mtorresm55/longcellpre repository overview

condaforge/miniforge3

docker run -it 2c2ad89f487d /bin/bash

apt-get update

apt install build-essential

apt-get install libboost-dev

apt-get install parallel

docker run -it 2c2ad89f487d /bin/bash

apt-get update

apt install build-essential

apt-get install libboost-dev

mamba install -c conda-forge -c bioconda -c r minimap2 samtools bedtools r-devtools bioconductor-iranges bioconductor-genomicranges r-rcppeigen bioconductor-rsamtools r-igraph r-rcppeigen bioconductor-bsgenome bioconductor-genomicfeatures r-parallelly r-listenv r-globals r-mass r-future r-data.table r-plyr r-proxy r-class r-future.apply r-nameneedle r-rcpphungarian r-transport r-e1071 r-reshape2 r-dbscan r-peakram r-spgs r-biocmanager

apt-get install dos2unix

mamba install -c conda-forge -c bioconda -c anaconda pysam pandas numpy pathos multiprocess

mamba install -c conda-forge -c bioconda -c r -c anaconda r-rcpp r-dbscan r-reshape2 r-tidyr r-transport r-rcpphungarian r-nameneedle r-igraph r-mass r-argparse bioconductor-genomicfeatures r-parallelly r-e1071 r-mknapsack

cd bin

git clone https://github.com/yuntianf/Longcell-pre.git⁠ cd ./Longcell-pre/scripts/ dos2unix Longcell-pre.sh chmod a+x Longcell-pre.sh cd ./BarcodeMatch/ g++ -O2 BarcodeMatch.cpp bc.cpp edit.cpp normal.cpp -o BarcodeMatch

docker commit 126b3b5c5021 mtorresm55/longcellpre:v1.0 docker push mtorresm55/longcellpre:v1.0

Version 2.3:

docker run -it 2c2ad89f487d /bin/bash

apt-get update

apt install build-essential

apt-get install libboost-dev

mamba install -c conda-forge -c bioconda -c r minimap2 samtools bedtools r-devtools bioconductor-iranges bioconductor-genomicranges r-rcppeigen bioconductor-rsamtools r-igraph r-rcppeigen bioconductor-bsgenome bioconductor-genomicfeatures r-parallelly r-listenv r-globals r-mass r-future r-data.table r-plyr r-proxy r-class r-future.apply r-nameneedle r-rcpphungarian r-transport r-e1071 r-reshape2 r-dbscan r-peakram r-spgs r-biocmanager bioconductor-bsgenome.mmusculus.ucsc.mm10

devtools::install_github("yuntianf/Longcellsrc")

devtools::install_github("yuntianf/LongcellPre")

docker commit 7bbf58df8419 mtorresm55/longcellpre:v2.3

docker push mtorresm55/longcellpre:v2.3