My username is shyamsundar19489(a)gmail.com
Galaxy main is not running jobs since today morning. They stay queued (gray) forever. I deleted and then re queued them twice. Still nothing.. Is the server down or is something wrong with my account??
Shyam S Jayaraman MD
Staff Research Associate
Division of Dermatology
LABioMed Research Institute
Dear Sir or Madam,
I have been attempting to upload a few datasets (>2Gb) for the past few
days but I cannot seem to login to the server. This has been the case
since the server crashed last week. Could you please restart the ftp server?
John R. Clayton, PhD
Université de Strasbourg
Anopheles Group, CNRS UPR-9022
"Réponse Immunitaire et Développement chez les Insectes"
Institut de Biologie Moléculaire et Cellulaire (IBMC)
15, rue René Descartes F-67084 CEDEX Strasbourg France
Tel: +33 188.8.131.52.96
Fax: +33 184.108.40.206.22
Applications are now being accepted for the 2012 GMOD Summer School
course, a five-day hands-on school aimed at teaching new GMOD
administrators how to install, configure and integrate popular GMOD
Components. The course will be held August 25-29 at the US National
Evolutionary Synthesis Center (NESCent) in Durham, North Carolina.
These components will be covered at the school:
Apollo or WebApollo - genome annotation editor
Chado - biological database schema
Galaxy - workflow system
GBrowse - genome viewer
GBrowse_syn - synteny viewer
GFF3 - genome annotation file format and tools
InterMine - biological data mining system
JBrowse - next generation genome browser
MAKER - genome annotation pipeline
Tripal - web front end to Chado databases
The deadline for applying is the end of July 9, 2012. Admission is
competitive and is based on the strength of the application,
especially the statement of interest. The 2011 school had over 70
applicants for the 25 slots. Any application received after deadline
will be automatically placed on the waiting list.
The course requires some knowledge of Linux as a prerequisite. The
registration fee will be $300 (only $60 per day). There will be a
limited number of scholarships available.
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
Can somebody please help me?
I'm trying for hours to connect to Galaxy on Amazon EC2. I did everything
according the instructions, but did not succeed.
The "Access Galaxy" button in the instance remains grey out.
I copied the screen print and the log to the attached file.
Can anyone help me please?
and another questions: I want to use it to analyze MiSeq results (to align
to the human genome). 100 Gb EBS and a large machine are enough? too much?
I am trying to upload 27.2 GB fastq file in Galaxy through FTP, but it
throws an error:
netout: Connection reset by peer
421 Service not available,remote server has closed connection.
Hi Galaxy team,
I have two instances of galaxy on the same host, and have enabled page
(I set enable_pages = True on universe_wsgi.ini file).
I have set the parameter "cookie_path" different for each instance.
I'm disconnected from galaxy when I try to edit a page content.
But when I comment out the "cookie_path" for one instance it works for this
Did I miss something when configuring my instance ?
Can someone give me some help ?
I've tried to have a look at in the code but I'm not familiar with python.
Thank you all,
1.) I am having trouble adding annotations to my Tophat and Cufflinks
I used the Mus.Musculus 9MM reference using the *built in index. *For the
Tophat mapping but no annotations were available in the output files.
I then tried converting the the Ref Genome from the UCSC to a SAM file
using Sam Tools. Tophat would not recognize this but Cufflinks did. The
Cufflinks output file did not have the annotation either.
Any thoughts on the proper way to add annotations?
2.) I am also trying to filter the single mapped reads from the multiple
mapped reads that resulted from Tophat. After converting the output file
from Tophat I used the filter tool in the Sam Tools choosing *0x100 map is
not primary. *Afterwards I tried to run Cufflinks on the filtered output
only to have it fail.
My ultimate goal is to look at RNA seq gene expression. I know that I have
to upload my files -> groom using FASTQ groomer -> download a reference
sequence from UCSC -> convert the reference genome file to a usable format
->Run Tophat for mapping using the groomed file and the converted reference
annotation -> Filter the single mapped reads -> Run cufflinks using the
filtered single mapped reads from Tophat.
>From here I will continue with some other statistical analysis but right
now I need to get this basic pipeline to work.
I have a personal galaxy instance with the runner as SGE. I am able to successfully submit jobs, and the output folder is created at $file_path. But I see that the SGE job log files ie., stdout and stderr - <job-name>.o and <job-name>.e are being removed in the cleanup function in sge.py. Is this right? Is galaxy capturing the jobs stdout and stderr some where else?
Also when I click on the link “Tool Standard Output” from galaxy web interface, it returns empty. Is there a setting that I should have to view jobs stdout, stderr from the web interface?