echoconda: Getting Started

Author: Brian M. Schilder

Updated: Mar-04-2022

Source: vignettes/echoconda.Rmd

Examples

Build env from yaml

Will build the “echoR” conda environment by default.

conda_env <- echoconda::yaml_to_env()
## echoconda:: Conda already installed.
## echoconda:: Retrieving conda env name from yaml.
## Identified yaml file stored in echoconda.
## Yaml contents:
## name: echoR
## channels:
##   - conda-forge
##   - bioconda
##   - nodefaults
## dependencies:
##   # Python
##   - python>=3.6.1
##   - pandas>=0.25.0
##   - fastparquet
##   - pyarrow
##   - scipy
##   - scikit-learn
##   - tqdm
##   - bitarray
##   - networkx
##   - rpy2
##   - requests
##   # Command line
##   - htslib
##   - plink
##   - bcftools
##   - wget
##   - axel
##   # R
##   - r>=4.0.0
##   - r-devtools
##   - r-susier
##   - r-reticulate
##   - r-rlang
##   - r-mvtnorm
##   - r-desctools
##   - r-exact
##   - r-later
##   - r-commonmark
##   - r-patchwork
##   - r-r.methodss3
##   - r-brew
##   - r-zip
##   - r-xfun
##   - r-credentials
##   - r-whisker
##   - r-gh
##   - r-xopen
##   - r-sessioninfo
##   - r-promises
##   - r-rex
##   - r-crosstalk
##   - r-roxygen2
##   - r-gert
##   - r-r.oo
##   - r-rversions
##   - r-rcmdcheck
##   - r-dt
##   - r-covr
##   - r-usethis
##   - r-openxlsx
##   - r-r.utils
##   - r-data.table
##   - r-ggplot2
##   - r-ckmeans.1d.dp
##   - r-tidyverse
##   - r-foreign
##   - r-refgenome
##   - r-xgr
##   - r-coloc
##   - r-susier
##   ### There's also this implementation of susieR which includes later versions
##   # - aksarkar::r-susier
##   - r-biocmanager
##   - bioconductor-snpstats
##   - bioconductor-ggbio
##   - bioconductor-ensdb.hsapiens.v75
##   - bioconductor-biomart
##   - radian
##   - pip
## 
## echoconda:: Conda environment already exists: echoR
## Time difference of 0.3 secs

Export 

yaml_path <- echoconda::env_to_yaml(conda_env = "echoR")
## echoconda:: Conda already installed.
## Exporting environment echoR as yaml file.
## * Environment 'echoR' exported to '/tmp/RtmpiLCesT/conda.yml'.

Activate conda env 

echoconda::activate_env(conda_env = "echoR")
## echoconda:: Conda already installed.
## echoconda:: Active conda env: 'echoR'
## echoconda:: Requested conda_env is already active: 'echoR'
## echoconda:: Attempting to activate conda env: 'echoR'
## [1] "echoR"

Find package path 

pkgs <- echoconda::find_packages(packages = c("dplyr","numpy","wget"),
                                 conda_env = "echoR")
## Searching for 3 package(s) across 1 conda environment(s):
##  -  echoR
## 3 unique package(s) found across 1 conda environment(s).
print(pkgs)
##    conda_env package version     requirement     channel
## 1:     echoR   numpy  1.22.2 py310h454958d_0 conda-forge
## 2:     echoR r-dplyr   1.0.7   r40h03ef668_0 conda-forge
## 3:     echoR    wget  1.20.3      ha56f1ee_1 conda-forge
##                                                         python
## 1: /github/home/.local/share/r-miniconda/envs/echoR/bin/python
## 2: /github/home/.local/share/r-miniconda/envs/echoR/bin/python
## 3: /github/home/.local/share/r-miniconda/envs/echoR/bin/python
##                                                         path
## 1:                                                      <NA>
## 2:                                                      <NA>
## 3: /github/home/.local/share/r-miniconda/envs/echoR/bin/wget

Find python path 

python <- echoconda::find_python_path(conda_env = "echoR")
print(python)
## [1] "/github/home/.local/share/r-miniconda/envs/echoR/bin/python"

Session Info 

utils::sessionInfo()
## R Under development (unstable) (2022-02-25 r81808)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
## 
## Matrix products: default
## BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] echoconda_0.99.4 BiocStyle_2.23.1
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.8          knitr_1.37          magrittr_2.0.2     
##  [4] rappdirs_0.3.3      lattice_0.20-45     R6_2.5.1           
##  [7] ragg_1.2.2          rlang_1.0.1         fastmap_1.1.0      
## [10] stringr_1.4.0       tools_4.2.0         grid_4.2.0         
## [13] data.table_1.14.2   xfun_0.30           png_0.1-7          
## [16] cli_3.2.0           jquerylib_0.1.4     systemfonts_1.0.4  
## [19] htmltools_0.5.2     yaml_2.3.5          digest_0.6.29      
## [22] rprojroot_2.0.2     pkgdown_2.0.2.9000  crayon_1.5.0       
## [25] bookdown_0.24       textshaping_0.3.6   Matrix_1.4-0       
## [28] BiocManager_1.30.16 purrr_0.3.4         sass_0.4.0         
## [31] fs_1.5.2            memoise_2.0.1       cachem_1.0.6       
## [34] evaluate_0.15       rmarkdown_2.12      stringi_1.7.6      
## [37] compiler_4.2.0      bslib_0.3.1         desc_1.4.0         
## [40] reticulate_1.24     jsonlite_1.8.0