Hi,
I think you can get reference genomes from UCSC,and then make Bowtie2 index
data by bowtie2-build.Other way you can try rsync to get the index files ,for
more information you can see
http://wiki.galaxyproject.org/Admin/Data%20Integration .
Hope to help you.
shenwiyn
From: Gerald Bothe
Il 2013-07-30 17:18 Peter Cock ha scritto:
Hello all,
Re:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010153.html
http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-October/011557.html
Something I raised during the GCC2013, and we talked about
via Twitter as well was a Galaxy
Hi Piotr,
In our proteomics lab, a protein sample is fractionated (by e.g. pH)
before analysis in a nr of sample fractions. The fractions are then run
through the mass spectrometer one at a time. Each fraction yields a data
file.
The mass spec data is then matched to peptides by searching a
On Mon, Jul 29, 2013 at 5:03 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
The issue with seq_rename incorrectly failing functional tests has been
resolved in 10266:fe04978dadac, and the test results will be corrected the
next time the automated testing framework runs. I'm still looking into
On Thu, Aug 1, 2013 at 11:43 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Jul 29, 2013 at 5:03 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
The issue with seq_rename incorrectly failing functional tests has been
resolved in 10266:fe04978dadac, and the test results will be
On Mon, Jul 29, 2013 at 3:10 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
I've created a Trello card where you can track this issue:
https://trello.com/c/wHXz9j0v/1018-toolshed-test-result-display-issue
Most of these look like display issues, the test results are correctly
recorded in the
Retitling thread to focus on a regression in the (Tool Shed) test framework
to do with input file types and sniffers.
On Thu, Aug 1, 2013 at 11:47 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Aug 1, 2013 at 11:43 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Jul 29, 2013 at
People,
I successfully installed NCBI_Blast_Plus from the toolshed
The tool, however, failed to work giving the following error:
Fatal error: Exit code 255 ()
Error: NCBI C++ Exception:
/usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp,
On Thu, Aug 1, 2013 at 6:49 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Aug 1, 2013 at 12:38 PM, Rodolfo Aramayo raram...@tamu.edu wrote:
People,
I successfully installed NCBI_Blast_Plus from the toolshed
The tool, however, failed to work giving the following error:
Fatal error:
On Thu, Aug 1, 2013 at 1:41 PM, Rodolfo Aramayo raram...@tamu.edu wrote:
On Thu, Aug 1, 2013 at 6:49 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Aug 1, 2013 at 12:38 PM, Rodolfo Aramayo raram...@tamu.edu wrote:
People,
I successfully installed NCBI_Blast_Plus from the toolshed
On Mon, Jul 29, 2013 at 10:27 PM, Nate Coraor n...@bx.psu.edu wrote:
On Jul 29, 2013, at 1:02 PM, Peter Cock wrote:
Hi all,
Is there a target date for the next Galaxy release, or should that
differ, the next update to the main Tool Shed?
Hi Peter,
The next release is planned for August
On Thu, Aug 1, 2013 at 8:40 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Aug 1, 2013 at 1:41 PM, Rodolfo Aramayo raram...@tamu.edu wrote:
On Thu, Aug 1, 2013 at 6:49 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Aug 1, 2013 at 12:38 PM, Rodolfo Aramayo raram...@tamu.edu
On Thu, Aug 1, 2013 at 2:47 PM, Rodolfo Aramayo raram...@tamu.edu wrote:
On Thu, Aug 1, 2013 at 8:40 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
I've seen that kind of error from NCBI BLAST+ before - do you
know which of the BLAST tools was this, and what the query
was?
The repo was:
Hi Peter,
The main tool shed was updated on schedule on Tuesday, July 30.
As Nate stated in his reply to you regarding your question about the target
date for the next Galaxy release, the next-stable branch was created on that
date. The release process is such that when the next-stable
Hi all
Apologies if I am in the wrong channel to post this. I have been using
Galaxy for a couple of months now and I'm still finding my way around the
mass of info
Some of the XML config file tags have a string interpolation type of
variable such as ${tool.name} in:
label=${tool.name} on
On Thu, Aug 1, 2013 at 2:58 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
The main tool shed was updated on schedule on Tuesday, July 30.
As Nate stated in his reply to you regarding your question about the target
date for the next Galaxy release, the next-stable branch was created on
This bug has been fixed in our code repository and will be included in our next
release, which is due out in a couple weeks.
Best,
J.
On Aug 1, 2013, at 1:25 AM, Philipe Moncuquet wrote:
Hi guys,
Since the last update of Galaxy. We are enable to edit pages on our local
instance. Pages
Rodolfo,
In order to simplify tracking down this issue, could you provide the
changeset revision of Galaxy that is running on tamu.edu? To retrieve
the revision, execute the following command in your galaxy root directory:
hg id
To clarify, our understanding is that you installed the
Hi there,
I'm looking for an elegant way to extract the metadata for a Galaxy history
item from a PostgreSQL database. My special interest lies in the path to the
output file and the input parameters. Has by any chance anybody already done
this and a ready to use python script at hand? ;)
Peter,
I have been able to duplicate the error on nlstradamus, and hope to have
a fix out soon.
--Dave B.
On 8/1/13 07:21:17.000, Peter Cock wrote:
Retitling thread to focus on a regression in the (Tool Shed) test framework
to do with input file types and sniffers.
On Thu, Aug 1, 2013
Hello,
I am running a local galaxy server and tried to add the downsampling script
for SAM/BAM files from Brad Longhorst which I found on Github. It uses a
modified picard_wrapper.py. I get everything running except that the end
file shows up empty. I realised when looking at the log file that
Hello,
I am trying to run GATK on a local galaxy installation. I get the following
error:
# ERROR
--
# ERROR A USER ERROR has occurred (version 1.5-21-g979a84a):
# ERROR The invalid
Hi Jorrit,
Thank you for your explanation. Would you be able to give us an example of what
do you mean by fractions and when the task_%d are being used to pick files.
Just want to make sure we have good understanding of the problem that you
solved.
Also, I vaguely remember seeing 'data
It shouldn't, unless the root cause of that error also affected the FTP
transfer. Does FileZilla say there are any transmission errors?
On Thu, Aug 1, 2013 at 1:16 AM, Mark Edward Fabreag merfabr...@gmail.comwrote:
Good day!
While I was uploading the file (through FileZilla), I encountered
Hi Ricardo,
do you run velvet on your own cluster with SGE? Sometimes, No Peak
found can also mean that velvet used to much resources and was killed
by your cluster engine. In that case it often happens to us that we get
no result. A solution is a give velvet more resources or adjust the
Here it is:
'pd.yaml' not found at paths.py load!
Set paths.P_GALAXY_HOME as '/mnt/galaxyTools/galaxy-central'
Python version: (2, 6)
Image configuration suports: {'apps': ['cloudman', 'galaxy']}
[DEBUG] app:54 2013-08-01 20:07:40,138: Initializing app
[DEBUG] app:55 2013-08-01 20:07:40,138:
Thanks for letting me know, my old credentials have been disabled.
Anyways, that is all the log contained. I clicked on show all. Does
launching it with this method work on your end?
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
The new volume update hasn't been released yet to fix those tool issues,
but the existing volume should actually appear in /mnt at launch.
On Thu, Aug 1, 2013 at 4:28 PM, Ravpreet Setia ravpreet.se...@oicr.on.cawrote:
Thanks for letting me know, my old credentials have been disabled.
Hi Piotr,
Regarding data parallelism - Galaxy can split a single large file into small
parts and process them in parallel, then merge outputs into single file.
That's not what we need, as we already have multiple input files. But as I
understand, there's a possibility to write our own
Hello,
My local cluster based galaxy installation was running fine till this
evening. Later I decided to test some workflows and got an error with
massive stack trace.
I can't make any sense of this. Here is the last part of the error. The
stack trace is literally 1000's of lines. Can
Here is the first part of the error (Traceback):
galaxy.tools ERROR 2013-08-01 22:56:16,590 Exception caught while
attempting tool execution:
Traceback (most recent call last):
File
/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/__init__.py,
line 1936, in
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