this folder has all the things that I don't know where to keep.
Note for me (and for others too?) so I don't need to remember or google.
See [issues] (https://github.com/hainm/bag_of_tips/issues)
coding
* font: Liberation Mono, 12
* builtin-in scheme: black on light yellow
* Text color: black
* bg color: light yellow
* Pallette: Linux console
pyspark
-
Use notebook remotely
- PYSPARK_DRIVER_PYTHON=ipython
PYSPARK_DRIVER_PYTHON_OPTS="notebook --no-browser --port=8889" ./bin/pyspark
- PYSPARK_DRIVER_PYTHON=ipython
GCC
Install gcc5.3
Common Error
-
libgmp.so.10: cannot open shared object file
- locate libgmp.so.10
- export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/libgmp/
How to use IPython, conda, ... in PHENIX
- Upgrade pip:
phenix.python -m pip install pip --upgrade
- Install readline:
phenix.python -m pip install readline
- Install Ipython:
phenix.python -m pip install IPython
. Alternate way is to useconda
- Run:
phenix.python -c 'from IPython import start_ipython;start_ipython()
- conda:
phenix.python -m pip install conda
- install via conda:
phenix.python -m conda install package
- update numpy >= 1.9.0:
phenix.python -m conda install numpy
- To use
jupyter
notebook, createpy2
env withanaconda
orminiconda
distribution. (man, too much work) - Check source_phenix_2376
Install pytraj with PHENIX
- cd $AMBERHOME/AmberTools/src/pytraj && phenix.python setup.py clean && phenix.python setup.py install
Notes: does not work with pytraj in $AMBERHOME/lib due to wrong Python version. (although two Pythons are 2.7, ack)
Crystal
Install coot
conda install coot -c mw
# update boots >= 1.59
conda install boost=1.59.0 -c omnia
npm
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- 401 error: ?