build quantas container

container/README.md

@@ -64,7 +64,7 @@ On occasion, you may see errors that a download or upload has failed while build
 | snpsift | [Link](http://pcingola.github.io/SnpEff/) | [Link](https://anaconda.org/bioconda/snpsift) | bioinfo | 5.1 | bioconda | LGPL‑3.0‑or‑later |
 | 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‑3.0‑or‑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 |
+| samtools | [Link](https://samtools.github.io/samtools/) | [Link](https://anaconda.org/bioconda/samtools) | dapars2, rna_quantification, leafcutter, quantas | 1.17 | bioconda | MIT |
 | 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‑2.0‑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‑3.0‑or‑later |
 | mofapy2 | [Link](https://anaconda.org/dnachun/mofapy2) | [Link](https://anaconda.org/dnachun/mofapy2) | factor_analysis | 0.7.0 | dnachun | GPL‑3.0‑or‑later |
@@ -113,6 +113,7 @@ On occasion, you may see errors that a download or upload has failed while build
 | polyfun | [Link](https://github.com/omerwe/polyfun) | [Link](https://anaconda.org/dnachun/polyfun) | polyfun | 1 | dnachun | MIT |
 | 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 |
+| quantas | [Link](https://github.com/chaolinzhanglab/quantas) | [Link](https://anaconda.org/dnachun/quantas) | quantas | 1.1.2 | dnachun | Other |
 | r-mashr | [Link](https://github.com/stephenslab/mashr) | [Link](https://anaconda.org/dnachun/r-mashr) | quantqtl | 0.2.73 | dnachun | BSD‑3‑Clause |
 | r-plink2r | [Link](https://github.com/gabraham/plink2R) | [Link](https://anaconda.org/dnachun/r-plink2r) | quantqtl | 1.1 | dnachun | Other |
 | r-profvis | [Link](https://rstudio.github.io/profvis/) | [Link](https://anaconda.org/conda-forge/r-profvis) | quantqtl | | conda‑forge | GPL‑3.0‑or‑later |

container/containers.csv

@@ -12,7 +12,7 @@ snpsift,http://pcingola.github.io/SnpEff/,Java,5.1,N/A,bioconda,bioinfo,LGPL-3.0
 bcftools,https://samtools.github.io/bcftools/,C/C++,1.17,N/A,bioconda,"bioinfo, apex, fastenloc, pcatools, rare_variation, factor_analysis",GPL-3.0-or-later,https://anaconda.org/bioconda/bcftools,
 r-igraph,https://cran.r-project.org/web/packages/igraph/index.html,R,1.5.1,N/A,conda-forge,bioinfo,GPL-2.0-or-later,https://anaconda.org/conda-forge/r-igraph,
 dapars2,https://github.com/cumc/xqtl-protocol,Python,1,b2fda460cc562aa80b5c1cd12e0d4d0305a40a88,dnachun,dapars2,Other,https://anaconda.org/dnachun/dapars2,
-samtools,https://samtools.github.io/samtools/,C/C++,1.17,N/A,bioconda,"dapars2, rna_quantification, leafcutter",MIT,https://anaconda.org/bioconda/samtools,
+samtools,https://samtools.github.io/samtools/,C/C++,1.17,N/A,bioconda,"dapars2, rna_quantification, leafcutter, quantas",MIT,https://anaconda.org/bioconda/samtools,
 dap-g,https://github.com/xqwen/dap,C/C++,1.0.0,875ba40b7b28d6972fb94e6d2fb352ce1aaa92a7,dnachun,fastenloc,AGPL-3.0-or-later,https://anaconda.org/dnachun/dap-g,
 fastenloc,https://github.com/xqwen/fastenloc,C/C++,2,N/A,dnachun,fastenloc,GPL-3.0-or-later,https://anaconda.org/dnachun/fastenloc,
 r-susier,https://github.com/stephenslab/susieR,R,0.14.7,N/A,conda-forge,"pecotmr, fastenloc",MIT,https://anaconda.org/conda-forge/r-susier,
@@ -85,8 +85,8 @@ r-gwasrapidd,https://cran.r-project.com/web/packages/gwasrapidd/index.html,R,0.9
 r-udr,https://github.com/stephenslab/udr,R,0.3.154,N/A,dnachun,"pecotmr, quantqtl",BSD-3-Clause,https://anaconda.org/dnachun/r-udr,
 multipy,https://github.com/puolival/multipy,Python,0.16,ef9d2e2ffd6a7e079e29268dfbd59e630dd346b4,dnachun,tensorqtl,BSD-3-Clause,https://anaconda.org/dnachun/multipy,
 tensorqtl,https://github.com/broadinstitute/tensorqtl,Python,1.0.8,N/A,dnachun,tensorqtl,BSD-3-Clause,https://anaconda.org/dnachun/tensorqtl,
-plink,https://www.cog-genomics.org/plink2,C/C++,1.90b6.21,N/A,bioconda,"bioinfo",GPL-3.0-or-later,https://anaconda.org/bioconda/plink,
-bioconductor-mofa2,https://bioconductor.org/packages/3.16/bioc/html/MOFA2.html,R/Python,1.10.0,N/A,bioconda,"factor_analysis",LGPL-3.0-or-later,https://anaconda.org/bioconda/bioconductor-mofa2,bioconda package is outdated
+plink,https://www.cog-genomics.org/plink2,C/C++,1.90b6.21,N/A,bioconda,bioinfo,GPL-3.0-or-later,https://anaconda.org/bioconda/plink,
+bioconductor-mofa2,https://bioconductor.org/packages/3.16/bioc/html/MOFA2.html,R/Python,1.10.0,N/A,bioconda,factor_analysis,LGPL-3.0-or-later,https://anaconda.org/bioconda/bioconductor-mofa2,bioconda package is outdated
 bioconductor-qvalue,https://www.bioconductor.org/packages/release/bioc/html/qvalue.html,R,2.32.0,N/A,bioconda,tensorqtl,LGPL-3.0-or-later,https://anaconda.org/bioconda/bioconductor-qvalue,
 qvalue,https://pypi.org/project/qvalue/,Python,0.1.3,N/A,bioconda,tensorqtl,BSD-3-Clause,https://anaconda.org/dnachun/qvalue,
 r-softimpute,https://github.com/cran/softImpute,R,1.4_1,N/A,conda-forge,factor_analysis,GPL-2.0-only,https://anaconda.org/conda-forge/r-softimpute,
@@ -134,3 +134,4 @@ bioconductor-edger,https://bioconductor.org/packages/3.18/bioc/html/edgeR.html,R
 bioconductor-limma,https://bioconductor.org/packages/3.18/bioc/html/limma.html,R,3.58.1,N/A,bioconda,seurat,GPL-2.0-or-later,https://anaconda.org/bioconda/bioconductor-limma,
 r-profvis,https://rstudio.github.io/profvis/,R,,N/A,conda-forge,quantqtl,GPL-3.0-or-later,https://anaconda.org/conda-forge/r-profvis,
 r-bigsnpr,https://privefl.github.io/bigsnpr/,R,1.12.2,N/A,conda-forge,pecotmr,GPL-3.0-or-later,https://anaconda.org/conda-forge/r-bigsnpr,
+quantas,https://github.com/chaolinzhanglab/quantas,Perl,1.1.2,N/A,dnachun,quantas,Other,https://anaconda.org/dnachun/quantas,

container/quantas/quantas.yml

@@ -0,0 +1,44 @@
+name: quantas
+channels:
+ - dnachun
+ - conda-forge
+ - bioconda
+ - nodefaults
+dependencies:
+ - quantas=1.1.2
+ - samtools=1.17
+ - 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

container/readme/containers.md

@@ -14,7 +14,7 @@
 | snpsift | [Link](http://pcingola.github.io/SnpEff/) | [Link](https://anaconda.org/bioconda/snpsift) | bioinfo | 5.1 | bioconda | LGPL‑3.0‑or‑later |
 | 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‑3.0‑or‑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 |
+| samtools | [Link](https://samtools.github.io/samtools/) | [Link](https://anaconda.org/bioconda/samtools) | dapars2, rna_quantification, leafcutter, quantas | 1.17 | bioconda | MIT |
 | 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‑2.0‑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‑3.0‑or‑later |
 | mofapy2 | [Link](https://anaconda.org/dnachun/mofapy2) | [Link](https://anaconda.org/dnachun/mofapy2) | factor_analysis | 0.7.0 | dnachun | GPL‑3.0‑or‑later |
@@ -63,6 +63,7 @@
 | polyfun | [Link](https://github.com/omerwe/polyfun) | [Link](https://anaconda.org/dnachun/polyfun) | polyfun | 1 | dnachun | MIT |
 | 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 |
+| quantas | [Link](https://github.com/chaolinzhanglab/quantas) | [Link](https://anaconda.org/dnachun/quantas) | quantas | 1.1.2 | dnachun | Other |
 | r-mashr | [Link](https://github.com/stephenslab/mashr) | [Link](https://anaconda.org/dnachun/r-mashr) | quantqtl | 0.2.73 | dnachun | BSD‑3‑Clause |
 | r-plink2r | [Link](https://github.com/gabraham/plink2R) | [Link](https://anaconda.org/dnachun/r-plink2r) | quantqtl | 1.1 | dnachun | Other |
 | r-profvis | [Link](https://rstudio.github.io/profvis/) | [Link](https://anaconda.org/conda-forge/r-profvis) | quantqtl | | conda‑forge | GPL‑3.0‑or‑later |