Hi Dave,
I made changes giving the suggestions of Ross, I got a different error and
that gave me insight as to what was going on. I uploaded new xml:
<action type="shell_command">export
<?xml version="1.0"?>
<tool_dependency>
<package name="requests" version="1.2.3">
<install version="1.0">
<actions>
<action
type="download_by_url">http://pypi.python.org/packages/source/r/requests/re
quests-1.2.3.tar.gz</action>
<action
type="make_directory">$INSTALL_DIR/lib/python</action>
PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
python setup.py install --home $INSTALL_DIR
--install-scripts $INSTALL_DIR/bin</action>
<action type="set_environment">
<environment_variable name="PYTHONPATH"
action="append_to">$INSTALL_DIR/lib/python</environment_variable>
<environment_variable name="PATH"
action="prepend_to">$INSTALL_DIR/bin</environment_variable>
</action>
</actions>And this worked for me. I'm thinking you may have downloaded after I
</install>
<readme>
</readme>
</package>
</tool_dependency>
made the changes.
-Curt
On 8/21/13 6:01 PM, "Dave Bouvier" <dave@bx.psu.edu> wrote:
>Curt,
>
>I tried installing the ingtest repository on a local instance of Galaxy,
>and the requests python module installed without errors. Which revision
>of Galaxy are you trying to install this repository into, and what kind
>of environment are you running on that system?
>
> --Dave B.
Try moving the <action
type="download_by_url">http://pypi.python.org/packages/source/r/requests/re
quests-1.2.3.tar.gz</action>
line so it's the one before
<action type="shell_command">python setup.py install --home $INSTALL_DIR
--install-scripts $INSTALL_DIR/bin</action>
I think I've been bitten by this - it seems download_by_url changes the
current path but only temporarily so you need to run setup.py immediately
as the next step?
If this works, please confirm to the entire list - I'm sending this to you
just in case I'm full of it :)
On Thu, Aug 22, 2013 at 9:12 AM, Curt Palm <cpalm@ingenuity.com> wrote:
I've just created a repository in the sandbox and have been trying to
test the installation of a dependency my tool needs. The tool needs the
python module "requests" and I've written code. I get an error:
STDERR
python: can't open file 'setup.py': [Errno 2] No such file or directory
I've modeled my code on examples I've found in the tool shed. I've
replaced the requests module with other python modules and these are
installed ok. I can also download and manually install requests with
"python setup.py install"
Any suggestions as to what I may be doing wrong?
--
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
>
>On 2013-08-21 19:12, Curt Palm wrote:
>> I've just created a repository in the sandbox and have been trying to
>>test the installation of a dependency my tool needs. The tool needs
>>the python module "requests" and I've written code. I get an error:
>> STDERR
>> python: can't open file 'setup.py': [Errno 2] No such file or directory
>>
>> I've modeled my code on examples I've found in the tool shed. I've
>>replaced the requests module with other python modules and these are
>>installed ok. I can also download and manually install requests with
>> "python setup.py install"
>>
>> Any suggestions as to what I may be doing wrong?
>>
>> tool_dependencies.xml:
>>
>> <?xml version="1.0"?>
>> <tool_dependency>
>> <package name="requests" version="1.2.3">
>> <install version="1.0">
>> <actions>
>> <action
>>type="download_by_url">http://pypi.python.org/packages/source/r/requests/
>>requests-1.2.3.tar.gz</action>
>> <action
>>type="make_directory">$INSTALL_DIR/lib/python</action>
>> <action type="make_directory">$INSTALL_DIR/bin</action>
>> <action type="set_environment">
>> <environment_variable name="PYTHONPATH"
>>action="append_to">$INSTALL_DIR/lib/python</environment_variable>
>> <environment_variable name="PATH"
>>action="prepend_to">$INSTALL_DIR/bin</environment_variable>
>> </action>
>> <action type="shell_command">python setup.py install
>>--home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
>> </actions>
>> </install>
>> <readme>
>> </readme>
>> </package>
>> </tool_dependency>
>>
>>
>> ingTest.xml:
>>
>> <tool id="ingTest" name="ingTest" version="1.0">
>> <description>Testing Tool Shed</description>
>> <requirements>
>> <requirement type="package"
>>version="1.2.3">requests</requirement>
>> </requirements>
>>
>>
>> <command interpreter="python">
>>
>> </command>
>>
>> <inputs>
>>
>>
>> </inputs>
>> <outputs>
>>
>> </outputs>
>> <help>
>>
>> .. class:: infomark
>>
>>
>>
>>
>> </help>
>> </tool>
>>
>>
>>
>> Thanks,
>>
>> -Curt
>> Curt Palm
>> Data Engineer
>> ________________________________________
>> INGENUITY SYSTEMS | www.ingenuity.com
>> 1700 Seaport Blvd., 3rd Floor | Redwood City, CA 94063
>> 650.381.5084
>>
>>
>> ___________________________________________________________
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>>
___________________________________________________________
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