IR/bin/|#!/usr/bin/env |' $INSTALL_DIR/bin/*
>
> I have uploaded it to the testtoolshed and to galaxytools.
> If this is working for you, also with depending repositories, I will try
> to add this to into the Tool Shed core to make this sed command implicit
> for all perl to
:04:
> Hi Renato,
>
> Am 30.07.2014 um 12:21 schrieb Renato Alves:
>> Hi everyone,
>>
>> Is there any standard or commonly used way to package tools that have
>> language specific dependencies.
>>
>> I know that with Python libraries one can use setup_virtualen
Hi Björn,
Thanks, this is exactly what I was looking for.
Cheers,
Renato
Quoting Björn Grüning on 30-07-2014 12:04:
> Hi Renato,
>
> Am 30.07.2014 um 12:21 schrieb Renato Alves:
>> Hi everyone,
>>
>> Is there any standard or commonly used way to package tools tha
Hi everyone,
Is there any standard or commonly used way to package tools that have
language specific dependencies.
I know that with Python libraries one can use setup_virtualenv and with
Java jars the JAVA_JAR_LIB strategy is used.
Is there anything equivalent for R, Perl and Ruby libraries?
Tha
but these are not really intended as public interfaces.
>
> (I did play with this a while back, but right now I forget which
> branch this was on...)
>
> Peter
>
> On Thu, Jul 17, 2014 at 6:53 PM, Renato Alves
> wrote:
>> Hi all,
>>
>>
>> TLDR - Last
Hi all,
TLDR - Last 2 lines of this email
Some time ago we created a wrapper script for breseq, a tool that
generates a friendly HTML report of mutations.
This was a perfect match for Galaxy given that we could simply set the
"summary.html" file to be displayed using Galaxy's HTML datatype and
Hi everyone,
I'm writing a wrapper that includes one text field.
I'm then passing the contents of this field to the underlying tool with
a simple:
command $textfield
However when a user inputs something like Test#1 the command ends up as:
command Test__pd__1
I did a quick search on the we
be a
> priority.
>
> https://trello.com/c/8K86l4Qk
>
> Thanks,
> -John
>
> On Wed, Feb 5, 2014 at 9:11 AM, Renato Alves
> wrote:
>> I'm trying to run functional tests on the stable branch of galaxy using:
>>
>> GALAXY_TEST_EXTERNAL=1 GALAXY_TEST_HOST=gala
I'm trying to run functional tests on the stable branch of galaxy using:
GALAXY_TEST_EXTERNAL=1 GALAXY_TEST_HOST=galaxy GALAXY_TEST_PORT=80
./run_functional_tests.sh
But I'm getting the error:
Traceback (most recent call last):
File "./scripts/functional_tests.py", line 457, in
sys.exit(
Hi everyone,
I've just recently decided to try out the automatic installation of
dependencies but ran into a few problems.
The first is that the machine that currently runs the web component
lacks most libraries which would be required for compilation.
I realize that this will make it hard/imposs
Quoting Renato Alves on 18-10-2013 03:18:
> Hi everyone,
>
> I'm currently setting up galaxy to run on top of AFS using torque for
> handling jobs.
>
> Everything is setup according to wiki documentation but I'm having a
> weird filesystem corruption problem.
Hi everyone,
I'm currently setting up galaxy to run on top of AFS using torque for
handling jobs.
Everything is setup according to wiki documentation but I'm having a
weird filesystem corruption problem.
The setup is the following:
machine A: runs galaxy. Galaxy home folder is on AFS.
machine B
Hi everyone,
When trying to adapt the init script for debian machines (provided in
contrib/) I started playing with paster directly. I was trying to get
some sort of help or list of commands/params that can be passed but
instead I was presented with the following output:
$ python ./scripts/paster
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