GenePeeks is hiring a Computational Geneticist
by Adam Cohn
Hello all,
GenePeeks is hiring a Computational Geneticist. The position description is
list below. We are also hiring a tools programmer and I will send another
note with that position description.
Thanks,
Adam
Position Description
GenePeeks is a unique genetic information company with a mission to help
families protect the health of their future children. We are searching for a
highly skilled scientist to join our growing team and help develop
leading-edge technologies in a fast-paced, early-stage environment.
Primary Duties:
*
* - Manipulate and analyze whole genome and high complexity genotype data,
including SNPs and Copy Number Variations (CNVs) from raw microarray data
files.
*
* - Develop computational and data mining approaches to combine genotype
information, molecular profiling data and other phenotypic information
derived from NCBI and other online databases.
*
* - Develop protocols to predict the probability and severity of particular
diseases and conditions related to SNP, CNV and other structural variations.
*
* - Participate in implementing a system to test for and identify those
diseases
*
* - Test and assure the quality of automated analysis systems
*
* - Efficiently manage experimental data and data workflows
*
* - Monitor trends and innovations in the fast-moving world of genomic
data, analytics, storage,
*
* and clinical diagnostics
*
* - Contribute to the ongoing design and development of GenePeeks
technology
*
* - Other duties as assigned
*
* Our ideal candidate would have the following training and technical
expertise:
*
* - Ph.D. in genetics, biostatistics, computer science or related field, or
comparable training
*
* - Familiarity with and experience using related publicly available
scientific datasources and tools
*
* (OMIM, DBSNP, GeneReviews, UCSC Genome Browser, Galaxy, HapMap)
*
* - Ability to implement tools using APIs that automatically interrogate
publicly available scientific
*
* datasources and tools such as OMIM, DBSNP, GeneReviews, UCSC Genome
Browser,
*
* Galaxy, HapMap
*
* - Familiarity with next-gen data analysis and whole genome data
*
* - Research experience with and /or knowledge of clinical aspects of the
genetic causes of
*
* Autism, Schizophrenia and other neurological disorders
*
* - Experience analyzing SNP, CNV, GWAS (or NGS) data
*
* - Experience using automated bioinformatics tools
*
* - Experience working with whole genome sequence data
*
* - Proficiency with scripting language such as Python or R
*
* - Familiarity with 1000 Genomes Project or similar exposure
*
* General Requirements:
*
* - Ability and motivation to work independently
* - Ability to interact proactively with a small group
* - Strong written and verbal communication skills
* - Desire to work in a fast-paced, loosely structured business environment
- Sense of humor
*
* Location:
*
* - Cambridge, MA or New York, NY - Some travel may be required
*
* Contact Information:
*
* If you are interested in this role and fulfill the requirements, please
send your CV and cover letter to jobs(a)genepeeks.com
--
Adam S. Cohn
Chief Technology Officer / Chief Operations Officer
GenePeeks
175 Varick Street, New York, NY
(646) 664-4268
(703) 473-8811 (mobile)
adamcohn(a)genepeeks.com
www.geenpeeks.com
9 years, 6 months
Urgent: Seems like tophat2 does not support "--transcriptome-mismatches"
by Sachit Adhikari
It seems like tophat2 does not support "--transcriptome-mismatches" option
but Galaxy is still configured to call tophat2 with this option when run
with "Full parameter setting" option within Galaxy. Is there new wrapper
with this fix? If not, how to remove this option from Galaxy so that
tophat2 is not call with this option. I am assuming that this is specified
somewhere in the wrapper.
Thanks,
Sachit
9 years, 6 months
Reference Genomes for NGS Tools - A Couple Questions
by greg
Hi all,
I'm finishing up installing Galaxy on our local cluster.
I'm at this step regarding setting up reference genomes:
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup#Setting_Up_the_Re...
But it looks like a whole lot of manual work that needs to be done by
a system administrator. I was kind of expecting this would be
something end users would be able to do. I'm actually not sure we
have the resources for a sys admin to install all of these reference
genomes every time someone needs one.
I guess here are my questions:
Am I misunderstanding the process?
Is there a different way that normal users can add reference genomes instead?
Is there anything in the works that lets users easily add these?
Is there a way to use NGS tools without installing reference genomes?
Thanks,
Greg
9 years, 6 months
liftOver Exception caught attempting conversion
by Nikoloas Sidiropoulos
Hi
I downloaded and extracted the .chain files for liftOver and edited the .loc file. After restarting Galaxy I have the option to convert my files to the respective coordinates but when running the job I get the same error for each.
"Traceback (most recent call last): File "/steno-internal/projects/galaxy/galaxy-dist/tools/extract/liftOver_wrapper.py", line 81, in raise Exception, 'Exception caught attempting conversion: ' + str( e ) Exception: Exception caught attempting conversion"
I also found this in the handler.log file:
"galaxy.tools DEBUG 2012-12-20 11:37:09,902 Error opening galaxy.json file: [Errno 2] No such file or directory: '/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/000/98/galaxy.json' "
Do you know how could this be sorted?
Thanks in advance,
Nikos
9 years, 6 months
Integrating generated graphics from cli tool?
by Samuel Lampa
Hi,
I'm looking into integrating some R scripts into Galaxy, which create
some graphics / plots. We are interested in integrating those in galaxy
somehow, or otherwise presenting them to the user in an as easy way as
possible.
I wanted to check if there is some support for this kind of
functionality there already, or if I'll need to hack something together
myself?
(I couldn't really find anything here on the mailing list).
Many TIA!
Best
// Samuel
--
Developer at SNIC-UPPMAX www.uppmax.uu.se
Developer at Dept of Pharm Biosciences www.farmbio.uu.se
9 years, 6 months
Extracting bacterial seq from cordinates
by shamsher jagat
I have a bacterial genome from ncbi and woulld like to extract seq from the
corresponding fasta file of bacterial genome. Since i have list of
coordinates so would not be possible to extract one by one. Is there any
interface within galxy that i can use.
Thanks
9 years, 6 months
feature or bug with the tool shed?
by David Gene Morgan
Hi,
I just installed a galaxy server and ran into something that may be a
deliberate feature or a genuine bug when trying to install a package
from the main tool shed. I got the Admin tab working, went to the
section dealing with tool sheds and selected "Search for valid tools" in
the Galaxy main too shed. I was able to find the tool I wanted (NCBI
Blast+, and I found multiple revisions) but I never found anything
remotely like an "Install" button. There are bare-bones instructions
for a manual install of the tool, but nothing automatic.
However, if I start with "Browse valid repositories" and _then_ search
for "ncbi blast" (and not "ncbi blast+"), I find a single revision that
has a "Preview and install" option and an "Install into local Galaxy"
button.
So the only question here is whether this behavior is a bug or a
feature. In other words, should I be able to automatically install
packages using my first approach, or does Galaxy prevent this deliberately?
--
David Gene Morgan
cryoEM Facility
320C Simon Hall
Indiana University Bloomington
812 856 1457 (office)
812 856 3221 (EM lab)
http://bio.indiana.edu/~cryo
9 years, 6 months
copying files via galaxy API
by Richard Park
Hi Everyone,
Is there a way to directly copy files from galaxy with the proper file
name? I'm currently using the galaxy API to download files via HTTP, but it
is very slow and would like to speed up the process of copying files
directly, but am having a hard time getting the proper file names.
Are there any suggestions on how to copy files directly from galaxy without
HTTP and with the proper filenames?
# Looking up files via API
$ ./display.py <api_key>
http://localhost:8080/api/libraries/86cf1d3beeec9f1c/contents/32ff5cf1b96...
Member Information
------------------
ldda_id: 32ff5cf1b96c1df7
misc_blurb: 10,028,615 lines
name: H3K9me3_L3_FE_2.wig
data_type: txt
file_name: /galaxy-central/database/files/000/dataset_733.dat
uploaded_by: rpark(a)bu.edu
template_data: {}
genome_build: ?
model_class: LibraryDataset
misc_info: uploaded txt file
file_size: 48439126
metadata_data_lines: 10028615
message:
id: 32ff5cf1b96c1df7
date_uploaded: 2012-12-15T01:53:08.655366
metadata_dbkey: ?
# Downloading files using a URL like
http://127.0.0.1:8080/datasets/a4975bc1e68708d4/display?to_ext=txt
thanks,
Richard
9 years, 6 months
Problems with Internet Explorer 9?
by Peter Cock
Hello all,
Are there (or were there) any known problems with Galaxy under
Microsoft Internet Explorer 9? One of our biologists is now having
problems with our local Galaxy server, probably after updating his
browser.
Specifically new history entries do not seem to automatically update
from queued to running to done, and also the "peep" functionality to
expand/collapse a history entry had stopped working. This was on a
large history of about 100 entries.
We installed Firefox 10, logged into Galaxy, and it was fine with this
same history.
A quick test on the public Galaxy with a single history entry seemed
to work in both browsers, so perhaps this is something you've already
fixed in the latest Galaxy - or perhaps it depends on the size of the
history.
Any ideas? Has anyone else seen something similar?
Thanks,
Peter
9 years, 6 months
help configuring tools in Galaxy
by Tilahun Abebe
Hi,
We installed a local galaxy a couple of days ago following the basic
installation instruction (http://wiki.galaxyproject.org/Admin/Get%20Galaxy).
The installation went well, all the tools are listed on the left. I can
also upload data to Galaxy. However, an error occurs when I try to run
RNA-seq analysis. I am thinking the tools are not configured properly. Can
you give me tips to configure NGS tools? An example file with setup syntax
will help as well.
Thanks.
Tilahun
9 years, 6 months
