From 1a660fc59ab2a614ded4fad612f3232f3bfb0c1c Mon Sep 17 00:00:00 2001 From: danielnachun Date: Mon, 11 Mar 2024 17:27:57 -0700 Subject: [PATCH 1/2] use r-flashier 1.0.21 --- container/containers.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/container/containers.csv b/container/containers.csv index 75cd7dae..f33bcb60 100644 --- a/container/containers.csv +++ b/container/containers.csv @@ -42,7 +42,7 @@ ldstore,http://christianbenner.com,C/C++,2,N/A,dnachun,polyfun,Other,https://ana polyfun,https://github.com/omerwe/polyfun,Python,1,de889bde9ce3d46326fc5ea568b623450f349569,dnachun,polyfun,MIT,https://anaconda.org/dnachun/polyfun, bioconductor-psichomics,https://bioconductor.org/packages/release/bioc/html/psichomics.html,R,1.26.0,N/A,bioconda,psichomics,MIT AND Other,https://anaconda.org/bioconda/bioconductor-psichomics, suppa,https://pypi.org/project/SUPPA/,Python,2.3,N/A,bioconda,psichomics,MIT,https://anaconda.org/bioconda/suppa, -r-flashier,https://github.com/willwerscheid/flashier,R,0.2.51,N/A,dnachun,"quantqtl, factor_analysis",GPL-3.0-or-later,https://anaconda.org/dnachun/r-flashier,This does not have a valid license on GitHub +r-flashier,https://github.com/willwerscheid/flashier,R,1.0.21,N/A,dnachun,"quantqtl, factor_analysis",GPL-3.0-or-later,https://anaconda.org/dnachun/r-flashier,This does not have a valid license on GitHub r-mashr,https://github.com/stephenslab/mashr,R,0.2.73,N/A,dnachun,quantqtl,BSD-3-Clause,https://anaconda.org/dnachun/r-mashr, r-plink2r,https://github.com/gabraham/plink2R,R,1.1,d74be015e8f54d662b96c6c2a52a614746f9030d,dnachun,quantqtl,Other,https://anaconda.org/dnachun/r-plink2r,Fix license info 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, From 5fd3202811aab01b8b775c74d9c0baadf1c6b3d1 Mon Sep 17 00:00:00 2001 From: danielnachun Date: Tue, 12 Mar 2024 00:29:09 +0000 Subject: [PATCH 2/2] Update YAML files and Markdown table --- container/README.md | 2 +- container/factor_analysis/factor_analysis.yml | 2 +- container/quantqtl/quantqtl.yml | 2 +- container/readme/containers.md | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/container/README.md b/container/README.md index 95522861..6f92fa89 100644 --- a/container/README.md +++ b/container/README.md @@ -114,7 +114,7 @@ On occasion, you may see errors that a download or upload has failed while build | r-qrank | [Link](https://CRAN.R-project.org/package=QRank) | [Link](https://anaconda.org/dnachun/r-qrank) | quantqtl | 1 | dnachun | 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 | | r-rfast | [Link](https://cran.r-project.org/web/packages/Rfast/index.html) | [Link](https://anaconda.org/conda-forge/r-rfast) | quantqtl | 2.0.8 | conda‑forge | GPL‑2.0‑or‑later | -| r-flashier | [Link](https://github.com/willwerscheid/flashier) | [Link](https://anaconda.org/dnachun/r-flashier) | quantqtl, factor_analysis | 0.2.51 | dnachun | GPL‑3.0‑or‑later | +| r-flashier | [Link](https://github.com/willwerscheid/flashier) | [Link](https://anaconda.org/dnachun/r-flashier) | quantqtl, factor_analysis | 1.0.21 | dnachun | GPL‑3.0‑or‑later | | ensembl-vep | [Link](https://github.com/Ensembl/ensembl-vep) | [Link](https://anaconda.org/bioconda/ensembl-vep) | rare_variation | 110.1 | 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/factor_analysis/factor_analysis.yml b/container/factor_analysis/factor_analysis.yml index 37d28d1b..4a7bc3ab 100644 --- a/container/factor_analysis/factor_analysis.yml +++ b/container/factor_analysis/factor_analysis.yml @@ -10,7 +10,7 @@ dependencies: - bioconductor-mofa2=1.10.0 - htslib - mofapy2=0.7.0 - - r-flashier=0.2.51 + - r-flashier=1.0.21 - r-missforest=1.5 - r-rcppeigen=0.3.3.9.3 - r-rlang=1.1.1 diff --git a/container/quantqtl/quantqtl.yml b/container/quantqtl/quantqtl.yml index 7abe652a..64038cdf 100644 --- a/container/quantqtl/quantqtl.yml +++ b/container/quantqtl/quantqtl.yml @@ -13,7 +13,7 @@ dependencies: - r-complexupset=1.3.3 - r-cowplot=1.1.1 - r-data.table=1.14.8 - - r-flashier=0.2.51 + - r-flashier=1.0.21 - r-genio=1.1.2 - r-gwasrapidd=0.99.14 - r-mashr=0.2.73 diff --git a/container/readme/containers.md b/container/readme/containers.md index c36dbafd..8cd3fa3a 100644 --- a/container/readme/containers.md +++ b/container/readme/containers.md @@ -64,7 +64,7 @@ | r-qrank | [Link](https://CRAN.R-project.org/package=QRank) | [Link](https://anaconda.org/dnachun/r-qrank) | quantqtl | 1 | dnachun | 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 | | r-rfast | [Link](https://cran.r-project.org/web/packages/Rfast/index.html) | [Link](https://anaconda.org/conda-forge/r-rfast) | quantqtl | 2.0.8 | conda‑forge | GPL‑2.0‑or‑later | -| r-flashier | [Link](https://github.com/willwerscheid/flashier) | [Link](https://anaconda.org/dnachun/r-flashier) | quantqtl, factor_analysis | 0.2.51 | dnachun | GPL‑3.0‑or‑later | +| r-flashier | [Link](https://github.com/willwerscheid/flashier) | [Link](https://anaconda.org/dnachun/r-flashier) | quantqtl, factor_analysis | 1.0.21 | dnachun | GPL‑3.0‑or‑later | | ensembl-vep | [Link](https://github.com/Ensembl/ensembl-vep) | [Link](https://anaconda.org/bioconda/ensembl-vep) | rare_variation | 110.1 | 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 |