Hi Alex
Now is an another problem. I now deal with two fastq files, there are Illumina
enconding 1.8 and pair-end, so I don't need to groom. But the fact is, I need
to use the filter by quality and Fastq interlacer and without groom thses
two tools can not regonize the files. Any idea to
You can just change the format of the data from fastq to fastqsanger if you're
sure about the error format (use the pencil, then datatype tab) note:
fastqsanger !=fastqcsanger
Brad
On Dec 7, 2012, at 3:20 AM, 泽 蔡
caizexi...@yahoo.com.cnmailto:caizexi...@yahoo.com.cn wrote:
Hi Alex
Now is an
Hi Brad,
I'm sorry, I can not quite follow you. The pencil and the datatype tab are
tools in galaxy?
发件人： Langhorst, Brad langho...@neb.com
收件人： 泽 蔡 caizexi...@yahoo.com.cn
抄送： galaxy-dev@lists.bx.psu.edu Dev galaxy-dev@lists.bx.psu.edu
发送日期： 2012年12月7日,
Hi Ido,
Is .sqlite a common compressed file type (i.e. zip, gzip, or bz2) just
with a different extension?
If it is, I think upload.py is always going to try to decompress it.
That that has long been a behavior I would like to be able to disable
on a per file type basis. If this is the problem
If I click on the small bug icon for a dataset in error state, I get this
message in the log:
URL: http://bbc.mdc-berlin.de/galaxy/dataset/errors?id=e96c6ce43a3d239a
File '/data/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line
143 in __call__
app_iter =
The specification does not mention zip, gzip or bz2 [1] and
I am pretty confident, that it does not in addition compresses
its content with zip etc..
It starts with a header SQLite format 3\000
which is visible in my file with less.
ido
[1]http://www.sqlite.org/fileformat.html
On Dec 7, 2012,
Thanks Thon. What is the TOOLSHED option?
As far as FASTQC, I downloaded and extracted it, but now what? Do I
dump all of those files and directories in tool-data/shared/jars?
wget
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.10.1.zip
unzip fastqc_v0.10.1.zip
ls
On Dec 6, 2012, at 7:16 PM, Smith, Therese wrote:
Dear Sir or Madam,
We are using DOS prompt ftp, we connected, we sent (8Gbytes), and we
received a succcessful completion message from ftp, we saw the file appearing
on your page as having been ftp'd to you, however, we received an
On Dec 7, 2012, at 9:54 AM, Andreas Kuntzagk wrote:
If I click on the small bug icon for a dataset in error state, I get this
message in the log:
URL: http://bbc.mdc-berlin.de/galaxy/dataset/errors?id=e96c6ce43a3d239a
File
Hi Nate. I do understand that this is not a bug directly stemming from the
Galaxy code base. Munge is really just a tool to pass user credentials between
systems during job submission to the PBS server. Galaxy is spooling jobs
through the PBS job runner, which presumably indirectly calls munge
I'm seeing some weird behavior in our local galaxy instance and am wondering if
anyone has seen anything similar.
I have a custom tool that I've written that generates a tab-delimted file.
When I click on the item name in the history, I can see the contents in the
preview window. However,
Hey Dave,
What revision are you running locally? And, just to confirm, in galaxy the
file is recognized as a 'tabular' file type?
-Dannon
On Dec 7, 2012, at 1:25 PM, Dave Walton dave.wal...@jax.org wrote:
I'm seeing some weird behavior in our local galaxy instance and am wondering
if
Galaxy dev:
I'm installing a local galaxy instance (Dec 4, 2012 vintage) and it is running
well under mySQL, but I'm having trouble getting it to work with a postgres
database.
I've done the following to create the db and provide permissions:
$ whoami
galaxy
$ createdb galaxy_prod4
$ psql
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