Volume modul builds - kooplex/kooplex-hub GitHub Wiki

CFLAGS="-m64" pip install ....

git clone https://github.com/openbabel/openbabel.git #tag 2.4.1
mkdir openbabel-build
cd openbabel-build
cmake ../openbabel/ -DCMAKE_INSTALL_PREFIX=/vol/molecularelectronics/
make -j4
make install

#### Set environmental variables
export MOLELEC_DIR=/vol/molecularelectronics

export PATH=$PATH:$MOLELEC_DIR/bin
export PYTHONPATH=$PYTHONPATH:$MOLELEC_DIR/lib/python3.6/site-packages/
export PATH=$PATH:$MOLELEC_DIR/=siesta/siesta-4.1-b3/Obj-parallel/
export ASE_DIR=$MOLELEC_DIR/ase_ext
export UTILS_DIR=$MOLELEC_DIR/Utils
export DREI_DIR=$UTILS_DIR
export YAEHMOPDIR=$MOLELEC_DIR/Yaehmop_build
export PYYAEHMOPDIR=$MOLELEC_DIR/molecularelectronics/Yaehmopy
export BABEL_EXE=$MOLELEC_DIR/bin/obabel
export OMP_NUM_THREADS=8
export DFTB_PREFIX=$MOLELEC_DIR/DFTB/DFTB_Parameters/mio-1-1/
export DFTB_COMMAND=$MOLELEC_DIR/DFTB/dftbplus-18.2.x86_64-linux/bin/dftb+
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MOLELEC_DIR/lib/:$MOLELEC_DIR/lib/x86_64-linux-gnu/
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MOLELEC_DIR/lib/openbabel/2.4.1
export SIESTA_COMMAND="mpirun -n 8 $MOLELEC_DIR/siesta-4.1-b3/Obj-parallel/siesta < %s > %s"
export SIESTA_PP_PATH=$MOLELEC_DIR/siesta-pseudos

DIR=/vol/python27/
FULLDIR=$DIR/condaenvs/python27

mkdir -p $DIR/condaenvs
conda create -p $FULLDIR python=2.7 ipykernel
source activate $FULLDIR

$CONDA_DIR/bin/conda install --quiet --yes pandas numpy scipy matplotlib seaborn plotly  bokeh pymysql sqlite ujson
$CONDA_DIR/bin/conda install --quiet --yes -c conda-forge  igraph lifelines folium
$CONDA_DIR/bin/conda install --quiet --yes -c conda-forge jupyter_dashboards; jupyter dashboards quick-setup --sys-prefix
$CONDA_DIR/bin/conda install --quiet --yes -c conda-forge jupyter_cms; jupyter cms quick-setup --sys-prefix

$CONDA_DIR/bin/conda install --quiet --yes -c conda-forge geopy
$CONDA_DIR/bin/conda install --quiet --yes biopython jinja2 
$CONDA_DIR/bin/conda install --quiet --yes -c bioconda ete3 
 
$CONDA_DIR/bin/conda install --quiet --yes -c conda-forge ipywidgets
jupyter nbextension enable --py widgetsnbextension --sys-prefix

echo "export CONDA_ENV_DIR=\$CONDA_ENV_DIR:$DIR/condaenvs" > $DIR/bashrc

DIR=/vol/python36/
FULLDIR=$DIR/condaenvs/python36

mkdir -p $DIR/condaenvs
conda create -p $FULLDIR python=3.6 ipykernel
source activate $FULLDIR

$CONDA_DIR/bin/conda install --quiet --yes pandas numpy scipy matplotlib seaborn plotly  bokeh pymysql sqlite ujson
$CONDA_DIR/bin/conda install --quiet --yes -c conda-forge  igraph lifelines folium
$CONDA_DIR/bin/conda install --quiet --yes -c conda-forge jupyter_dashboards; jupyter dashboards quick-setup --sys-prefix
$CONDA_DIR/bin/conda install --quiet --yes -c conda-forge jupyter_cms; jupyter cms quick-setup --sys-prefix

$CONDA_DIR/bin/conda install --quiet --yes -c conda-forge geopy
$CONDA_DIR/bin/conda install --quiet --yes biopython jinja2 
$CONDA_DIR/bin/conda install --quiet --yes -c bioconda ete3 

$CONDA_DIR/bin/conda install --quiet --yes -c conda-forge ipywidgets bqplot
jupyter nbextension enable --py widgetsnbextension --sys-prefix

echo "export CONDA_ENV_DIR=\$CONDA_ENV_DIR:$DIR/condaenvs" > $DIR/bashrc

DIR=/vol/r_env/
FULLDIR=$DIR/condaenvs/r_env

mkdir -p $DIR/condaenvs
conda create -p $FULLDIR python=2.7 ipykernel
source activate $FULLDIR

conda create -p $DIR/condaenvs  -c r r-essentials

echo "export CONDA_ENV_DIR=\$CONDA_ENV_DIR:$DIR/condaenvs" > $DIR/bashrc

DIR=/vol/bio/
FULLDIR=$DIR/condaenvs/bio

mkdir -p $DIR/condaenvs
conda create -p $FULLDIR --quiet --yes python=3.4 ipykernel
source activate $FULLDIR

# THIS ENABLES THE NOTEBOOK EXTENSION TO FIND THE CONDA ENV
echo "export CONDA_ENV_DIR=\$CONDA_ENV_DIR:$DIR/condaenvs" > $DIR/bashrc

# MAKING NON PYTHON PACKAGES ACCESSIBLE
echo "export PATH=\$PATH:$DIR/usr/bin" >> $DIR/bashrc
echo "export LD_LIBRARY_PATH=\$LD_LIBRARY_PATH:$DIR/usr/bin" >> $DIR/bashrc

# CONDA PACKAGES
for CP in pandas numpy scipy matplotlib seaborn plotly  bokeh pymysql sqlite ujson biopython jinja2 xvfbwrapper r rpy2 
do
    $CONDA_DIR/bin/conda install --quiet --yes $CP
done

# CONDA-FORGE PACKAGES
for CP in igraph lifelines folium jupyter_dashboards jupyter_cms geopy
do
    $CONDA_DIR/bin/conda install --quiet --yes -c conda-forge $CP
done

# OTHER CONDA PACKAGES
$CONDA_DIR/bin/conda install --quiet --yes -c bioconda ete3 bowtie dendropy 
$CONDA_DIR/bin/conda install --quiet --yes -c etetoolkit ete3_external_apps

# ACTIVATING PACKAGES
jupyter dashboards quick-setup --sys-prefix
jupyter cms quick-setup --sys-prefix

# NON CONDA PYTHON PACKAGES
pip install sklearn-pandas

$CONDA_DIR/bin/conda install --quiet --yes -c conda-forge ipywidgets
jupyter nbextension enable --py widgetsnbextension --sys-prefix

pip install pybel

# TEMPORARY DIR FOR DOWNLOADS
TMP=/tmp/pkg
mkdir -p $TMP
cd $TMP

for PP in openjdk-8-jdk clustalw clustalo mafft mrbayes mrbayes-doc mrbayes-mpi libtbb2 libncurses5-dev libncursesw5-dev zlib1g-dev
do
  apt-rdepends $PP |grep -v "^ "| awk '{TT=$1;if(system("bash -c '\'' dpkg -l |grep "$1" '\''")) system("bash -c '\'' apt download "TT" '\''")  }'
done
ls *deb | xargs -n 1 echo | awk -v DD=$DIR '{TT=$1;system("bash -c '\'' dpkg -X "TT" "DD" '\''")}'
rm *deb

cd $TMP; git clone git://github.com/samtools/samtools.git
git clone https://github.com/samtools/bcftools.git
git clone https://github.com/samtools/htslib.git
git clone https://github.com/lh3/bwa.git
cd $TMP/samtools; git checkout tags/1.5; make; make install -e prefix=$DIR/install/samtools
cd $TMP/bcftools; git checkout tags/1.5; make; make install -e prefix=$DIR/install/bcftools
cd $TMP/htslib;   git checkout tags/1.5; make; make install -e prefix=$DIR/install/htslib
cd $TMP/bwa;      git checkout tags/v0.7.16; make; cp $TMP/bwa $DIR/install/bwa

cd $TMP; wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.6.0+-x64-linux.tar.gz
mkdir $DIR/install/blast
tar -xf ncbi-blast-2.6.0+-x64-linux.tar.gz -C $DIR/install/blast

# NEEDS ACCEPTING UELA (user end license agreement)
# Get GenomeAnalysisTK.jar  picard.jar
echo " Get GenomeAnalysisTK.jar  picard.jar"
# cp *jar /vol/bio/usr/bin/
echo " cp *jar /vol/bio/usr/bin/"

# EXTRA PATH ADDITIONS
echo "export PATH=\$PATH:$DIR/install/samtools/bin/:$DIR/install/blast/ncbi-blast-2.6.0+/bin/:$DIR/
install/bwa/bwakit" >>  $DIR/bashrc