Dear all,
When running Simulate (version 1.0.0)I am missing a graph in the initial
display. Is this a bug or is it my instance problem. On a side note, when
running Simulate I found out that if you don't place parameters in
"Frequency/ies for minor allele:" and "Detection thresholds:" the job
Here's some specific information about what the PATH variable is for UNIX
systems and how to set it: http://kb.iu.edu/data/acar.html
Many folks do the following so that you only need to add a single directory to
your path:
(a) install all tools in one directory;
(b) create a "bin" directory in
Take a look at the item_tags API controller; you can manage (add/delete/show)
history, dataset, and workflow tags using it. There's not much documentation
for it yet, but it should be pretty straight-forward. Let us know if you have
questions.
Best,
J.
On Jun 20, 2013, at 9:59 AM, Philip Mabon
I guess one more question for today. Our lab will be taking care of all
library preps and so we want to simplify and remove a few options including
Multiplexing/barcodes, library construction, and library validation. Where
would I change that in nglims? I can't seem to hack it in the yaml file.
After a lot of head banging and then realizing that you stressed
"sequencing" I realized I had a capitalization error. Case-sensitive!
Everything seems to be working fine now, and I will be customizing it some
more via the yaml file.
Thank you Brad. You are awesome that you are so responsive.
Hi Marco,
You'll need to enable some missing tool data tables in
tool_data_table_conf.xml. i.e. adding:
value, dbkey, name, path
value, name, gatk_value, tools_valid_for
Also make sure the files exist at the listed , they probably
Hi Elwood,
It sounds like you are getting closer, and that the instructions a few
days ago from Jeremy are helping:
http://dev.list.galaxyproject.org/transferring-Trapnell-et-al-programs-into-a-one-user-instance-of-Galaxy-tc4660245.html#none
For each of these tools in #2, you will need to inst
The .dat file *is* the dataset file, so you can use it directly with your tool.
J.
On Jun 20, 2013, at 2:52 PM, vijayalakshmi wrote:
> Hi all,
>
> I have written a java tool to which I have to pass an existing file's name.
> In the XML wrapper, I am choosing the file from the history using
Hi all,
I have written a java tool to which I have to pass an existing file's
name. In the XML wrapper, I am choosing the file from the history using
.
Even though the tool is receiving the filename as an input, it is looking
for a ".dat" file from \database\000\
How do I retrieve t
> [http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies] under
> "Local Jobs"
>
> I would appreciate any specific advice on this.
>
> Sincerely,
>
> Elwood Linney
> DUMC
> -- next part ---
Display applications are extensively documented here:
http://wiki.galaxyproject.org/Admin/Tools/External%20Display%20Applications%20Tutorial
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Thu, Jun 20, 2013 at 2:20 AM, shashi shekhar wrote:
> Hi james,
>
> can you share s
I am sorry, i posted the wrong configuration file above. I am posting now the
updated proftpd.conf , the differences is that some things are commented out
and others are not.
# This is a basic ProFTPD configuration file (rename it to
# 'proftpd.conf' for actual use. It establishes a single se
Hi Mr. Tobias,
We are having a similar problem. It seems that when the galaxy code was
updates, new created/updated passwords are using a different encryption mode.
This new mode, PBKDF2 SHA256 is NOT supported by proftpd 1.3.4d that you see to
be using. We had to compile proftpd from source
I have:
1) downloaded the Galaxy framework into a Mac Pro desktop with 64gb ram
2) downloaded Mac OS versions of Tophat2, Bowtie2, and the Cufflink suite
to the mac
3) have looked at the Galaxy wiki on connecting these
[http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies]
4) I have gott
On Wed, Jun 19, 2013 at 3:32 PM, Jordi Vaquero wrote:
> the shared and publish option of history but they don't work as I wanted.
Published histories should be accessible to anonymous users, under the
Shared Data tab. Can you provide more information on why this is not
working for you?
(Data li
Hi Eveybody,
We have notice the problem with logging on our galaxy ftpserver after
galaxy server upgrade. The only users who created new account or
modified password have the problem with logging to ftp. I have found out
that this is caused by modified password hashing. Now galaxy uses PBKDF2
Thank you. The tool guide seems to have a good sample to begin with.
Saliya
On Thu, Jun 20, 2013 at 2:53 AM, Björn Grüning <
bjoern.gruen...@pharmazie.uni-freiburg.de> wrote:
> Hi Saliya,
>
> the Galaxy documentation is a good starting point for your questions:
>
> http://wiki.galaxyproject.org
Hello, Shashi
It looks like TreeViewX was written in C++ as a desktop program. In this
case, there is no way that it can be used with the display_application code
without major modification.
One option is to not use TreeViewX from within Galaxy but simply have it
installed on your users' computer
Hey,
I was curious if it was possible to allow the API to change tags associated
with a history? At the moment in the galaxy code it's forbidden.
Having the ability to add tags using the API would be helpful of
associating multiple histories to a particular project. So later, it would
be easier t
Lee;
> Hi, what roles are embedded in nglims? (am I calling it by the right
> name?)
>
> I have a "sequencing" role which will be given to anyone submitting a
> request, and that seems to be working just fine. I am also using the yaml
> form to edit the submission form, and I think it's beautifu
Hi Ross,
i am using display application as visualization in galaxy.
display id="ucsc_interval_as_bed" version="1.0.0" name="display at UCSC">
http://genome.ucsc.edu/cgi-bin/hgTracks?db=${qp($bed_file.dbkey)}&position=${position.qp}&hgt.customText=${bed_file.qp}
what is the meaninng
and
Hello Joachim,
It looks like you have an invalid URL you are attempting to us for your top
shed (this looks to me like your Galaxy paster log, not your tool shed paster
log). Is your tool shed running at 'http://localhost:9009/, or some other port?
Also, when this error occurs, you can point y
Hi,
with the new frameless layout we have found a regression that makes it
impossible to work with different histories at the same time.
Steps to reproduce:
- Open History A, uploading some datasets, doing some calculations,
reload one tool
- Open Histpry B in a second tab
- Go back to History A
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