Hi Guys,
I tried to install flexbar from toolshed, but upon running, error said it
could
not find it.
I checked and found
idtoolshed.g2.bx.psu.edu/repos/jtilman/flexbar/flexbar/2.4/id
in the config file, but this path does not exist.
Is it that I need to install the dependency on my own? I
is not effective.
But why is this? btw I'm using the 1.1.19 version of nginx that comes with
ubuntu.
Could anyone give me a hint? I'll be really grateful.
Thanks,
Rui
On Fri, May 16, 2014 at 12:29 PM, ruiwang.sz ruiwang...@gmail.com wrote:
Hi All,
I have been trying to get the visualization through
, at least redirect works, but I don't know why there is only one
server
block in use at a time. How do I solve this? Any help would be greatly
appreciated.
Thanks,
Rui
On Sat, May 17, 2014 at 7:36 PM, ruiwang.sz ruiwang...@gmail.com wrote:
Hi Guys,
I did a little further investigation. I found
Just to answer myself...
Those 2 location blocks should be in the same server block!
Hope this could help someone else...
:)
Rui
On Sat, May 17, 2014 at 8:54 PM, ruiwang.sz ruiwang...@gmail.com wrote:
Hi Guys,
I just switch to 1.6.0 of nginx, but the behavior is the same. I also
tried
Hi All,
I have been trying to get the visualization through ucsc main working, thus
I installed the nginx on our ubuntu(the one comes with update), then I
configured it according to the wiki
https://wiki.galaxyproject.org/Admin/Config/nginxProxy
Here is the section in my nginx.conf
now for testing
Am 08.03.2014 00:48, schrieb ruiwang.sz:
Hi Guys,
I'm sorry to post multiple times for the same question. Now I removed all
the specifics of my problem and I only want someone to point me to the
right documentation. Admins, I know you are busy, but don't you want more
people
Hi John,
Thanks for the note. Please see inline.
On Fri, Mar 7, 2014 at 7:18 PM, John Chilton jmchil...@gmail.com wrote:
Hmm... I am not certain but it sounds like the migration script ripped
something out of your Galaxy tool panel that you did not want it to? This
is unfortunate - but I
Hi Guys,
Sorry for the duplicate posting...nobody saw my original one seems and I'm
still wondering what the proper way is. I searched around the wiki but
didn't find much.
Originally, I installed macs dependency for galaxy myself. The version is
1.4.2. It worked well.
Now, after galaxy
Hi Guys,
I'm sorry to post multiple times for the same question. Now I removed all
the specifics of my problem and I only want someone to point me to the
right documentation. Admins, I know you are busy, but don't you want more
people to benefit from this platform?
When galaxy upgraded it
Hi Guys,
Our galaxy instance has been in use for a couple years but since Feb 2014
it started to show us some weird behavior. Recently the upload function
suddenly stopped working properly. We are getting messages like the
following. I'm not sure if this only happens to us. If someone has seen
Hi Guys,
Are there anyone who is using Cistrome?
I tried to merge Cistrome's setting into our own galaxy instance. A new
entry is
# Path to the static library files for assembly, ceaslib, chromLen,
conservation, liftOver and MAT-lib
# Then in other tool configuration xml file, we can use 'from
Hi All,
A quick question on the indices. Here is the information provided by the
sample file:
#Your bowtie_indices.loc file should include an entry per line for each
#index set you have stored. The file in the path does not actually
#exist, but it is the prefix for the actual index files. For
this tool run successfully, in Galaxy, on the type without span included.
If you find that the span variable is problematic after correcting any
other format issue issues, switch to the format without span.
Good luck,
Jen
Galaxy team
On 1/14/14 9:52 PM, ruiwang.sz wrote:
Hi All,
I'm having
Hi All,
I'm having an error at this:
*Dataset 18: Wig/BedGraph-to-bigWig on data 12*
Tool execution generated the following error message:
grep: writing output: Broken pipe
grep: writing output: Broken pipe
grep: writing output: Broken pipe
grep: writing output: Broken pipe
..
put: Broken
,
Rui
On Mon, Nov 18, 2013 at 10:40 AM, Nate Coraor n...@bx.psu.edu wrote:
On Sat, Nov 16, 2013 at 12:27 PM, ruiwang.sz ruiwang...@gmail.com wrote:
Hi All,
I‘m seeing some weird error messages...I googled but didn't see anything
useful:
So, it is during the wigToBigwig conversion
Hi All,
I‘m seeing some weird error messages...I googled but didn't see anything
useful:
So, it is during the wigToBigwig conversion:
Dataset generation errors
Dataset 47: Wig/BedGraph-to-bigWig on data 43
Tool execution generated the following error message:
grep: writing output: Broken
Hi Peter,
Thanks! I got it working by putting a suppressMessages() around the
function call.
I might have some questions on how to generate output file names on the
fly...let me make some attempts
first. :-)
Best,
Rui
On Sun, Sep 29, 2013 at 10:54 PM, ruiwang.sz ruiwang...@gmail.com wrote
Hi Guys,
I'm doing a very simple test about deseq2...there is a weird situation
always happening:
It looks like the deseq2 tool executed just fine, without any error, and
the result files were created, but after the set_metadata, galaxy always
'set dataset state to ERROR'.
The xml file for this
to suppress them as well -- but how come they are on stderr
not stdout?
Thanks,
Rui
On Sun, Sep 29, 2013 at 3:36 PM, Peter Cock p.j.a.c...@googlemail.comwrote:
On Sun, Sep 29, 2013 at 8:47 PM, ruiwang.sz ruiwang...@gmail.com wrote:
Hi Guys,
I'm doing a very simple test about deseq2
Cheers,
Joachim
Joachim Jacob
Contact details:
http://www.bits.vib.be/index.**php/about/80-teamhttp://www.bits.vib.be/index.php/about/80-team
On 09/11/2013 01:15 AM, ruiwang.sz wrote:
Hi All,
we are making a wrapper for deseq2, and there is a step where
control/experimental conditions
/deseq2
Cheers,
Joachim
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
On 09/11/2013 01:15 AM, ruiwang.sz wrote:
Hi All,
we are making a wrapper for deseq2, and there is a step where
control/experimental conditions
need to be determined
Hi All,
we are making a wrapper for deseq2, and there is a step where
control/experimental conditions
need to be determined. For example, it would be a column like the following
in the input file
Type
CTC
CTC
LM
LM
PT
PT
and we want the select list to contain
CTC
LM
PT
In other words, we want
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