Skip to content

Commit

Permalink
Add KING (#956)
Browse files Browse the repository at this point in the history 
* Add KING

* add KING

* Update YAML files and Markdown table

---------

Co-authored-by: danielnachun <daniel.nachun@gmail.com>
Co-authored-by: danielnachun <danielnachun@users.noreply.github.com>
  • Loading branch information
@gaow @danielnachun
3 people authored Apr 4, 2024
1 parent 96c425d commit f5b2413
Show file tree
Hide file tree
Showing 4 changed files with 46 additions and 0 deletions.
1 change: 1 addition & 0 deletions container/README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -64,6 +64,7 @@ On occasion, you may see errors that a download or upload has failed while build
| bcftools | [Link](https://samtools.github.io/bcftools/) | [Link](https://anaconda.org/bioconda/bcftools) | bioinfo, apex, fastenloc, pcatools, rare_variation, factor_analysis | 1.17 | bioconda | GPL&#x2011;3.0&#x2011;or&#x2011;later |
| dapars2 | [Link](https://github.com/cumc/xqtl-protocol) | [Link](https://anaconda.org/dnachun/dapars2) | dapars2 | 1 | dnachun | Other |
| samtools | [Link](https://samtools.github.io/samtools/) | [Link](https://anaconda.org/bioconda/samtools) | dapars2, rna_quantification, leafcutter | 1.17 | bioconda | MIT |
| king | [Link](http://people.virginia.edu/~wc9c/KING/) | [Link](https://anaconda.org/bioconda/king) | dnachun | 2.3.0 | bioconda | GPL&#x2011;3.0&#x2011;or&#x2011;later |
| bioconductor-impute | [Link](https://bioconductor.org/packages/3.18/bioc/html/impute.html) | [Link](https://anaconda.org/bioconda/bioconductor-impute) | factor_analysis | 1.76.0 | bioconda | GPL&#x2011;2.0&#x2011;only |
| bioconductor-mofa2 | [Link](https://bioconductor.org/packages/3.16/bioc/html/MOFA2.html) | [Link](https://anaconda.org/bioconda/bioconductor-mofa2) | factor_analysis | 1.10.0 | bioconda | LGPL&#x2011;3.0&#x2011;or&#x2011;later |
| mofapy2 | [Link](https://anaconda.org/dnachun/mofapy2) | [Link](https://anaconda.org/dnachun/mofapy2) | factor_analysis | 0.7.0 | dnachun | GPL&#x2011;3.0&#x2011;or&#x2011;later |
Expand Down
1 change: 1 addition & 0 deletions container/containers.csv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@ apex,https://github.com/corbinq/apex,C/C++,0.2-alpha,63b605e00766141693a69eee6d6
htslib,http://www.htslib.org/,C/C++,,N/A,bioconda,"apex, factor_analysis, bioinfo, methylation, pcatools, pecotmr, quantqtl, tensorqtl",MIT,https://anaconda.org/bioconda/htslib,
gcta,https://yanglab.westlake.edu.cn/software/gcta/#Overview,C/C++,1.94.1,N/A,bioconda,bioinfo,GPL-3.0-only,https://anaconda.org/bioconda/gcta,
plink2,https://www.cog-genomics.org/plink/2.0/,C/C++,2.00a3.7,N/A,bioconda,bioinfo,GPL-3.0-or-later,https://anaconda.org/bioconda/plink2,
king,http://people.virginia.edu/~wc9c/KING/,C/C++,2.3.0,N/A,bioconda,dnachun,GPL-3.0-or-later,https://anaconda.org/bioconda/king,
qtl,https://pypi.org/project/qtl/,Python,0.1.9,N/A,dnachun,bioinfo,BSD-3-Clause,https://anaconda.org/dnachun/qtl,Fix license info
r-bedtoolsr,https://github.com/PhanstielLab/bedtoolsr,R,2.30.0.2,N/A,bioconda,bioinfo,MIT,https://anaconda.org/bioconda/r-bedtoolsr,
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,
Expand Down
43 changes: 43 additions & 0 deletions container/dnachun/dnachun.yml
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,43 @@
name: dnachun
channels:
- dnachun
- conda-forge
- bioconda
- nodefaults
dependencies:
- king=2.3.0
- altair
- awscli
- bash_kernel
- feather-format
- formulaic
- imageio
- ipykernel
- jupyter_contrib_nbextensions
- jupyterlab
- jupyterlab-sos
- markdown-kernel
- matplotlib
- nbdime
- notebook
- numpy
- openpyxl
- pandas
- parallel
- plotnine
- ptpython
- pytables
- r-irkernel
- r-languageserver
- r-tidyverse
- rpy2
- scikit-learn
- scipy
- seaborn
- sos
- sos-bash
- sos-notebook
- sos-pbs
- sos-python
- statsmodels
- wand
1 change: 1 addition & 0 deletions container/readme/containers.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
| bcftools | [Link](https://samtools.github.io/bcftools/) | [Link](https://anaconda.org/bioconda/bcftools) | bioinfo, apex, fastenloc, pcatools, rare_variation, factor_analysis | 1.17 | bioconda | GPL&#x2011;3.0&#x2011;or&#x2011;later |
| dapars2 | [Link](https://github.com/cumc/xqtl-protocol) | [Link](https://anaconda.org/dnachun/dapars2) | dapars2 | 1 | dnachun | Other |
| samtools | [Link](https://samtools.github.io/samtools/) | [Link](https://anaconda.org/bioconda/samtools) | dapars2, rna_quantification, leafcutter | 1.17 | bioconda | MIT |
| king | [Link](http://people.virginia.edu/~wc9c/KING/) | [Link](https://anaconda.org/bioconda/king) | dnachun | 2.3.0 | bioconda | GPL&#x2011;3.0&#x2011;or&#x2011;later |
| bioconductor-impute | [Link](https://bioconductor.org/packages/3.18/bioc/html/impute.html) | [Link](https://anaconda.org/bioconda/bioconductor-impute) | factor_analysis | 1.76.0 | bioconda | GPL&#x2011;2.0&#x2011;only |
| bioconductor-mofa2 | [Link](https://bioconductor.org/packages/3.16/bioc/html/MOFA2.html) | [Link](https://anaconda.org/bioconda/bioconductor-mofa2) | factor_analysis | 1.10.0 | bioconda | LGPL&#x2011;3.0&#x2011;or&#x2011;later |
| mofapy2 | [Link](https://anaconda.org/dnachun/mofapy2) | [Link](https://anaconda.org/dnachun/mofapy2) | factor_analysis | 0.7.0 | dnachun | GPL&#x2011;3.0&#x2011;or&#x2011;later |
Expand Down

0 comments on commit f5b2413

Please sign in to comment.