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Merge pull request #730 from danielnachun/update_bioinfo_container2
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update bioinfo container
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@danielnachun
danielnachun authored Oct 24, 2023
2 parents 1f0cb1f + 3b0b5ab commit 3514da4
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3 changes: 2 additions & 1 deletion container/README.md
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Expand Up @@ -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 |
Expand Down Expand Up @@ -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 |
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1 change: 1 addition & 0 deletions container/bioinfo/bioinfo.yml
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Expand Up @@ -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
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3 changes: 2 additions & 1 deletion container/containers.csv
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Expand Up @@ -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,
3 changes: 2 additions & 1 deletion container/readme/containers.md
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Expand Up @@ -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 |
Expand Down Expand Up @@ -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 |
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