From 14ad6069028b000c339cc10c4974294a1fda4a5d Mon Sep 17 00:00:00 2001
From: Hadi <53904259+hforoughmand@users.noreply.github.com>
Date: Wed, 5 Feb 2025 14:12:49 +0100
Subject: [PATCH] create corona_lineage_dynamics (#53522)

* create corona_lineage_dynamics

* Update recipes/corona_lineage_dynamics/build.sh

Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com>

* Update recipes/corona_lineage_dynamics/meta.yaml

Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com>

* 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 <martin-g@users.noreply.github.com>
---
 recipes/corona_lineage_dynamics/build.sh  |  23 +++++
 recipes/corona_lineage_dynamics/meta.yaml | 101 ++++++++++++++++++++++
 2 files changed, 124 insertions(+)
 create mode 100644 recipes/corona_lineage_dynamics/build.sh
 create mode 100644 recipes/corona_lineage_dynamics/meta.yaml

diff --git a/recipes/corona_lineage_dynamics/build.sh b/recipes/corona_lineage_dynamics/build.sh
new file mode 100644
index 0000000000000..fe982241e15a3
--- /dev/null
+++ 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
new file mode 100644
index 0000000000000..0b5df977444b2
--- /dev/null
+++ 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