Commit 93156364 authored by Tru  HUYNH's avatar Tru HUYNH
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parent 2de8caa9
Anaconda2: provides python2 with its own conda package management system,
that can be user installed. If you happen you have non python3 friendly code.
+ easy way to take care of python2
+ one shot installation
+ one can use pip to add non anaconda packaged python modules (caveat don't overwrite conda managed packages!)
- as any package management system, you depend on a 3rd party
- some conda packages might have non compatible requirements
see list of installed anaconda2 packages at:
(conda list output)
https://gitlab.pasteur.fr/tru/ISB2017/raw/master/ISB2017/installation_notes/anaconda2-list
1) Download and install
```
cd /ISB2017/sources/
wget https://repo.continuum.io/archive/Anaconda2-4.3.1-Linux-x86_64.sh
sh /ISB2017/sources/Anaconda2-4.3.1-Linux-x86_64.sh -b -p /ISB2017/anaconda2
```
2) create the modulefile
```
wget -O /ISB2017/modulefiles/anaconda2 https://gitlab.pasteur.fr/tru/ISB2017/raw/master/ISB2017/modulefiles/anaconda2
```
3) update and add more packages
```
module use /ISB2017/modulefiles
module add anaconda2
conda update -y conda
conda update -y --all
conda install biopython
```
Anaconda3: provides python3 with its own conda package management system,
that can be user installed.
+ easy way to take care of python3
+ one shot installation
+ one can use pip to add non anaconda packaged python modules (caveat don't overwrite conda managed packages!)
- as any package management system, you depend on a 3rd party
- some conda packages might have non compatible requirements
Provides Jupyter Notebook
see list of installed anaconda2 packages at:
(conda list output)
https://gitlab.pasteur.fr/tru/ISB2017/raw/master/ISB2017/installation_notes/anaconda3-list
1) Download and install
```
# Jupyter Notebook and Python/anaconda
cd /ISB2017/sources/
wget https://docs.continuum.io/anaconda/hashes/Anaconda3-4.3.1-Linux-x86_64.sh-hash
wget https://repo.continuum.io/archive/Anaconda3-4.3.1-Linux-x86_64.sh
# 4447b93d2c779201e5fb50cfc45de0ec96c3804e7ad0fe201ab6b99f73e90302 sha256
# 9209864784250d6855886683ed702846 md5
sh Anaconda3-4.3.1-Linux-x86_64.sh -b -p /ISB2017/anaconda3
```
2) create the modulefile
```
wget -O /ISB2017/modulefiles/anaconda3 https://gitlab.pasteur.fr/tru/ISB2017/raw/master/ISB2017/modulefiles/anaconda3
```
3) update and add more packages
```
module use /ISB2017/modulefiles
module add anaconda3
conda update -y conda
conda update -y --all
conda install biopython
```
# CCP4 -7.0 64 bits for linux
- http://www.ccp4.ac.uk/download/index.php#os=linux
- CCP4 Program Suite v7.0 including SHELX (64 bit) -> ccp4-7.0-shelx-linux-x86_64.tar.bz2
```
cd /ISB2017 && tar xjf ccp4-7.0-shelx-linux-x86_64.tar.bz2
cd /ISB2017/ccp4-7.0/ && ./BINARY.setup
```
Before using for bash users:
```
source /ISB2017/ccp4-7.0/bin/ccp4.setup-sh
```
# chimera 64 bits linux
- https://www.cgl.ucsf.edu/chimera/download.html
- chimera-1.11.2-linux_x86_64.bin
```
chmod +x chimera-1.11.2-linux_x86_64.bin
./chimera-1.11.2-linux_x86_64.bin -q -d /dev/shm/
UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs@lists.wku.edu).
Valid options are -tfupcz and -d <exdir>; modifiers are -abjnoqCLMVX.
[centos@salle3-35 sources]$ ./chimera-1.11.2-linux_x86_64.bin -q -d /dev/shm/
UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs@lists.wku.edu).
Original path: '/ISB2017/sources'
Enter install location: /ISB2017/chimera-1.11.2-linux_x86_64
Extracting files. This may take a few minutes.
Executing command: './chimera.bin -q -d /ISB2017/chimera-1.11.2-linux_x86_64'
UnZipSFX 5.52 of 28 February 2005, by Info-ZIP (http://www.info-zip.org).
...
```
# grace
- http://plasma-gate.weizmann.ac.il/Grace/
```
wget ftp://plasma-gate.weizmann.ac.il/pub/grace/src/grace5/grace-5.1.25.tar.gz
tar xzvf grace-5.1.25.tar.gz
cd grace-5.1.25/
./configure --prefix=/ISB2017/grace-5.1.25
sed -i -e 's,/ISB2017/grace-5.1.25,grace,/ISB2017/grace-5.1.25,g' Make.conf
make -j 8
make check && make install
```
# IMP from https://integrativemodeling.org
- using a separate conda installation tree to avoid conflict from the main anaconda2 tree
- https://integrativemodeling.org/download-anaconda.html
```
sh /ISB2017/sources/Anaconda2-4.3.1-Linux-x86_64.sh -b -p /ISB2017/IMP-co-anaconda2
export PATH=/ISB2017/IMP-co-anaconda2/bin:$PATH
conda config --add channels salilab
conda install imp
Fetching package metadata ...........
Solving package specifications: .
Package plan for installation in environment /ISB2017/IMP-co-anaconda2:
The following NEW packages will be INSTALLED:
boost: 1.61.0-py27_0
cgal: 4.9.1-1 salilab
fftw: 3.3.4-0 salilab
gmp: 6.1.0-0
gsl: 1.16-0 salilab
imp: 2.7.0-py27_2 salilab
libtau: 1.0.1-0 salilab
mpfr: 3.1.5-0
opencv: 3.1.0-np111py27_1
system: 5.8-2
The following packages will be UPDATED:
anaconda: 4.3.1-np111py27_0 --> custom-py27_0
conda: 4.3.14-py27_0 --> 4.3.22-py27_0
The following packages will be DOWNGRADED due to dependency conflicts:
jpeg: 9b-0 --> 8d-2
libtiff: 4.0.6-3 --> 4.0.6-2
pillow: 4.0.0-py27_0 --> 3.4.2-py27_0
qt: 5.6.2-3 --> 5.6.2-2
Proceed ([y]/n)? y
...
[centos@salle3-35 sources]$ conda upgrade --all
Fetching package metadata ...........
Solving package specifications: .
Package plan for installation in environment /ISB2017/IMP-co-anaconda2:
The following NEW packages will be INSTALLED:
asn1crypto: 0.22.0-py27_0
bkcharts: 0.2-py27_0
bleach: 1.5.0-py27_0
html5lib: 0.999-py27_0
packaging: 16.8-py27_0
pandocfilters: 1.4.1-py27_0
pywavelets: 0.5.2-np112py27_0
sphinxcontrib: 1.0-py27_0
sphinxcontrib-websupport: 1.0.1-py27_0
testpath: 0.3.1-py27_0
typing: 3.6.1-py27_0
The following packages will be UPDATED:
alabaster: 0.7.9-py27_0 --> 0.7.10-py27_0
anaconda-client: 1.6.0-py27_0 --> 1.6.3-py27_0
anaconda-navigator: 1.5.0-py27_0 --> 1.6.3-py27_0
anaconda-project: 0.4.1-py27_0 --> 0.6.0-py27_0
astropy: 1.3-np111py27_0 --> 1.3.3-np112py27_0
babel: 2.3.4-py27_0 --> 2.4.0-py27_0
beautifulsoup4: 4.5.3-py27_0 --> 4.6.0-py27_0
bokeh: 0.12.4-py27_0 --> 0.12.6-py27_0
boto: 2.45.0-py27_0 --> 2.47.0-py27_0
bottleneck: 1.2.0-np111py27_0 --> 1.2.1-np112py27_0
cffi: 1.9.1-py27_0 --> 1.10.0-py27_0
chardet: 2.3.0-py27_0 --> 3.0.4-py27_0
colorama: 0.3.7-py27_0 --> 0.3.9-py27_0
contextlib2: 0.5.4-py27_0 --> 0.5.5-py27_0
cryptography: 1.7.1-py27_0 --> 1.8.1-py27_0
dask: 0.13.0-py27_0 --> 0.15.0-py27_0
dill: 0.2.5-py27_0 --> 0.2.6-py27_0
entrypoints: 0.2.2-py27_0 --> 0.2.2-py27_1
flask: 0.12-py27_0 --> 0.12.2-py27_0
fontconfig: 2.12.1-2 --> 2.12.1-3
futures: 3.0.5-py27_0 --> 3.1.1-py27_0
gevent: 1.2.1-py27_0 --> 1.2.2-py27_0
greenlet: 0.4.11-py27_0 --> 0.4.12-py27_0
h5py: 2.6.0-np111py27_2 --> 2.7.0-np112py27_0
hdf5: 1.8.17-1 --> 1.8.17-2
idna: 2.2-py27_0 --> 2.5-py27_0
ipykernel: 4.5.2-py27_0 --> 4.6.1-py27_0
ipython: 5.1.0-py27_0 --> 5.3.0-py27_0
ipython_genutils: 0.1.0-py27_0 --> 0.2.0-py27_0
ipywidgets: 5.2.2-py27_1 --> 6.0.0-py27_0
isort: 4.2.5-py27_0 --> 4.2.15-py27_0
jedi: 0.9.0-py27_1 --> 0.10.2-py27_2
jinja2: 2.9.4-py27_0 --> 2.9.6-py27_0
jsonschema: 2.5.1-py27_0 --> 2.6.0-py27_0
jupyter_client: 4.4.0-py27_0 --> 5.1.0-py27_0
jupyter_console: 5.0.0-py27_0 --> 5.1.0-py27_0
jupyter_core: 4.2.1-py27_0 --> 4.3.0-py27_0
lazy-object-proxy: 1.2.2-py27_0 --> 1.3.1-py27_0
libgcc: 4.8.5-2 --> 5.2.0-0
llvmlite: 0.15.0-py27_0 --> 0.18.0-py27_0
lxml: 3.7.2-py27_0 --> 3.8.0-py27_0
matplotlib: 2.0.0-np111py27_0 --> 2.0.2-np112py27_0
mistune: 0.7.3-py27_0 --> 0.7.4-py27_0
mkl: 2017.0.1-0 --> 2017.0.3-0
nbconvert: 4.2.0-py27_0 --> 5.2.1-py27_0
nbformat: 4.2.0-py27_0 --> 4.3.0-py27_0
nltk: 3.2.2-py27_0 --> 3.2.4-py27_0
notebook: 4.3.1-py27_0 --> 5.0.0-py27_0
numba: 0.30.1-np111py27_0 --> 0.33.0-np112py27_0
numexpr: 2.6.1-np111py27_2 --> 2.6.2-np112py27_0
numpy: 1.11.3-py27_0 --> 1.12.1-py27_0
opencv: 3.1.0-np111py27_1 --> 3.1.0-np112py27_1
openpyxl: 2.4.1-py27_0 --> 2.4.7-py27_0
openssl: 1.0.2k-1 --> 1.0.2l-0
pandas: 0.19.2-np111py27_1 --> 0.20.2-np112py27_0
partd: 0.3.7-py27_0 --> 0.3.8-py27_0
path.py: 10.0-py27_0 --> 10.3.1-py27_0
pathlib2: 2.2.0-py27_0 --> 2.2.1-py27_0
ply: 3.9-py27_0 --> 3.10-py27_0
prompt_toolkit: 1.0.9-py27_0 --> 1.0.14-py27_0
psutil: 5.0.1-py27_0 --> 5.2.2-py27_0
py: 1.4.32-py27_0 --> 1.4.34-py27_0
pyasn1: 0.1.9-py27_0 --> 0.2.3-py27_0
pycosat: 0.6.1-py27_1 --> 0.6.2-py27_0
pycrypto: 2.6.1-py27_4 --> 2.6.1-py27_6
pygments: 2.1.3-py27_0 --> 2.2.0-py27_0
pyopenssl: 16.2.0-py27_0 --> 17.0.0-py27_0
pytables: 3.3.0-np111py27_0 --> 3.3.0-np112py27_0
pytest: 3.0.5-py27_0 --> 3.1.2-py27_0
pytz: 2016.10-py27_0 --> 2017.2-py27_0
qtawesome: 0.4.3-py27_0 --> 0.4.4-py27_0
qtconsole: 4.2.1-py27_1 --> 4.3.0-py27_0
requests: 2.12.4-py27_0 --> 2.14.2-py27_0
scandir: 1.4-py27_0 --> 1.5-py27_0
scikit-image: 0.12.3-np111py27_1 --> 0.13.0-np112py27_0
scikit-learn: 0.18.1-np111py27_1 --> 0.18.2-np112py27_0
scipy: 0.18.1-np111py27_1 --> 0.19.1-np112py27_0
sphinx: 1.5.1-py27_0 --> 1.6.2-py27_0
spyder: 3.1.2-py27_0 --> 3.1.4-py27_0
sqlalchemy: 1.1.5-py27_0 --> 1.1.11-py27_0
statsmodels: 0.6.1-np111py27_1 --> 0.8.0-np112py27_0
tornado: 4.4.2-py27_0 --> 4.5.1-py27_0
traitlets: 4.3.1-py27_0 --> 4.3.2-py27_0
werkzeug: 0.11.15-py27_0 --> 0.12.2-py27_0
widgetsnbextension: 1.2.6-py27_0 --> 2.0.0-py27_0
wrapt: 1.10.8-py27_0 --> 1.10.10-py27_0
Proceed ([y]/n)?
```
# remove the channel (persistent across anaconda versions)
```
conda config --show-sources
conda config --add channels salilab
conda config --remove channels salilab
```
# phenix
- https://www.phenix-online.org/
```
To download the PHENIX distribution with a web browser go to:
https://www.phenix-online.org/download/phenix/
When prompted for a user name and password enter:
User Name: download
Password: ********
The password is changed every Monday at 00:05 PST/PDT. (If the password
is expired, simply request a new one at: www.phenix-online.org)
This is an automatically generated message. Please do not reply to
this email. If you experience problems please contact:
download@phenix-online.org
Citing PHENIX:
PHENIX: a comprehensive Python-based system for macromolecular
structure solution. P.D. Adams, P.V. Afonine, G. Bunkoczi, V.B. Chen,
I.W. Davis, N. Echols, J.J. Headd, L.-W. Hung, G.J. Kapral,
R.W. Grosse-Kunstleve, A.J. McCoy, N.W. Moriarty, R. Oeffner,
R.J. Read, D.C. Richardson, J.S. Richardson, T.C. Terwilliger and
P.H. Zwart. Acta Cryst. D66, 213-221 (2010).
```
```
tar xjf /ISB2017/sources/phenix-installer-1.11.1-2575-intel-linux-2.6-x86_64-centos6.tar.gz
cd phenix-installer-1.11.1-2575-intel-linux-2.6-x86_64-centos6/
alias pymol=/ISB2017/anaconda2/bin/pymol
./install --prefix=/ISB2017/
# will install into /ISB2017/phenix-1.11.1-2575
```
Usage:
```
source /ISB2017/phenix-1.11.1-2575/phenix_env.sh
phenix
```
# pymol
```
cd /ISB2017/sources
wget -O pymol-v1.8.6.0.tar.bz2 https://sourceforge.net/projects/pymol/files/pymol/1.8/pymol-v1.8.6.0.tar.bz2/download
sudo yum -y install glew-devel glew msgpack-devel
tar -C ~/build -xjvf /ISB2017/sources/pymol-v1.8.6.0.tar.bz2
cd ~/build/pymol
python setup.py build
python setup.py install --bundled-pmw
```
Alternatively, you can pull the subsersion code with:
```
svn checkout https://svn.code.sf.net/p/pymol/code/trunk pymol-code
```
python3(anaconda3) will need Pmw2(https://downloads.sourceforge.net/project/pmw/Pmw-2.0.0.tar.gz?) instead of the bundled pwm.
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