
these problems. Galaxy is a popular Web-based platform for performing
accessible, reproducible, and transparent genomics research. Galaxy provides
a collaborative environment for performing complex analyses with automatic
and unobtrusive provenance tracking; these features allow transparent
sharing of both the precise computational details underlying an analysis and
also intent, context, and narrative. Based on experiences with Galaxy,
Jeremy will discuss some open problems that might be addressed using
artificial intelligence methods and techniques.
I was trying to extract FASTA sequences using the following tab separated data for Chicken on the Galaxy Main server:
chr5 47258168 47259240
chr18 1938527 1939965
chr2 101973625 101974007
chr4 75653898 75674045
chr19 4258837 4263299
chr4 39330049 39372715
chr4 9606881 9610083
chr15 7264937 7265599
chr21 6659189 6667015
chr2 351239 352821
I got the following galaxy output:
7: Extract Genomic DNA on data 6
format: fasta, database: galGal3
Info: 10 warnings, 1st is: Unable to fetch the sequence from '47258168' to '1072' for build 'galGal3'.
Skipped 10 invalid lines, 1st is #1, "chr5 47258168 47259240"
Any ideas what I am doing wrong?
> 1. Is there any help file explaining directory structure and what
> configuration files used for?
The Galaxy wiki is the best place to go for these things, as
Louise-Amelie said. You should be able to ignore most things in the
config files initially as they will "just work". You can ignore most of
the directory structure as well, except perhaps the "tools" directory.
> 2. I got list of all dependencies from website, Do I have to install
> tools in /usr/local/bin/ or can be installed at any custom location?
Mostly, the install should (again) "just work" (install the tarball or
distrib and run). I've a got a Galaxy installation checklist here:
It's a bit peculiar to my own situation, but it might give you another
Paul Agapow (paul-michael.agapow(a)hpa.org.uk)
Bioinformatics, Centre for Infections, Health Protection Agency
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Looking at the output of the SplicingDiff files of CuffDiff, me and my
colleagues are preplexed about the output of the p_values and q_values.
We've tried different inputs of different samples to compare but never seem
to manage to get p_values smaller than 0.50 and we keep getting higher than
1 q_values (also smaller which we expect) which we think is strange too.
The input files we use for the CuffDiff are the CuffCompare of a combined
CuffCompare of a dataset, or the CuffCompare of just the two samples we want
to analyse. For the samples input files we use the TopHat files
Could you please help us get meaningful results for the SplicingDiff files
or help us understand the data?
The top 5 rows of our typical SplicingDiff file:
test_id gene_id gene locus sample_1 sample_2
1583 TSS11905 XLOC_028193 - chr5:134910259-134914719 q1 q2
2385 TSS12870 XLOC_030892 - chr7:29976178-30008608 q1 q2
8005 TSS6887 XLOC_016656 - chr18:47803031-47807892 q1 q2
10214 TSS9761 XLOC_022527 - chr20:43128822-43138649 q1 q2
2818 TSS13383 XLOC_032450 - chr8:100899717-100905900 q1 q2
status value_1 value_2 sqrt.JS. test_stat p_value q_value
1583 OK 0 0 0.000771867 0.797878 0.501645 164.5400
2385 OK 0 0 0.001548470 0.797809 0.505482 82.8991
8005 OK 0 0 0.003288510 0.797717 0.508184 55.5615
10214 OK 0 0 0.001414180 0.797620 0.510277 41.8427
2818 OK 0 0 0.007112780 0.797416 0.513678 33.6973
Thanks in advance for your most appreciated help,
Does anyone know how to get SRMA to work properly in galaxy? I've used the pre-built 0.1.15 jar as well as a 0.1.16 jar I built from source, but the result of an SRMA re-alignment job in both instances is a python process which only takes a few percent CPU (or less, since it only seems to be outputting timestamps to the terminal). Here are my system's specs if they're important: 2.8Ghz Intel i5, 4 core; 4GB 1333MHz DDR3; 1TB HDD (430GB free). The OS is OS X 10.6.7. I've also built the required indices and placed them in path/to/galaxy-dist/hg19/srma_path/hg19.dict, hg19.fa.fai, and hg19.fa; the hg19 is a concatenated version of the various chromosome and contig files, and I've followed the sample files in adding these locations to the .loc files (both srma and picard tools).
The NGS installation page seems to suggest that SRMA does work, so I'm not sure if I'm overreacting, but I'd really appreciate any advice on this, since I imagine others have had similar problems.