Hello Jeremy !
Could you tell me how to find the version number of the current galaxy-dist
to know if I have the latest one or no ?
Thanks
Amine
2012/7/20 Chebbi Mohamed Amine
> Ok. Thanks for your clarifications. So I will wait for your upcoming
> distribution of Galaxy and redo the test.
>
> B
Hi,
I have a question related to this Galaxy threads:
http://dev.list.galaxyproject.org/Populating-tool-select-menu-with-database
-data-tp4139069.html
I implemented the example with the deprecated tag which is working
fine. But I do not invest time in a tag which might vanish soon. What is
the re
Which .loc file corresponds to tophat? I looked through the .xml file for
the wrapper and it made no reference to any .loc file.
--
Andre Gatorano
847-845-9284
University of California San Diego
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Dear All,
I successfully install Galaxy onto my new MBP with 16Gb or Ram but when
I tried to use Galaxy, it is painfully slow! The first test I did was to
create Admin and import data (RNA-seq fastq, about 6Gb in size) into
database and then history. The second test was to run fasqgroomer on
Dear all,
I am not sure whether the following issue is related to development or
bug report. In main galaxy website, I generated bcf files using
mpileup, and now would like to convert bcf files to vcf files.
However, I cannot find this conversion tool. Oddly, I find this tool
in test galaxy websit
Hello,
I'm running a local installation of galaxy. While loading a bam file (2GB)
to galaxy, I get the following error:
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 403, in
__main__()
File "/home/galaxy/galaxy-dist/tools/da
The key lines in the wrapper are:
--
--
This code refers to the tool_data_table_conf.xml file, where tophat_indexes is
defined:
--
value, dbkey, name, path
--
So you can see that Tophat uses the tool-data/bowtie_indices.loc file, which is
reason
Assuming that you're using Mercurial, which is highly recommended, you can type
this at the command line:
% hg tip
You probably know that we released a new distribution last week that you can
update to:
http://wiki.g2.bx.psu.edu/News
Best,
J.
On Jul 25, 2012, at 7:13 AM, Chebbi Mohamed Amine
Ok Jeremy ; So I will test the latest release.
Thanks
Amine
2012/7/25 Jeremy Goecks
> Assuming that you're using Mercurial, which is highly recommended, you can
> type this at the command line:
>
> % hg tip
>
> You probably know that we released a new distribution last week that you
> can update
Bonsoir,
Une nouvelle version de Galaxy vient de sortir. D’après le Monsieur du
maling list de Galaxy, les bugs de crash liés à l'utilisation du
visualiseur Trackster devraient être résolus.
Pourriez vous me dire vos recommandations à ce propos.
Merci
Amine
Back on the topic again, I found another real issue with toolshed tools. I can
configure the toolshed tool to be used by drmaa in universe_wsgi.ini, then
restart Galaxy and everything's good. However, if I modify the tool .xml file
and reload it using the Admin link, it goes back to the defaul
I recently switched from galaxy-dist to galaxy-central as the source of my
local install (version 7427:cb9272041d95). When I delete a dataset from a
history, all the delete icons disappear from the datasets. They come back if I
refresh the page. Has anyone else noticed this?
David Hoover
Hel
On Wed, Jul 25, 2012 at 9:35 PM, David Hoover wrote:
> I recently switched from galaxy-dist to galaxy-central as the source
> of my local install (version 7427:cb9272041d95). When I delete a
> dataset from a history, all the delete icons disappear from the
> datasets. They come back if I refresh
Is there a work flow/ tutorial how to call SNP and get significant SNP
followed by their annotation.
Thanks
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Hi,
I'm newbie in Galaxy. In fact, this is my first post.
I'd like to create a web-interface to run a C program. It is necessary a
config file which is used as input to this program. Therefore, the values
of parameters are informed by user through this web-interface. Its output
is some files.
I
Hi guys,
Recently we have discovered there is a bug in the database dump utility.
And we had used the same utility to migrate the galaxy mysql database once.
That resulted the on the current galaxy database, two tables are missing:
genome_index_tool_data
tool_dependency
I am wondering if there
ar..
Just saw the news brief, will that be possible that these two tables are
added as part of the Tool Shed and Admin Genome Indexing update??
Regards,
D
On Thu, Jul 26, 2012 at 12:18 PM, Derrick Lin wrote:
> Hi guys,
>
> Recently we have discovered there is a bug in the database dump utility
Hi Rodrigo,
You can try this tutorial:
http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial
Although I dont do c/c++ development myself, you might want to want to make
sure that the c/c++ tools you create have been compiled for the platform
you are working on, especially when you switch fr
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