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fulcrumgenomics / fgbio

Tools for working with genomic and high throughput sequencing data.
http://fulcrumgenomics.github.io/fgbio/
MIT License
309 stars 67 forks source link

The `fgbio` conda package should not require R dependencies #986

Closed msto closed 3 months ago

msto commented 3 months ago 
  + _r-mutex          1.0.1  anacondar_1  conda-forge/noarch     Cached
  + curl              8.7.1  h726d00d_0   conda-forge/osx-64      153kB
  + fgbio             2.2.1  hdfd78af_0   bioconda/noarch        Cached
  + gsl                 2.7  h93259b0_0   conda-forge/osx-64     Cached
  + icu                73.2  hf5e326d_0   conda-forge/osx-64     Cached
  + jpeg                 9e  hb7f2c08_3   conda-forge/osx-64     Cached
  + libgcc            4.8.5  1            conda-forge/osx-64     Cached
  + libiconv           1.17  hd75f5a5_2   conda-forge/osx-64     Cached
  + libpng           1.6.43  h92b6c6a_0   conda-forge/osx-64     Cached
  + libtiff           4.2.0  h1167814_3   conda-forge/osx-64     Cached
  + libwebp-base      1.4.0  h10d778d_0   conda-forge/osx-64      355kB
  + libxml2          2.12.7  h3e169fe_0   conda-forge/osx-64      620kB
  + pcre               8.45  he49afe7_0   conda-forge/osx-64     Cached
  + r                 3.3.1  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-assertthat        0.1  r3.3.1_4     pkgs/r/osx-64          Cached
  + r-base            3.3.1  0            pkgs/r/osx-64          Cached
  + r-boot           1.3_18  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-class          7.3_14  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-cluster         2.0.4  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-codetools      0.2_14  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-colorspace      1.2_6  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-dichromat       2.0_0  r3.3.1_2     pkgs/r/osx-64          Cached
  + r-digest          0.6.9  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-foreign        0.8_66  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-ggplot2         2.2.1  r3.3.1_0     bioconda/osx-64        Cached
  + r-gtable          0.2.0  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-kernsmooth    2.23_15  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-labeling          0.3  r3.3.1_2     pkgs/r/osx-64          Cached
  + r-lattice       0.20_33  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-lazyeval        0.2.0  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-magrittr          1.5  r3.3.1_2     pkgs/r/osx-64          Cached
  + r-mass           7.3_45  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-matrix          1.2_6  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-mgcv           1.8_12  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-munsell         0.4.3  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-nlme          3.1_128  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-nnet           7.3_12  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-plyr            1.8.4  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-rcolorbrewer    1.1_2  r3.3.1_3     pkgs/r/osx-64          Cached
  + r-rcpp           0.12.5  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-recommended     3.3.1  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-reshape2        1.4.1  r3.3.1_2     pkgs/r/osx-64          Cached
  + r-rpart          4.1_10  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-scales          0.4.1  r3.3.1_1     bioconda/osx-64        Cached
  + r-spatial        7.3_11  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-stringi         1.1.1  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-stringr         1.1.0  r3.3.1_0     bioconda/osx-64        Cached
  + r-survival       2.39_4  r3.3.1_0     pkgs/r/osx-64          Cached
  + r-tibble            1.2  r3.3.1_1     bioconda/osx-64        Cached
  + zlib             1.2.13  h8a1eda9_5   conda-forge/osx-64     Cached

I'm surprised to see that R and numerous R packages are a required dependency when installing fgbio via conda. Could these dependencies be made optional, or could an fgbio-minimal package be created?

clintval commented 3 months ago

Some one beat ya to it! https://bioconda.github.io/recipes/fgbio-minimal/README.html

nh13 commented 3 months ago

Who has two thumbs and beat you to it?