Hi,
I'm trying the add tool tutorial at
http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial . It works, but
how do I designate the path of the tool if it's not dropped into the same
directory as the tool config xml? Some executable may not be in the
directory. Surely it couldn't
Thanks, this helps. I was running with an interpreter and I didn't realize I
had to had the full path in there. I was expecting that $PATH which contains
the directory the script was located in to take care of it. Thanks you very
much for the clarification.
Timothy
Hi,
I'm putting my own tool into Galaxy. Suppose I have an command line option
that is designated by a switch. Such as
$executable.py -a option input output
The -a option is an optional argument. I want to make sure when the option
is not given, -a option is entirely taken out.
I tried Cheetah
Hi,
I'm trying to wrap up my own tool in Galaxy. The input to my tool include
the set of EST (such as the entire human collection). I tried using UCSC
genome browser but it doesn't seem to let me download the whole human
collection due to the size of the data.
I tried to implement my own FTP
On Wed, Sep 14, 2011 at 5:21 PM, Hans-Rudolf Hotz h...@fmi.ch wrote:
On 09/14/2011 10:39 AM, Timothy Wu wrote:
//
Alternatively, I can just ask user to download from NCBI ftp themselves,
decompress them, and upload it to galaxy.
What's the best approach here?
How about: you download
On Thu, Sep 15, 2011 at 4:58 PM, Peter Cock p.j.a.c...@googlemail.comwrote:
On Thu, Sep 15, 2011 at 9:32 AM, Timothy Wu 2hug...@gmail.com wrote:
I think I need some kind of data source implementation that allow user
to
obtain the data themselves. However with the current tool XML
On Thu, Sep 15, 2011 at 5:32 PM, Timothy Wu 2hug...@gmail.com wrote:
On Thu, Sep 15, 2011 at 4:58 PM, Peter Cock p.j.a.c...@googlemail.comwrote:
On Thu, Sep 15, 2011 at 9:32 AM, Timothy Wu 2hug...@gmail.com wrote:
I think I need some kind of data source implementation that allow user
Hi,
Looking under the tools directory I realized that some tools comes with
*_wrapper.py. I wonder under what circumstances is this needed?
I'm trying to do a quickie for RepeatMasker. It looks to me like the tool
does not allow one to specify the name of the output files. It also appears
to me
Hi,
I'm implementing my own tools. In one tool I may have hundreds of input
files. (or maybe I'm doing it wrong?) I'm copying off the tool conf xml code
from the concatenate dataset tool. But this requires adding files one by
one. Is there a quicker way in which I can just specify these files
On Thu, Sep 22, 2011 at 4:36 PM, Peter Cock p.j.a.c...@googlemail.comwrote:
How does your tool handle this at the command line (ignoring Galaxy)?
Does it expect a directory name or pattern, or just a really long
command line string with many many file names?
Originally I have this config
Hi,
I thought I had already asked this question a while ago, but I can't find it
so I guess I haven't.
When porting my own tool, is there anyway to customize the name of the
output?
Timothy
___
Please keep all replies on the list by using
On Wed, Oct 12, 2011 at 4:50 PM, Timothy Wu 2hug...@gmail.com wrote:
Hi,
I thought I had already asked this question a while ago, but I can't find
it so I guess I haven't.
When porting my own tool, is there anyway to customize the name of the
output?
Timothy
I have another perhaps
On Wed, Oct 12, 2011 at 5:23 PM, Hans-Rudolf Hotz h...@fmi.ch wrote:
Hi Timothy
Are you talking about the name as it will appear in the history?
Then have a look at the following wiki page:
http://wiki.g2.bx.psu.edu/**Admin/Tools/Tool%20Config%**
Hi,
I'm executing a R script via Python's os.system() (using Rscript executable
which allow executing R script in the command line). This script makes use
of library that will attempt to load up Tcl/Tk interface. Though I don't
see anything even if I'm running the commands on Windows interactive
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