From e3cde9aaf8dfef17299987590db11aa1f4df418b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 29 May 2021 07:25:08 +0200
Subject: 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.
---
 .../patches/mosaicatcher-unbundle-htslib.patch     | 49 ++++++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100644 gnu/packages/patches/mosaicatcher-unbundle-htslib.patch

(limited to 'gnu/packages/patches')

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
-- 
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