diff --git a/container/README.md b/container/README.md index 3aa8c2788..607d16cb3 100644 --- a/container/README.md +++ b/container/README.md @@ -55,6 +55,7 @@ On occasion, you may see errors that a download or upload has failed while build | gcta | [Link](https://yanglab.westlake.edu.cn/software/gcta/#Overview) | [Link](https://anaconda.org/bioconda/gcta) | bioinfo | 1.94.1 | bioconda | GPL‑3.0‑only | | plink2 | [Link](https://www.cog-genomics.org/plink/2.0/) | [Link](https://anaconda.org/bioconda/plink2) | bioinfo | 2.00a3.7 | bioconda | GPL‑3.0‑or‑later | | qtl | [Link](https://pypi.org/project/qtl/) | [Link](https://anaconda.org/dnachun/qtl) | bioinfo | 0.1.9 | dnachun | BSD‑3‑Clause | +| r-foreach | [Link](https://cran.r-project.org/web/packages/foreach/index.html) | [Link](https://anaconda.org/conda-forge/r-foreach) | bioinfo | 1.5.2 | conda‑forge | Apache‑2.0 | | r-igraph | [Link](https://cran.r-project.org/web/packages/igraph/index.html) | [Link](https://anaconda.org/conda-forge/r-igraph) | bioinfo | 1.5.1 | conda‑forge | GPL‑2.0‑or‑later | | snpeff | [Link](http://pcingola.github.io/SnpEff/) | [Link](https://anaconda.org/bioconda/snpeff) | bioinfo | 5.1 | bioconda | LGPL‑3.0‑or‑later | | snpsift | [Link](http://pcingola.github.io/SnpEff/) | [Link](https://anaconda.org/bioconda/snpsift) | bioinfo | 5.1 | bioconda | LGPL‑3.0‑or‑later | @@ -91,7 +92,7 @@ On occasion, you may see errors that a download or upload has failed while build | bioconductor-psichomics | [Link](https://bioconductor.org/packages/release/bioc/html/psichomics.html) | [Link](https://anaconda.org/bioconda/bioconductor-psichomics) | psichomics | 1.26.0 | bioconda | MIT AND Other | | suppa | [Link](https://pypi.org/project/SUPPA/) | [Link](https://anaconda.org/bioconda/suppa) | psichomics | 2.3 | bioconda | MIT | | r-qrank | [Link](https://CRAN.R-project.org/package=QRank) | [Link](https://anaconda.org/dnachun/r-qrank) | quantqtl | 1.0 | dnachun | GPL‑2.0‑or‑later | -| r-quantreg | [Link](https://www.r-project.org) | [Link](https://anaconda.org/conda-forge/r-quantreg) | quantqtl | 5.97 | conda‑forge | GPL‑2.0‑or‑later | +| r-quantreg | [Link](https://cran.r-project.org/web/packages/quantreg/index.html) | [Link](https://anaconda.org/conda-forge/r-quantreg) | quantqtl | 5.97 | conda‑forge | GPL‑2.0‑or‑later | | ensembl-vep | [Link](https://github.com/Ensembl/ensembl-vep) | [Link](https://anaconda.org/bioconda/ensembl-vep) | rare_variation | 103.1 | dnachun | Apache‑2.0 | | r-watershedr | [Link](https://github.com/nicolerg/WatershedR) | [Link](https://anaconda.org/dnachun/r-watershedr) | rare_variation | 1.0.0 | dnachun | MIT | | bamtools | [Link](https://github.com/pezmaster31/bamtools) | [Link](https://anaconda.org/bioconda/bamtools) | rna_quantification | 2.5.2 | bioconda | MIT | diff --git a/container/bioinfo/bioinfo.yml b/container/bioinfo/bioinfo.yml index 62827ce81..c7c15f6bb 100644 --- a/container/bioinfo/bioinfo.yml +++ b/container/bioinfo/bioinfo.yml @@ -11,6 +11,7 @@ dependencies: - plink=1.90b6.21 - plink2=2.00a3.7 - qtl=0.1.9 + - r-foreach=1.5.2 - r-igraph=1.5.1 - snpeff=5.1 - snpsift=5.1 diff --git a/container/containers.csv b/container/containers.csv index 9590b0e8d..b9178fa0b 100644 --- a/container/containers.csv +++ b/container/containers.csv @@ -103,5 +103,6 @@ scikit-learn,https://pypi.org/project/scikit-learn/,Python,,N/A,conda-forge,univ hello,https://www.gnu.org/software/hello/,C/C++,2.12.1,N/A,dnachun,hello,GPL-3.0-or-later,https://anaconda.org/dnachun/hello, deeptools,https://github.com/deeptools/deepTools,Python,3.5.4,N/A,Bioconda,rna_quantification,GPL-3.0-or-later,https://anaconda.org/bioconda/deeptools, r-ape,https://github.com/emmanuelparadis/ape,R,5.7,N/A,conda-forge,rna_quantification,GPL-3.0-or-later,https://anaconda.org/conda-forge/r-ape, -r-quantreg,https://www.r-project.org,R,5.97,N/A,conda-forge,quantqtl,GPL-2.0-or-later,https://anaconda.org/conda-forge/r-quantreg, +r-quantreg,https://cran.r-project.org/web/packages/quantreg/index.html,R,5.97,N/A,conda-forge,quantqtl,GPL-2.0-or-later,https://anaconda.org/conda-forge/r-quantreg, r-qrank,https://CRAN.R-project.org/package=QRank,R,1.0,N/A,dnachun,quantqtl,GPL-2.0-or-later,https://anaconda.org/dnachun/r-qrank, +r-foreach,https://cran.r-project.org/web/packages/foreach/index.html,R,1.5.2,N/A,conda-forge,bioinfo,Apache-2.0,https://anaconda.org/conda-forge/r-foreach, diff --git a/container/readme/containers.md b/container/readme/containers.md index dbdf583ab..f91789cd2 100644 --- a/container/readme/containers.md +++ b/container/readme/containers.md @@ -5,6 +5,7 @@ | gcta | [Link](https://yanglab.westlake.edu.cn/software/gcta/#Overview) | [Link](https://anaconda.org/bioconda/gcta) | bioinfo | 1.94.1 | bioconda | GPL‑3.0‑only | | plink2 | [Link](https://www.cog-genomics.org/plink/2.0/) | [Link](https://anaconda.org/bioconda/plink2) | bioinfo | 2.00a3.7 | bioconda | GPL‑3.0‑or‑later | | qtl | [Link](https://pypi.org/project/qtl/) | [Link](https://anaconda.org/dnachun/qtl) | bioinfo | 0.1.9 | dnachun | BSD‑3‑Clause | +| r-foreach | [Link](https://cran.r-project.org/web/packages/foreach/index.html) | [Link](https://anaconda.org/conda-forge/r-foreach) | bioinfo | 1.5.2 | conda‑forge | Apache‑2.0 | | r-igraph | [Link](https://cran.r-project.org/web/packages/igraph/index.html) | [Link](https://anaconda.org/conda-forge/r-igraph) | bioinfo | 1.5.1 | conda‑forge | GPL‑2.0‑or‑later | | snpeff | [Link](http://pcingola.github.io/SnpEff/) | [Link](https://anaconda.org/bioconda/snpeff) | bioinfo | 5.1 | bioconda | LGPL‑3.0‑or‑later | | snpsift | [Link](http://pcingola.github.io/SnpEff/) | [Link](https://anaconda.org/bioconda/snpsift) | bioinfo | 5.1 | bioconda | LGPL‑3.0‑or‑later | @@ -41,7 +42,7 @@ | bioconductor-psichomics | [Link](https://bioconductor.org/packages/release/bioc/html/psichomics.html) | [Link](https://anaconda.org/bioconda/bioconductor-psichomics) | psichomics | 1.26.0 | bioconda | MIT AND Other | | suppa | [Link](https://pypi.org/project/SUPPA/) | [Link](https://anaconda.org/bioconda/suppa) | psichomics | 2.3 | bioconda | MIT | | r-qrank | [Link](https://CRAN.R-project.org/package=QRank) | [Link](https://anaconda.org/dnachun/r-qrank) | quantqtl | 1.0 | dnachun | GPL‑2.0‑or‑later | -| r-quantreg | [Link](https://www.r-project.org) | [Link](https://anaconda.org/conda-forge/r-quantreg) | quantqtl | 5.97 | conda‑forge | GPL‑2.0‑or‑later | +| r-quantreg | [Link](https://cran.r-project.org/web/packages/quantreg/index.html) | [Link](https://anaconda.org/conda-forge/r-quantreg) | quantqtl | 5.97 | conda‑forge | GPL‑2.0‑or‑later | | ensembl-vep | [Link](https://github.com/Ensembl/ensembl-vep) | [Link](https://anaconda.org/bioconda/ensembl-vep) | rare_variation | 103.1 | dnachun | Apache‑2.0 | | r-watershedr | [Link](https://github.com/nicolerg/WatershedR) | [Link](https://anaconda.org/dnachun/r-watershedr) | rare_variation | 1.0.0 | dnachun | MIT | | bamtools | [Link](https://github.com/pezmaster31/bamtools) | [Link](https://anaconda.org/bioconda/bamtools) | rna_quantification | 2.5.2 | bioconda | MIT |