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View Code? Open in Web Editor NEWSingularity Container for Hail (hail.is)
License: MIT License
Singularity Container for Hail (hail.is)
License: MIT License
when adding path to anaconda3/bin
into the system path via .bashrc
and run conda activate
conda activate
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
If your shell is Bash or a Bourne variant, enable conda for the current user with
$ echo ". /root/anaconda3/etc/profile.d/conda.sh" >> ~/.bashrc
or, for all users, enable conda with
$ sudo ln -s /root/anaconda3/etc/profile.d/conda.sh /etc/profile.d/conda.sh
The options above will permanently enable the 'conda' command, but they do NOT
put conda's base (root) environment on PATH. To do so, run
$ conda activate
in your terminal, or to put the base environment on PATH permanently, run
$ echo "conda activate" >> ~/.bashrc
Previous to conda 4.4, the recommended way to activate conda was to modify PATH in
your ~/.bashrc file. You should manually remove the line that looks like
export PATH="/root/anaconda3/bin:$PATH"
^^^ The above line should NO LONGER be in your ~/.bashrc file! ^^^
The above message will be printed out.
/opt/spark-2.2.0-bin-hadoop2.7//bin/spark-class: line 71: /usr/lib/jvm/java-8-oracle/bin/java: No such file or directory
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/opt/hail/python/hail/typecheck/check.py", line 547, in wrapper
return f(*args_, **kwargs_)
File "/opt/hail/python/hail/context.py", line 160, in init
default_reference, force_ir)
File "/opt/hail/python/hail/typecheck/check.py", line 547, in wrapper
return f(*args_, **kwargs_)
File "/opt/hail/python/hail/context.py", line 35, in __init__
SparkContext._ensure_initialized()
File "/opt/spark-2.2.0-bin-hadoop2.7/python/pyspark/context.py", line 283, in _ensure_initialized
SparkContext._gateway = gateway or launch_gateway(conf)
File "/opt/spark-2.2.0-bin-hadoop2.7/python/pyspark/java_gateway.py", line 95, in launch_gateway
raise Exception("Java gateway process exited before sending the driver its port number")
Exception: Java gateway process exited before sending the driver its port number
error found while trying hl.init()
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