Re: [galaxy-dev] Problem with conda on galaxy 16.07

[John Chilton]

Any follow up on this? I have never seen this - but it would be worth
specifying a full absolute path for conda_prefix in galaxy.ini and see
if that fixes it. If it does - I can open a PR that makes sure this
variable is always an absolute path.

On Thu, Sep 1, 2016 at 11:37 PM, Léo Biscassi  wrote:
> Hi folks,
> Today after perform some tests with conda on galaxy 16.07 the follow message
> was returned in my terminal:
>
> "Conda dependency seemingly installed but failed to build job environment."
>
> The error occurs when build_isolated_environment() function is call. Below
> some variable values:
>
> is_installed = True
> job_directory = /home/leobiscassi/programs/galaxy/job_work_dir/000/17
> env_path = /home/leobiscassi/programs/galaxy/job_work_dir/000/17/conda-env
> exit_code = 127
>
> Analyzing inside of the build_isolated_environment(), the exec_create()
> function is executed because path variable
> (/home/leobiscassi/programs/galaxy/job_work_dir/000/17/conda-env) don't
> exists, the command executed by exec_create is showed below:
>
> deps/_conda/bin/conda create -y --unknown --offline --prefix
> /home/leobiscassi/programs/galaxy/job_work_dir/000/17/conda-env --file
> ./database/tmp/jobdepsIGslWfe2bd2345d2ec1bb4aeb81211183570bae7db28a3bea4f7ff9e8e75074719a7ee/__mgltools@1.5.6
>> /dev/null
>
> Some important values:
>
> env = {'HOME': 'deps/_conda', 'CONDARC':
> '/home/leobiscassi/programs/galaxy/deps/_condarc'}
>
> The command return is '/bin/sh: 1: deps/_conda/bin/conda: not found', but
> the binary exist. Anyone can help me with this?
>
> Thanks in advance.
> --
> Best regards,
> Léo Biscassi
>
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[galaxy-dev] Problem with conda on galaxy 16.07

[Léo Biscassi]

Hi folks,
Today after perform some tests with conda on galaxy 16.07 the follow
message was returned in my terminal:

"*Conda dependency seemingly installed but failed to build job environment.*
"

The error occurs when *build_isolated_environment()* function is call.
Below some variable values:

*is_installed* = *True*
*job_directory* = */home/leobiscassi/programs/galaxy/job_work_dir/000/17*
*env_path* =
*/home/leobiscassi/programs/galaxy/job_work_dir/000/17/conda-env*
*exit_code* = *127*

Analyzing inside of the *build_isolated_environment()*, the
*exec_create() *function
is executed because *path* variable (
*/home/leobiscassi/programs/galaxy/job_work_dir/000/17/conda-env*) don't
exists, the command executed by *exec_create* is showed below:

*deps/_conda/bin/conda create -y --unknown --offline --prefix
/home/leobiscassi/programs/galaxy/job_work_dir/000/17/conda-env --file
./database/tmp/jobdepsIGslWfe2bd2345d2ec1bb4aeb81211183570bae7db28a3bea4f7ff9e8e75074719a7ee/__mgltools@1.5.6
> /dev/null*

Some important values:

*env* = *{'HOME': 'deps/_conda', 'CONDARC':
'/home/leobiscassi/programs/galaxy/deps/_condarc'}*

The command return is '*/bin/sh: 1: deps/_conda/bin/conda: not found*', but
the binary exist. Anyone can help me with this?

Thanks in advance.
-- 
Best regards,
*Léo Biscassi*
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