Hi Assaf, On Thu, Apr 28, 2011 at 7:55 PM, Assaf Gordon <gordon@cshl.edu> wrote:
Leandro Hermida wrote, On 04/28/2011 08:55 AM:
Hi galaxy developers,
Just want to double-check, there is no way to import some kind of galaxy tool context info into python code you are running for a tool?
Nothing is impossible... just depends on how messy you want to get :)
for me, the following works: === python_path.xml === <tool id="cshl_python_path_test" name="pythonpath" description="" > <command>echo '$input1' > '$output'</command> <inputs> <param name="input1" type="text" value="10" label="Dummy"/> </inputs> <code file="python_path_code.py" /> <outputs> <data name="output" format="txt" /> </outputs> </tool> ======
==== python_path_code.py ===== from os import path import sys
def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): tool_path = path.abspath(tool.tool_dir); sys.stderr.write("!!!!! path = %s\n" % (tool_path)) ========================
When the tool runs, the following line is printed to STDERR: ====== !!!!! path = /home/gordon/projects/galaxy_dev/tools/cshl_tests ======
Help this helps, -gordon
Thanks so much, I never knew of the page https://bitbucket.org/galaxy/galaxy-central/wiki/CustomCode until seeing what you wrote and searching now. But I have one complication I guess. My tool is already running a Python code file to dynamically create a drop-down menu using the dynamic_options attribute a la: <param type="select" dynamic_options="my_options()"> ... <code file="my_options.py"/> In this function my_options I would need the tool dir path. How would I be able to combine what you did with this? Which function runs at the right time before my_options() is executed is it exec_before_process?
best, leandro
On Fri, Apr 15, 2011 at 8:03 PM, Leandro Hermida <
softdev@leandrohermida.com <mailto:softdev@leandrohermida.com>> wrote:
On Fri, Apr 15, 2011 at 7:27 PM, Peter Cock <
p.j.a.cock@googlemail.com <mailto:p.j.a.cock@googlemail.com>> wrote:
On Thu, Apr 14, 2011 at 2:56 PM, Leandro Hermida <softdev@leandrohermida.com <mailto:softdev@leandrohermida.com>>
wrote:
> On Thu, Apr 14, 2011 at 3:17 PM, Peter Cock <
p.j.a.cock@googlemail.com <mailto:p.j.a.cock@googlemail.com>>
> wrote: >> >> For standard Python tools in Galaxy, I'm using >> os.path.split(sys.argv[0])[0] >> to get the path, which on reflection probably should be
written as
>> os.path.dirname(sys.argv[0]) as you suggest. >> >> What do __file__ and sys.argv[0] give you? The simplest way to
debug
>> this is to add a print statement, since Galaxy will show the
stdout.
>> > > Hi Peter, > > __file__ throws an error: global name '__file__' is not defined
I guess the script is being loaded as a string, and run with
eval(...)
or something like that. It would also explain why sys.argv[0]
would
be one of the Galaxy script files.
> os.path.abspath(os.path.dirname(sys.argv[0])) gives me > /path/to/galaxy/scripts directory which is two levels up from
what the tool
> directory I want for example /path/to/galaxy/tools/mytool
So combine that with ../tools/mytool/ and you're done? OK, you
have
to know the name of the folder your tool *should* be in... so not
a
perfect solution.
Thanks Peter, yes that's the same idea I did as a quick fix.... also
don't like the fact that my tool directory is hard-coded but oh well. There must be a way within Python in Galaxy importing something from Galaxy that has the current tool directory path, it would seem that Galaxy needs to know this and would store it anyway?
best, Leandro