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sra-tools: add version 3.0.3 and fix build (#34965)

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Glenn Johnson 2023-01-16 20:29:52 -06:00 committed by GitHub
parent b2cc36109f
commit b7e416046f
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2 changed files with 21 additions and 0 deletions
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16
var/spack/repos/builtin/packages/sra-tools/ngs-java.patch Normal file
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@ -0,0 +1,16 @@
--- a/ngs/ngs-java/CMakeLists.txt 2023-01-12 17:48:48.901017181 -0600
+++ b/ngs/ngs-java/CMakeLists.txt 2023-01-12 18:46:26.833359507 -0600
@@ -140,11 +140,8 @@
set(SRC_FILES "${SRC_FILES} ${f}")
endforeach()
- if( ${OS} STREQUAL "windows" )
- set( NGS_JAVADOC_DIR ${TARGDIR} )
- else()
- set( NGS_JAVADOC_DIR ${TARGDIR}/obj )
- endif()
+ set( NGS_JAVADOC_DIR ${TARGDIR} )
+
if ( Java_JAR_EXECUTABLE AND NOT (${OS} STREQUAL "windows") )
add_custom_target(
ngs-doc-jar ALL COMMAND

5
var/spack/repos/builtin/packages/sra-tools/package.py
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@ -13,6 +13,7 @@ class SraTools(CMakePackage):
homepage = "https://github.com/ncbi/sra-tools" homepage = "https://github.com/ncbi/sra-tools"
git = "https://github.com/ncbi/sra-tools.git" git = "https://github.com/ncbi/sra-tools.git"
version("3.0.3", tags="3.0.3")
version("3.0.0", tags="3.0.0") version("3.0.0", tags="3.0.0")
depends_on("openjdk") depends_on("openjdk")
@ -20,6 +21,10 @@ class SraTools(CMakePackage):
depends_on("libxml2") depends_on("libxml2")
depends_on("ncbi-vdb") depends_on("ncbi-vdb")
# The CMakeLists.txt file set the path to ${TARGDIR}/obj but the code
# actually uses ${TARGDIR}.
patch("ngs-java.patch")
def cmake_args(self): def cmake_args(self):
args = [ args = [
self.define("VDB_INCDIR", format(self.spec["ncbi-vdb"].prefix) + "/include"), self.define("VDB_INCDIR", format(self.spec["ncbi-vdb"].prefix) + "/include"),