The 2012 Systems Bioinformatics Workshop will be held at the Institute
for Systems Biology in Seattle on September 10th & 11th. We invite
The workshop will be a two day meeting featuring talks, tutorials and
a hackathon, bringing together engineers and scientists building
software for biological data analysis. Themes for this year's workshop
include networks, visualization, and software architecture for
collaborative research computing.
Paramvir Dehal, Computational Research Scientist/Engineer, MicrobesOnline, KBase
Max Franz, Software Engineer and User Interface Designer, Cytoscape Web
Michael Kellen, Director of Technology at Sage Bionetworks
Mike Smoot, Chief Architect of the Cytoscape project
James Taylor, The Galaxy project
Matt Wood, Amazon Web Services
Regulatory network inference with cMonkey
Cloud Computing with EC2
Graph data storage with Neo4j
Visualization and D3
More information can be found on the workshop website:
hopefully this is a simple question: How can I include a folder into the
The backgroud is, that I installed Galaxy on one of out server, which
has access to the data folders used everywhere at our institute. So,
instead of uploading and copying serveral big files (and waisting space
on servers) I want to make a link to the appropiate folder, so it can be
used like as the data has been uploaded. I hope I explained enough
details... The question is: is it possible?
Thanks for help, Norbert
Institute of Bioinformatics
Faculty of Medicine
University of Muenster, Germany
Use *BSD because Linux is a patch for Linux
Bowtie and BWA jobs seem to be forever on queue, but other jobs run
normally. Is there a problem or is this expected? Thank you.
Antony M Jose,
Dept. of Cell Biology & Molecular Genetics,
University of Maryland,
Rm 2116, Bioscience Research Building,
College Park, MD - 20742.
I submitted Bowtie and BWA alignment jobs on two relatively small fastq
files, and the jobs still appear as gray after multiple hours. can you
please check and see if the system if functioning properly?
Hello Di Nguyen,
Without seeing your history, my initial guess is that the SAM output
from the mapping runs need to be sorted before running Cufflinks.
(Tophat, which is designed to map spliced RNA-seq data, sorts the SAM
output as part of the data processing, but BWA and Bowtie do not).
The workflow provided on this FAQ can be followed to sort SAM files for
If you continue to have problems, please submit a bug report (click on
"green bug" icon from the error Cufflinks dataset as run on the main
public Galaxy instance (http://usegalaxy.org), leave all inputs and the
error dataset undeleted, note this email address in the comments if it
differs from your Galaxy account email address (so that I can link the
two issues together), and we can provide more feedback.
Hopefully this helps,
On 6/20/12 1:28 PM, Di Nguyen wrote:
> Hi Jen,
> I mapped with BWA and Bowtie for my RNAseq but Cufflink DID not run.
> This is the error message:
> "An error occurred running this job: /cufflinks v1.3.0
> cufflinks -q --no-update-check -I 300000 -F 0.100000 -j 0.150000 -p 8
> -b /galaxy/data/hg19/sam_index/hg19.fa
> Error running cufflinks.
> return code = 1
> cufflinks: /lib64/libz.so.1: no version information available
> (required by cufflinks)"
> /What should I do?/
> Di Nguyen
I installed bowtie2 and when running tophat I get the following error:
Error in tophat:
[2012-06-19 14:02:39] Beginning TopHat run (v2.0.3)
[2012-06-19 14:02:39] Checking for Bowtie
Bowtie version: 220.127.116.11
[2012-06-19 14:02:39] Checking for Samtools
Samtools version: 0.1.18.0
[2012-06-19 14:02:39] Checking for Bowtie index files
Error: Could not find Bowtie 2 index files
I was wondering if I can create the index files using bowtie2 via command
line and then change the universe_wsgi.ini to:
# Temporary files are stored in this directory.
new_file_path = database/tmp
and put the index files there. Anyway, why is it not creating the indexes?
I created links to all bowtie2 executable files. If I remove bowtie 0.12.8,
then I get a error from tophat (bowtie not installed). Is it creating the
index with bowtie 0.12.8?
I am trying to do variants call with "generate pileup".
My steps where:
2. select only lines with the pattern Matching pattern: XT:A:U
4. then I tried to use "Generate
However, it does not work, and I get the error message:
114: Generate pileup on data 97: converted pileup
An error occurred running this job: *Samtools Version: 0.1.16 (r963:234)
Error running Samtools pileup tool
Floating point exception*
Did I do anything wrong, or is it a bug?
The parameters are copied below.
The parameters are:
Tool: Generate pileup Name:Generate pileup on data 97: converted pileup
Created:Jun 14, 2012 Filesize:0 bytes Dbkey:hg_g1k_v37 Format:tabular Tool
Tool Standard Output:stdout<https://main.g2.bx.psu.edu/datasets/d038161e3fe9072e/stdout>
Input Parameter Value Conditional (refOrHistory) 0 Select the BAM file
to generate the pileup file for 97: SAM-to-BAM on data 94: converted
or not to print the mapping quality as the last column Do not print the
mapping quality as the last column Whether or not to print only output
pileup lines containing indels Print all lines Where to cap mapping quality
60 Conditional (c) 1 Theta parameter (error dependency coefficient) in
the MAQ consensus calling model 0.85 Number of haplotypes in the
sample 2 Expected
fraction of differences between a pair of haplotypes 0.001 Phred
probability of an indel in sequencing/prep 40
I have been unable to get a solid FTP connection to main.g2.bx.psu.edu
for ~24hrs. Two things have occurred: 1) I get the error "530 Sorry,
the maximum number of clients (3) for this user are already connected"
or 2) when finally connected, some files fail during transfer with
'incorrect password' while others continue uploading and eventually the
entire connection is lost where attempts to reconnect give the 530 error
in situation 1. To troubleshoot, I have tried all suggestions through
FileZilla and Cyberduck, essentially limiting number of connections and
disabling all before connecting, to no avail. It seems likely that this
might be a server issue.
Any insight is appreciated.
The cufflinks and cuffdiff results are not consistent with each other. This is killing me.
Does it make sense?
<< Obseration >>
We have 3 control samples and 3 treated sample. For many genes, their FPKM in cufflinks and cuffdiff are far from consistent. In cufflinks result, for a gene’s FPKM are
control group (sample: 1,2,3)：0， 0， 4.8
treated group(sample: 1,2,3)：0， 0， 6.0
In cuffdiff, the estimated FPKM are
control group： 12.6
Use ucsc gene annotation gtf file, mm9, downloaded from UCSC table database
Use cufflinks on each individual sample.
Cufflinks: galaxy mirror at cistrome, minimal count:10, no quantile normalization, use gtf as reference, no background correction
Use cufflinks on treated groups (3 biological replicates) and control groups (3 biological replicates)
Cuffdiff: galaxy mirror at cistrome, minimal count:10, no normalization, use gtf as reference, no background correction
Cufflinks returns 55350 transcripts, while cuffdiff return 55418 transcripts, even though they use the same gene annotation gtf file.
For the 6 cufflinks results (corresponding to 6 samples), the transcript ids are all the same, but the order are not,
Does it make sense? Or did I do anything wrong?
I uploaded a couple small files via ftp to do some basic text
manipulation on them in the main galaxy server. I have queued up
several jobs (including just importing the files I uploaded into a
history) but after two hours of waiting they are still gray and "waiting
to run." I have been using galaxy regularly lately and have never had
to wait very long for a job to start running (usually a matter of
seconds). I am not above my quota so this is not the problem. Is there
something else I need to do or is there a problem with the servers that
would explain why jobs aren't being run?
All the best,