Update svdss to 2.0.0 (#51519)

* Update svdss to 2.0.0 * add run_exports * edit build.sh * edit build.sh * edit build.sh * revert to skipping osx --------- Co-authored-by: mencian <joshua.zhuang@yahoo.com>
bioconda · Oct 21, 2024 · 44de0dc · 44de0dc
1 parent 8363caf
commit 44de0dc
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diff --git a/recipes/svdss/build.sh b/recipes/svdss/build.sh
@@ -1,10 +1,24 @@
-#!/usr/bin/env bash
-
-mkdir -p build
-cd build
-cmake -DCMAKE_BUILD_TYPE=Release -DCONDAPREFIX=${PREFIX} ..
-make
-cd ..
+#!/bin/bash
 
 mkdir -p ${PREFIX}/bin
-cp SVDSS ${PREFIX}/bin
+export INCLUDE_PATH="${PREFIX}/include"
+export LIBRARY_PATH="${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CFLAGS="${CFLAGS} -O3 -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
+
+if [[ `uname` == "Darwin" ]]; then
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+	export CONFIG_ARGS=""
+fi
+
+cmake -S. -B build -DCMAKE_BUILD_TYPE=Release \
+	-DCONDAPREFIX="${PREFIX}" -DCMAKE_CXX_COMPILER="${CXX}" \
+	-DCMAKE_CXX_FLAGS="${CXXFLAGS}" -DCMAKE_C_COMPILER="${CC}" \
+	-DCMAKE_C_FLAGS="${CFLAGS}" \
+	"${CONFIG_ARGS}"
+cmake --build build -j "${CPU_COUNT}" -v
+
+chmod 0755 SVDSS
+mv SVDSS ${PREFIX}/bin
diff --git a/recipes/svdss/build_failure.linux-64.yaml b/recipes/svdss/build_failure.linux-64.yaml
diff --git a/recipes/svdss/meta.yaml b/recipes/svdss/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "1.0.5" %}
-{% set sha256 = "98345630451e98a43af9c807c9cf739cce58f6582d860ceb5daa00bdb50950df" %}
+{% set version = "2.0.0" %}
+{% set sha256 = "825324dbdd70474b2a527925a25dea94b597ef579dee117645f285d678985652" %}
 
 package:
   name: svdss
@@ -10,8 +10,10 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 3
+  number: 0
   skip: True  # [osx]
+  run_exports:
+    - {{ pin_subpackage('svdss', max_pin="x") }}
 
 requirements:
   build:
@@ -20,16 +22,20 @@ requirements:
     - make
     - automake
     - autoconf
-    - coreutils
-    - cmake >=3.14
+    - libtool
+    - cmake
     - git
   host:
+    - libgomp  # [linux]
+    - llvm-openmp  # [osx]
     - htslib
     - gsl
     - zlib
     - bzip2
     - xz
   run:
+    - libgomp  # [linux]
+    - llvm-openmp  # [osx]
     - samtools >=1.9
     - bcftools >=1.9
 
@@ -38,12 +44,17 @@ test:
     - SVDSS --version
 
 about:
-  home: https://github.com/Parsoa/SVDSS
+  home: "https://github.com/Parsoa/SVDSS"
   license: MIT
-  summary: Structural Variant Discovery from Sample-specific Strings
+  license_family: MIT
+  license_file: LICENSE
+  summary: "Structural Variant Discovery from Sample-specific Strings."
+  dev_url: "https://github.com/Parsoa/SVDSS"
+  doc_url: "https://github.com/Parsoa/SVDSS/blob/v{{ version }}/README.md"
 
 extra:
   identifiers:
     - biotools:svdss
+    - doi:10.1038/s41592-022-01674-1
   recipe-maintainers:
     - ldenti