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 <leo.biscassi@gmail.com> 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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