program_paths

kallisto v0.49.0 (newest version of kallisto):
/home/dsullivan/kallisto-bf/build/src/kallisto

kallisto v0.48.0 (previous version of kallisto):
/home/dsullivan/kallisto/build/src/kallisto

bustools v0.41.1 (newest version of bustools)
/home/dsullivan/bustools/build/src/bustools

Cell Ranger v3.1.0 (Released July 24, 2019. Downloaded November 22, 2022)
/home/kristjan/cellranger/cellranger-3.1.0/cellranger

Cell Ranger v4.0.0 (Released July 7, 2020. Downloaded November 22, 2022)
/home/kristjan/cellranger/cellranger-4.0.0/cellranger

Cell Ranger v5.0.1 (Released December 16, 2020. Downloaded November 22, 2022)
/home/kristjan/cellranger/cellranger-5.0.1/cellranger

Cell Ranger v6.1.6 (Released October 25, 2021. Downloaded October 7, 2022)
/home/kristjan/cellranger/cellranger-6.1.2/cellranger

Cell Ranger v7.0.1 (Released August 18, 2022. Downloaded October 7, 2022)
/home/kristjan/cellranger/cellranger-7.0.1/cellranger


salmon v1.9.0 (Released Jun 23, 2022. Download Oct 11, 2022) # Downloaded via: wget https://github.com/COMBINE-lab/salmon/releases/download/v1.9.0/salmon-1.9.0_linux_x86_64.tar.gz && tar -xzvf salmon-1.9.0_linux_x86_64.tar.gz
/home/dsullivan/salmon-1.9.0_linux_x86_64/bin/salmon

alevin-fry 0.8.0 (Released Oct 11, 2022. Download Oct 11, 2022; installation instructions below)
/home/dsullivan/.cargo/bin/alevin-fry

Install rust and alevin-fry:
export RUSTUP_HOME=./.rustup/
export CARGO_HOME=./.cargo/
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
./.cargo/bin/cargo install alevin-fry

Install pyroe:
python3.9 -m pip install pyroe

kbpy installation:
pip install kb-python