create corona_lineage_dynamics (#53522)

* create corona_lineage_dynamics * Update recipes/corona_lineage_dynamics/build.sh Co-authored-by: Martin Grigorov <[email protected]> * Update recipes/corona_lineage_dynamics/meta.yaml Co-authored-by: Martin Grigorov <[email protected]> * fixing errors by bio-conda * fixing errors * Fixed issues as per review comments * Fixed issues as per review comments * library link changed * Fixed issues as per review comments * Fixed issues as per review comments * Fixed issues as per review comments * Fixed issues as per review comments * Fixed issues as per review comments * Cleanup meta.yaml * Update meta.yaml * Remove the version range for r-base For some reason conda-build does not like it: ``` conda.exceptions.InvalidVersionSpec: Invalid version '>=4': invalid character(s) ``` * Do not build aarch64 and arm64. r-binom is not yet available for them --------- Co-authored-by: Martin Grigorov <[email protected]>
bioconda · Feb 5, 2025 · 14ad606 · 14ad606
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diff --git a/recipes/corona_lineage_dynamics/build.sh b/recipes/corona_lineage_dynamics/build.sh
@@ -0,0 +1,23 @@
+#!/bin/bash
+
+${CXX} --std=c++17 scripts/count_lineages_country.cpp -o scripts/count_lineages_country -lstdc++ -lboost_regex ${CXXFLAGS} ${LDFLAGS}
+
+# Define the target directory
+TARGET_DIR=$PREFIX/share/corona_lineage_dynamics
+
+# Create the target directory
+mkdir -p $TARGET_DIR
+
+# Copy the entire repository to the target directory
+cp -r * $TARGET_DIR/
+
+# Create the proxy script in $PREFIX/bin
+mkdir -p $PREFIX/bin
+cat > $PREFIX/bin/corona_lineage_dynamics <<EOF 
+#!/bin/bash
+bash $TARGET_DIR/SDPlots_lineages_local.sh "\$@"
+EOF
+
+# Make the proxy script executable
+chmod +x $PREFIX/bin/corona_lineage_dynamics
+
diff --git a/recipes/corona_lineage_dynamics/meta.yaml b/recipes/corona_lineage_dynamics/meta.yaml
@@ -0,0 +1,101 @@
+{% set version = "0.1.5" %}
+
+package:
+  name: corona_lineage_dynamics
+  version: {{ version }}
+
+source:
+  url: https://github.com/hzi-bifo/corona_lineage_dynamics/releases/download/v{{ version }}/corona_lineage_dynamics-v{{ version }}.tgz
+  sha256: c8afa72a1645036b69772bb4d2a2e02372f1f5c72fe46e1ba6d215a26c805f5f
+
+build:
+  number: 0
+  run_exports:
+    - corona_lineage_dynamics >=0.1.2,<0.2
+
+requirements:
+    build:
+        - {{ compiler('c') }} 
+        - {{ compiler('cxx') }} 
+        - make 
+        - pkg-config 
+    host:
+        - r-base >=4
+        - zlib
+        - r-mass 
+        - r-matrix 
+        - r-xml2 
+        - r-systemfonts 
+        - r-ragg 
+        - r-pkgdown 
+        - r-devtools
+        - r-binom
+        - r-plotly
+        - r-htmlwidgets
+        - r-countrycode
+        - r-doparallel
+        - r-dplyr
+        - r-foreach
+        - r-htmltools
+        - r-plyr
+        - r-rcpp
+        - r-rcurl
+        - r-readr
+        - r-stringr
+        - r-tictoc
+        - r-tidyr
+        - r-xtable
+        - ta-lib # ['osx']
+        - r-lifecycle
+        - r-scales
+        - r-withr
+        - r-knitr
+        - r-d3heatmap
+        - libboost-devel
+    run:
+        - ta-lib # ['osx']
+        - boost 
+        - zlib 
+        - r-base 
+        - r-mass 
+        - r-matrix 
+        - r-xml2 
+        - r-systemfonts 
+        - r-ragg 
+        - r-pkgdown 
+        - r-devtools
+        - r-binom
+        - r-plotly
+        - r-htmlwidgets
+        - r-countrycode
+        - r-doparallel
+        - r-dplyr
+        - r-foreach
+        - r-htmltools
+        - r-plyr
+        - r-rcpp
+        - r-rcurl
+        - r-readr
+        - r-stringr
+        - r-tictoc
+        - r-tidyr
+        - r-xtable
+        - r-lifecycle
+        - r-scales
+        - r-withr
+        - r-knitr
+        - r-d3heatmap
+test:
+  commands:
+    - $PREFIX/share/corona_lineage_dynamics/scripts/count_lineages_country -h
+    - Rscript -e "library(scales); library(evaluate); library(knitr); library(lifecycle); library(fs); library(glue); library(gtable); library(withr)"
+    - corona_lineage_dynamics -h
+
+
+about:
+  home: https://github.com/hzi-bifo/corona_lineage_dynamics
+  dev_url: https://github.com/hzi-bifo/corona_lineage_dynamics
+  license: ASL
+  license_file: LICENSE.md
+  summary: Analyzing and visualizing pangolin lineages of GISAID metadata.
+  license_family: OTHER