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| author | Ricardo Wurmus <rekado@elephly.net> | 2021-05-29 07:25:08 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2021-05-29 07:26:15 +0200 |
| commit | e3cde9aaf8dfef17299987590db11aa1f4df418b (patch) | |
| tree | 85a8d8038c371cc9a910cc9c923af4b07e57c502 /gnu/packages/patches | |
| parent | 64907645ec86be4a12db66c98343a9e1ea6f781d (diff) | |
| download | guix-e3cde9aaf8dfef17299987590db11aa1f4df418b.tar guix-e3cde9aaf8dfef17299987590db11aa1f4df418b.tar.gz | |
gnu: Add mosaicatcher.
* gnu/packages/patches/mosaicatcher-unbundle-htslib.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/bioinformatics.scm (mosaicatcher): New variable.
Diffstat (limited to 'gnu/packages/patches')
| -rw-r--r-- | gnu/packages/patches/mosaicatcher-unbundle-htslib.patch | 49 |
1 files changed, 49 insertions, 0 deletions
diff --git a/gnu/packages/patches/mosaicatcher-unbundle-htslib.patch b/gnu/packages/patches/mosaicatcher-unbundle-htslib.patch new file mode 100644 index 0000000000..262895ddcf --- /dev/null +++ b/gnu/packages/patches/mosaicatcher-unbundle-htslib.patch @@ -0,0 +1,49 @@ +--- a/src/CMakeLists.txt 2021-05-28 13:07:25.655107983 +0200 ++++ b/src/CMakeLists.txt 2021-05-28 13:09:55.764025497 +0200 +@@ -21,24 +21,6 @@ + + + +-### Link HTSlib +- +-ExternalProject_Add(htslib +- PREFIX ${CMAKE_BINARY_DIR}/htslib +- GIT_REPOSITORY "https://github.com/samtools/htslib.git" +- GIT_TAG "1.3.1" +- UPDATE_COMMAND "" +- BUILD_IN_SOURCE 1 +- CONFIGURE_COMMAND "" +- BUILD_COMMAND make +- INSTALL_COMMAND make install prefix=${CMAKE_BINARY_DIR}/htslib +- LOG_DOWNLOAD 1 +-) +-link_directories (${CMAKE_BINARY_DIR}/htslib/lib) +-include_directories (${CMAKE_BINARY_DIR}/htslib/include) +- +- +- + ### Set version + + # Get the current working branch +@@ -64,13 +46,6 @@ + + # 2. Boost version from find_package (Boost_VERSION) + +-# 3. Get HTSlib version from git +-execute_process( +- COMMAND git describe --always +- WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/htslib +- OUTPUT_VARIABLE HTSLIB_VERSION +- OUTPUT_STRIP_TRAILING_WHITESPACE +-) + set(HTSLIB_VERSION "1.3.1 ${HTSLIB_VERSION}") + + # 4. write version.hpp file +@@ -105,7 +80,6 @@ + add_executable (mosaic main.cpp ${HEADER_FILES}) + target_link_libraries (mosaic LINK_PUBLIC ${Boost_LIBRARIES}) + target_link_libraries (mosaic LINK_PUBLIC hts) +-add_dependencies (mosaic htslib) + + + ### Doxygen API documentation |