setup for mmcloud

container/course_packages_conda.csv

@@ -1,76 +1,60 @@
 Package,Homepage,Language,Version,Channel,Evironment,Link,Notes
-plink,https://www.cog-genomics.org/plink/2.0/,C/C++,1.90b6.21,bioconda,"clumping, epistasis, fastlmm-gcta, ldpred2, pleiotropy, plink-r-nothnagel, plink, regenie, twas, vat",https://anaconda.org/bioconda/plink,
-plink2,https://www.cog-genomics.org/plink/2.0/,C/C++,2.00a3.7,bioconda,"clumping, regenie",https://anaconda.org/bioconda/plink2,
-gcta,https://yanglab.westlake.edu.cn/software/gcta/#Overview	,C/C++,1.94.1,bioconda,fastglmm-gcta,https://anaconda.org/bioconda/gcta,
-FaSTLMM,http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/fastlmm/,,0.2.32,bioconda,fastglmm-gcta,https://anaconda.org/bioconda/fastlmm,
-corrplot,https://github.com/taiyun/corrplot,R,,conda-forge,finemap,https://anaconda.org/conda-forge/r-corrplot,
-gemini,https://github.com/arq5x/gemini,,0.30.2-0,bioconda,gemini,https://anaconda.org/bioconda/gemini,in python=2.7
-vt,,,2015.11.10,bioconda,gemini,https://anaconda.org/bioconda/vt,in python=2.7
-variant-effect-predictor,,,87-0,bioconda,gemini,https://anaconda.org/bioconda/variant-effect-predictor,in python=2.7
-igv,http://www.broadinstitute.org/software/igv/home,,,bioconda,igv,https://anaconda.org/bioconda/igv,exercise can be removed
-data.table,https://r-datatable.com,R,,conda-forge,"ldpred2, twas",https://anaconda.org/conda-forge/r-data.table,
-tidyverse,https://tidyverse.tidyverse.org,R,,conda-forge,ldpred2,https://anaconda.org/conda-forge/r-tidyverse,
-bigsnpr,https://privefl.github.io/bigsnpr/,R,,conda-forge,ldpred2,https://anaconda.org/conda-forge/r-bigsnpr,
-bigsparser,https://github.com/privefl/bigsparser,R,,conda-forge,ldpred2,https://anaconda.org/conda-forge/r-bigsparser,
-ggplot2,"http://ggplot2.tidyverse.org, https://github.com/tidyverse/ggplot2",R,,conda-forge,"ldpred2, statgen-equations",https://anaconda.org/conda-forge/r-ggplot2,
-gplots,https://CRAN.R-project.org/package=gplots,R,,conda-forge,ldpred2,https://anaconda.org/conda-forge/r-gplots,
-R.utils,https://github.com/HenrikBengtsson/R.utils,R,,conda-forge,ldpred3,https://anaconda.org/conda-forge/r-r.utils,
-curl,http://curl.haxx.se/,,,conda-forge,"nps, quanto",https://anaconda.org/conda-forge/libcurl,
-make,https://www.gnu.org/software/make/,C/C++,,conda-forge,nps,https://anaconda.org/conda-forge/make,
-gcc,https://gcc.gnu.org/onlinedocs/gccint/Libgcc.html,C/C++,,conda-forge,nps,https://anaconda.org/conda-forge/libgcc-ng,
-g++,https://github.com/conda-forge/ctng-compiler-activation-feedstock,C/C++,,conda-forge,nps,https://anaconda.org/conda-forge/gxx,
-libreadline-dev,https://tiswww.case.edu/php/chet/readline/rltop.html,,,conda-forge,"nps, saige",https://anaconda.org/conda-forge/m2-libreadline,
-libz-dev,http://zlib.net/,,,conda-forge,"nps, saige",https://anaconda.org/conda-forge/libzlib,
-libbz2-dev,http://www.bzip.org,C/C++,,conda-forge,nps,https://anaconda.org/conda-forge/m2-libbz2,
-liblzma-dev,https://tukaani.org/xz/,C/C++,,conda-forge,nps,https://anaconda.org/conda-forge/m2-liblzma,
-libpcre3-dev,http://www.pcre.org/,,,conda-forge,"nps, saige",https://anaconda.org/conda-forge/m2-libpcre32,
-libssl-dev,,,,zegami,nps,https://anaconda.org/zegami/libssl-libcryptso6,
-libopenblas-dev,http://www.openblas.net/,,,conda-forge,nps,https://anaconda.org/conda-forge/libopenblas,
-unzip,,,,conda-forge,nps,https://anaconda.org/conda-forge/unzip,
-libboost-all-dev,http://www.boost.org/,C/C++,,conda-forge,"nps, saige",https://anaconda.org/conda-forge/libboost,
-libpng-dev,http://www.libpng.org/pub/png/libpng.html,,,conda-forge,"nps, saige",https://anaconda.org/conda-forge/libpng,
-tabix,https://github.com/samtools/htslib,C/C++,,bioconda,"nps, saige",https://anaconda.org/bioconda/tabix,
-pROC,http://expasy.org/tools/pROC/,R,,conda-forge,nps,https://anaconda.org/conda-forge/r-proc,
-DescTools,https://andrisignorell.github.io/DescTools/,R,,conda-forge,nps,https://anaconda.org/conda-forge/r-desctools,
-mediation,https://CRAN.R-project.org/package=RMediation,R,,r,pleiotropy,https://anaconda.org/r/r-rmediation,
-BiocManager,https://CRAN.R-project.org/package=BiocManager,,,cona-forge,plink-r-nothnagel,https://anaconda.org/conda-forge/r-biocmanager,
-multtest,https://bioconductor.org/packages/3.18/bioc/html/multtest.html,,,bioconda,plink-r-nothnagel,https://anaconda.org/bioconda/bioconductor-multtest,
+plink,https://www.cog-genomics.org/plink/2.0/,C/C++,,bioconda,plink,https://anaconda.org/bioconda/plink,
+plink2,https://www.cog-genomics.org/plink/2.0/,C/C++,,bioconda,plink,https://anaconda.org/bioconda/plink2,
+KING,http://people.virginia.edu/~wc9c/KING/,C/C++,,bioconda,plink,https://anaconda.org/bioconda/king,
+gcta,https://yanglab.westlake.edu.cn/software/gcta/#Overview,C/C++,1.94.1,bioconda,fastglmm-gcta,https://anaconda.org/bioconda/gcta,
+FaSTLMM,http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/fastlmm/,python,0.2.32,bioconda,fastglmm-gcta,https://anaconda.org/bioconda/fastlmm,
+corrplot,https://github.com/taiyun/corrplot,R,,conda-forge,,https://anaconda.org/conda-forge/r-corrplot,
+data.table,https://r-datatable.com,R,,conda-forge,,https://anaconda.org/conda-forge/r-data.table,
+tidyverse,https://tidyverse.tidyverse.org,R,,conda-forge,,https://anaconda.org/conda-forge/r-tidyverse,
+bigsnpr,https://privefl.github.io/bigsnpr/,R,,conda-forge,,https://anaconda.org/conda-forge/r-bigsnpr,
+bigsparser,https://github.com/privefl/bigsparser,R,,conda-forge,,https://anaconda.org/conda-forge/r-bigsparser,
+ggplot2,"http://ggplot2.tidyverse.org, https://github.com/tidyverse/ggplot2",R,,conda-forge,,https://anaconda.org/conda-forge/r-ggplot2,
+gplots,https://CRAN.R-project.org/package=gplots,R,,conda-forge,,https://anaconda.org/conda-forge/r-gplots,
+R.utils,https://github.com/HenrikBengtsson/R.utils,R,,conda-forge,,https://anaconda.org/conda-forge/r-r.utils,
+mediation,https://CRAN.R-project.org/package=RMediation,R,,conda-forge,,https://anaconda.org/conda-forge/r-rmediation,
+BiocManager,https://CRAN.R-project.org/package=BiocManager,R,,cona-forge,,https://anaconda.org/conda-forge/r-biocmanager,
+multtest,https://bioconductor.org/packages/3.18/bioc/html/multtest.html,R,,bioconda,,https://anaconda.org/bioconda/bioconductor-multtest,
 plinkseq,https://atgu.mgh.harvard.edu/plinkseq/,C/C++,,hcc,pseq,https://anaconda.org/hcc/plinkseq,
 regenie,https://rgcgithub.github.io/regenie/,C/C++,,bioconda,regenie,https://anaconda.org/bioconda/regenie,
-ggrepel,http://github.com/slowkow/ggrepel,,,conda-forge,regenie,https://anaconda.org/conda-forge/r-ggrepel,
-qqman,https://CRAN.R-project.org/package=qqman,,,conda-forge,regenie,https://anaconda.org/conda-forge/r-qqman,
-wget,https://www.gnu.org/software/wget/,,,conda-dorge,saige,https://anaconda.org/conda-forge/wget,
-cmake,http://www.cmake.org/,,,conda-dorge,saige,https://anaconda.org/conda-forge/cmake,
-cget,,,,conda-dorge,saige,https://anaconda.org/conda-forge/cget,
-bgen,https://github.com/limix/bgen,,,conda-dorge,saige,https://anaconda.org/conda-forge/bgen,
-bgen-reader,http://github.com/limix/bgen-reader-py,,,conda-dorge,saige,https://anaconda.org/conda-forge/bgen-reader,
-remotes,https://github.com/r-lib/remotes#readme,R,,conda-forge,saige,https://anaconda.org/conda-forge/r-remotes,
-Rcpp,http://www.rcpp.org,R,,conda-forge,saige,https://anaconda.org/conda-forge/r-rcpp,
-RcppArmadillo,https://dirk.eddelbuettel.com/code/rcpp.armadillo.html,R,,conda-forge,saige,https://anaconda.org/conda-forge/r-rcpparmadillo,
-RcppParallel,"http://rcppcore.github.io/RcppParallel, https://github.com/RcppCore/RcppParallel",R,,conda-forge,saige,https://anaconda.org/conda-forge/r-rcppparallel,
-SPAtest,https://CRAN.R-project.org/package=SPAtest,R,,conda-forge,saige,https://anaconda.org/conda-forge/r-spatest,
-RcppEigen,http://dirk.eddelbuettel.com/code/rcpp.eigen.html,R,,conda-forge,"saige, twas",https://anaconda.org/conda-forge/r-rcppeigen,
-BH,,R,,conda-forge,saige,https://anaconda.org/conda-forge/r-bh,
-optparse,https://github.com/trevorld/r-optparse,R,,conda-forge,"saige, twas",https://anaconda.org/conda-forge/r-optparse,
-SKAT,https://CRAN.R-project.org/package=SKAT,R,,conda-forge,saige,https://anaconda.org/conda-forge/r-skat,
-MetaSKAT,https://CRAN.R-project.org/package=MetaSKAT,R,,conda-forge,saige,https://anaconda.org/conda-forge/r-metaskat,
-saige,https://github.com/saigegit/SAIGE,R,,bioconda,saige,https://anaconda.org/bioconda/r-saige,
-reshape2,https://github.com/hadley/reshape,R,,conda-forge,statgen-equations,https://anaconda.org/conda-forge/r-reshape2,
-grid,https://github.com/pmur002/gridgraphics,R,,conda-forge,statgen-equations,https://anaconda.org/conda-forge/r-gridgraphics,
-gridExtra,https://github.com/baptiste/gridextra,R,,conda-forge,statgen-equations,https://anaconda.org/conda-forge/r-gridextra,
-RColorBrewer,,R,,conda-forge,"statgen-equations, twas",https://anaconda.org/conda-forge/r-rcolorbrewer,
-scales,"https://scales.r-lib.org, https://github.com/r-lib/scales",R,,conda-forge,statgen-equations,https://anaconda.org/conda-forge/r-scales,
-dplyr,"https://dplyr.tidyverse.org, https://github.com/tidyverse/dplyr",R,,conda-forge,statgen-equations,https://anaconda.org/conda-forge/r-dplyr,
-rgl,https://r-forge.r-project.org/projects/rgl/,R,,conda-forge,statgen-equations,https://anaconda.org/conda-forge/r-rgl,
-MASS,,R,,conda-forge,statgen-equations,https://anaconda.org/conda-forge/r-mass,
-mgcv,,R,,conda-forge,statgen-equations,https://anaconda.org/conda-forge/r-mgcv,
-pandas,http://pandas.pydata.org,python,,conda-forge,twas,https://anaconda.org/conda-forge/pandas,
-scipy,http://www.scipy.org/,python,,conda-forge,twas,https://anaconda.org/conda-forge/scipy,
-abind,https://cran.r-project.org/package=abind,R,,conda-forge,twas,https://anaconda.org/conda-forge/r-abind,
-tibble,"https://tibble.tidyverse.org/, https://github.com/tidyverse/tibble",R,,conda-forge,twas,https://anaconda.org/conda-forge/r-tibble,
-modelr,"https://modelr.tidyverse.org, https://github.com/tidyverse/modelr",R,,conda-forge,twas,https://anaconda.org/conda-forge/r-modelr,
-purrr,https://purrr.tidyverse.org,R,,conda-forge,twas,https://anaconda.org/conda-forge/r-purrr,
-RSQLite,https://github.com/r-dbi/RSQLite,R,,conda-forge,twas,https://anaconda.org/conda-forge/r-rsqlite,
-glmnet,"https://glmnet.stanford.edu, https://dx.doi.org/10.18637/jss.v033.i01, https://dx.doi.org/10.18637/jss.v039.i05",R,,conda-forge,twas,https://anaconda.org/conda-forge/r-glmnet,
-HDCI,https://CRAN.R-project.org/package=HDCI,R,,conda-forge,twas,https://anaconda.org/conda-forge/r-hdci,
-r-pecotmr,https://github.com/cumc/pecotmr,R,,dnachun,"finemap, twas",https://anaconda.org/dnachun/r-pecotmr,
+ggrepel,http://github.com/slowkow/ggrepel,R,,conda-forge,,https://anaconda.org/conda-forge/r-ggrepel,
+qqman,https://CRAN.R-project.org/package=qqman,R,,conda-forge,,https://anaconda.org/conda-forge/r-qqman,
+bgen,https://github.com/limix/bgen,,,conda-dorge,regenie,https://anaconda.org/conda-forge/bgen,
+bgen-reader,http://github.com/limix/bgen-reader-py,,,conda-dorge,regenie,https://anaconda.org/conda-forge/bgen-reader,
+reshape2,https://github.com/hadley/reshape,R,,conda-forge,,https://anaconda.org/conda-forge/r-reshape2,
+grid,https://github.com/pmur002/gridgraphics,R,,conda-forge,,https://anaconda.org/conda-forge/r-gridgraphics,
+gridExtra,https://github.com/baptiste/gridextra,R,,conda-forge,,https://anaconda.org/conda-forge/r-gridextra,
+RColorBrewer,,R,,conda-forge,,https://anaconda.org/conda-forge/r-rcolorbrewer,
+scales,"https://scales.r-lib.org, https://github.com/r-lib/scales",R,,conda-forge,,https://anaconda.org/conda-forge/r-scales,
+dplyr,"https://dplyr.tidyverse.org, https://github.com/tidyverse/dplyr",R,,conda-forge,,https://anaconda.org/conda-forge/r-dplyr,
+rgl,https://r-forge.r-project.org/projects/rgl/,R,,conda-forge,,https://anaconda.org/conda-forge/r-rgl,
+MASS,,R,,conda-forge,,https://anaconda.org/conda-forge/r-mass,
+mgcv,,R,,conda-forge,,https://anaconda.org/conda-forge/r-mgcv,
+pandas,http://pandas.pydata.org,python,,conda-forge,,https://anaconda.org/conda-forge/pandas,
+scipy,http://www.scipy.org/,python,,conda-forge,,https://anaconda.org/conda-forge/scipy,
+abind,https://cran.r-project.org/package=abind,R,,conda-forge,,https://anaconda.org/conda-forge/r-abind,
+tibble,"https://tibble.tidyverse.org/, https://github.com/tidyverse/tibble",R,,conda-forge,,https://anaconda.org/conda-forge/r-tibble,
+purrr,https://purrr.tidyverse.org,R,,conda-forge,,https://anaconda.org/conda-forge/r-purrr,
+pecotmr,https://github.com/cumc/pecotmr,R,,dnachun,,https://anaconda.org/dnachun/r-pecotmr,
+htslib,http://www.htslib.org/,C/C++,,bioconda,,https://anaconda.org/bioconda/htslib,
+r-bedtoolsr,https://github.com/PhanstielLab/bedtoolsr,R,2.30.0.2,bioconda,,https://anaconda.org/bioconda/r-bedtoolsr,
+bcftools,https://samtools.github.io/bcftools/,C/C++,1.17,bioconda,,https://anaconda.org/bioconda/bcftools,
+r-igraph,https://cran.r-project.org/web/packages/igraph/index.html,R,1.5.1,conda-forge,,https://anaconda.org/conda-forge/r-igraph,
+r-matrixstats,https://cran.rstudio.com/web/packages/matrixStats/index.html,R,1.0.0,conda-forge,,https://anaconda.org/conda-forge/r-matrixstats,
+r-flashpcar,https://github.com/gabraham/flashpca,R,2.1,dnachun,,https://anaconda.org/dnachun/r-flashpcar,
+r-rlang,https://cran.r-project.org/web/packages/rlang/index.html,R,1.1.1,conda-forge,,https://anaconda.org/conda-forge/r-rlang,
+bioconductor-pcatools,https://www.bioconductor.org/packages/release/bioc/html/PCAtools.html,R,2.12.0,bioconda,,https://anaconda.org/bioconda/bioconductor-pcatools,
+bioconductor-biocsingular,https://bioconductor.org/packages/release/bioc/html/BiocSingular.html,R,1.16.0,bioconda,,https://anaconda.org/bioconda/bioconductor-biocsingular,
+r-rmtstat,https://cran.r-project.org/web/packages/RMTstat/index.html,R,0.3.1,conda-forge,,https://anaconda.org/conda-forge/r-rmtstat,
+finemap,http://christianbenner.com,Python,1.4.1,bioconda,finemap,https://anaconda.org/bioconda/finemap,
+ldstore,http://christianbenner.com,C/C++,2,dnachun,finemap,https://anaconda.org/dnachun/ldstore,
+polyfun,https://github.com/omerwe/polyfun,Python,1,dnachun,finemap,https://anaconda.org/dnachun/polyfun,
+r-flashier,https://github.com/willwerscheid/flashier,R,1.0.21,dnachun,,https://anaconda.org/dnachun/r-flashier,
+r-mashr,https://github.com/stephenslab/mashr,R,0.2.73,dnachun,,https://anaconda.org/dnachun/r-mashr,
+r-plink2r,https://github.com/gabraham/plink2R,R,1.1,dnachun,,https://anaconda.org/dnachun/r-plink2r,
+r-rfast,https://cran.r-project.org/web/packages/Rfast/index.html,R,2.0.8,conda-forge,,https://anaconda.org/conda-forge/r-rfast,
+ensembl-vep,https://github.com/Ensembl/ensembl-vep,Perl,110.1,dnachun,annovar,https://anaconda.org/bioconda/ensembl-vep,
+bedtools,https://github.com/arq5x/bedtools2,C/C++,2.31.0,bioconda,,https://anaconda.org/bioconda/bedtools,
+tensorqtl,https://github.com/broadinstitute/tensorqtl,Python,1.0.8,dnachun,,https://anaconda.org/dnachun/tensorqtl,
+bioconductor-qvalue,https://www.bioconductor.org/packages/release/bioc/html/qvalue.html,R,2.32.0,bioconda,,https://anaconda.org/bioconda/bioconductor-qvalue,
+qvalue,https://pypi.org/project/qvalue/,Python,0.1.3,bioconda,,https://anaconda.org/dnachun/qvalue,