README.md

Conda recipes

This repository contains conda recipies to build single cell computation pipeline developed by KrasnitzLab.

Build SCGV viewer

Example building of SCGV viewer:

conda-build SCGV

To convert linux package into OSX-64 package use:

conda convert --platform osx-64 ~/anaconda/envs/sgains3/conda-bld/linux-64/scgv-1.0.2-py36h39e3cac_0.tar.bz2 -o build/ 

To upload conda packages into Anaconda Cloud channel for KrasnitzLab use:

anaconda upload -u krasnitzlab ~/anaconda/envs/sgains3/conda-bld/linux-64/scgv-1.0.2-py36h39e3cac_0.tar.bz2
anaconda upload -u krasnitzlab build/osx-64/scgv-1.0.2-py36h39e3cac_0.tar.bz2

To install SCGV use:

conda install -c krasnitzlab scgv

Build SCclust package

We need to build using krasnitzlab channel because of bioconductor-dnacopy dependency:

conda build -c krasnitzlab -c r -c bioconda bioconductor-dnacopy

conda build -c krasnitzlab SCclust

To convert linux package into OSX-64 package use:

conda convert --platform osx-64 ~/anaconda/envs/sgains3/conda-bld/linux-64/scclust-1.0.0RC3-r341_1.tar.bz2 -o build/ 

To upload conda packages into Anaconda Cloud channel for KrasnitzLab use:

anaconda upload -u krasnitzlab ~/anaconda/envs/sgains3/conda-bld/linux-64/scclust-1.0.0RC3-r341_1.tar.bz2
anaconda upload -u krasnitzlab build/osx-64/scclust-1.0.0RC3-r341_1.tar.bz2

To install SCclust package use:

conda install -c krasnitzlab scclust

Build sGAINS pipeline

Example building of sGAINS:

# conda build sgains
conda build -c bioconda -c krasnitzlab sgains

To upload conda package into Anaconda Cloud channel for KrasnitzLab use:

anaconda upload -u krasnitzlab /home/lubo/anaconda3/conda-bld/linux-64/sgains-1.0.0-py36h39e3cac_1.tar.bz2

To install use:

conda install -c bioconda -c krasnitzlab sgains