Hi all, I was wondering if it was possible for a user to specify the number
of files to upload in Galaxy and have multiple file input boxes to upload
updated on the wrapper page accordingly.
A user will have from one to many files needed to be uploaded from a job.
Right now I can see that galaxy
Hi,
I tried to use Barcode Splitter in Galaxy and could not get it work. In the
Library to split pull down list, I could not get anything. I would expect it
provides me information just like Barcodes to use pulldown list. Is this a bug?
Yunling
Hi everybody,
I'm currently trying to create a wrapper for one of my program.
This program generates several output file and the name of each output
file is derived from the name of the main input file.
_In the .xml file I try to get my output files with the following tag_:
outputs
data
Aurelien,
The particular behavior that you need isn't currently supported because the
value of from_work_dir isn't treated as a template. To work around this
limitation, you can do the move/copy operations in your tool wrapper; see the
wrappers for Bowtie and Sicer for examples on how to do
On Nov 21, 2011, at 11:09 AM, Toqa Manasrah wrote:
Hi everybody,
I am integrating my software ViSpA inside galaxy and I have two questions:
1: the main program is a shell script (.sh) which call another shell script,
which call Java executables. should I include any interpreter inside the
Hi Jeremy,
I'm trying to view boxplots (png) and FastQC (html) output. I can view
other output types like tabular in the published histories, but not png or
html.
Thanks,
Liisa
Liisa Koski
Bioinformatics Programmer
Phone: 518-309-3079, E-Mail: liisa.ko...@dnalandmarks.ca
Postal Address: DNA
On Nov 23, 2011, at 11:10 AM, Giota Kottara wrote:
Dear galaxy developers,
I am trying to integrate an executable tool in a private instance of galaxy.
I stored the configuration .xml file and the executable in tools folder of
Galaxy and the tool appears in the homepage. Nevertheless
On Nov 25, 2011, at 8:23 AM, Toqa Manasrah wrote:
Hello everybody,
I am trying to run my tool Vispa but every time i try to i got this error
messages:
An error occurred running this job:
/home/galaxy/galaxy-dist/tools/vispa/main.bash: line 13: ./parser_v.2.sh: No
such file or
Dear List,
I am new to developing for Galaxy and haven't found a good answer to this
question yet. Does Galaxy Test Toolshed use or recognize Shogun Toolbox
(http://www.shogun-toolbox.org/)? I'm considering writing a module for Galaxy,
but the underlying Python code relies on Shogun, and I
Dear Kipper,
We are running most of our tools with the help of Shogun toolbox. Just
configure a recent version of Shogun toolbox to your local machine and add
the python path to your program. By doing this you will be able to call
shogun functionalities in your programs. (Depends on the
Liisa,
I'm not able to reproduce your issue on our public server. For instance, here's
a history that includes both FastQC output and a boxplot; both display
correctly:
http://main.g2.bx.psu.edu/u/jeremy/h/unnamed-history-2
(Note that I just committed a fix to galaxy-central so that the
Hi Kipper,
Sorry I got confused, Yes you are right, both ways are fine I think.
--Vipin
Vipin,
Thanks for quick reply. Pardon my asking, as I said I am new to Galaxy
development, but if I wanted to share my module, would other users need to
install Shogun separately, or could I include it
hi matthias,
i've also been getting metadata errors (below) for several weeks, but it
works with the set_metadata_externally option (in the universe config file)
set to False. for large files, it could take many minutes for your job
server to check the metadata, and no new jobs will be run or
Ed,
we had the classic goof on our cluster with this. 4 nodes could not see the
/home/galaxy folder due to a missing entry in /etc/fstab. When the jobs hit
those nodes (which explains the randomness) we got the error message.
Bothersome was the lack of good logs to go on. The error message was
Vipin,
Thanks for quick reply. Pardon my asking, as I said I am new to Galaxy
development, but if I wanted to share my module, would other users need to
install Shogun separately, or could I include it as a dependency or 'egg'?
On Nov 28, 2011, at 2:28 PM, Vipin TS vipin...@gmail.com wrote:
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