These are chat archives for dereneaton/ipyrad
@jlmcdaniel A few quick questions and/or tips:
The error you received is due to the
python call in your bash script
If you're switching from pyrad to ipyrad you have to restart from step 1. Have you run steps 1 and 2 with ipyrad already?
The installation instructions for ipyrad include the command
source ~/.bashrc after you install miniconda and ipyrad. This command re-loads the file .bashrc which is usually automatically called when you open a new terminal. Once it is 'sourced' you don't have to type the full path to the programs anymore, just the name. So instead of the long path
/mnt/gluster/jlmcdaniel/miniconda2/bin/ipyrad, you can simply type
ipyrad. If you type
ipyrad and it says that the command is not recognized, then your system must not automatically source .bashrc (though this is rare), but you can fix this by running
Once ipyrad is callable, you can simply call it with a single line of code as follows:
ipyrad -p params.txt -s 123
If you want to make a submission script like in your example that can be run on condor I would make it like the following: https://gist.github.com/dereneaton/6c6bfe6e487eec49cb0731bc9c3565ac
ipcluster code in your example is used to set up an advanced cluster setup, usually involving many nodes. If you are connecting to CPUs on a single node you are unlikely to have need of it.
Does that make things more clear? Thanks for the questions.