1 files changed, 0 insertions, 121 deletions
diff --git a/sci-biology/sailfish/files/sailfish-no-curl.patch b/sci-biology/sailfish/files/sailfish-no-curl.patch
deleted file mode 100644
index 2ec97808e..000000000
--- a/sci-biology/sailfish/files/sailfish-no-curl.patch
+++ /dev/null
@@ -1,121 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 1be4117..ee4b34c 100755
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -230,9 +230,6 @@ elseif(FETCH_BOOST)
-     message("Build system will fetch and build Boost")
-     message("==================================================================")
-     ExternalProject_Add(libboost
--        DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--        DOWNLOAD_COMMAND curl -k -L  http://downloads.sourceforge.net/project/boost/boost/1.59.0/boost_1_59_0.tar.gz -o boost_1_59_0.tar.gz &&
--                               tar xzf boost_1_59_0.tar.gz
-         SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_59_0
-         INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-         #PATCH_COMMAND patch -p2 < ${CMAKE_CURRENT_SOURCE_DIR}/external/boost156.patch
-@@ -292,10 +289,6 @@ if (NOT JELLYFISH_FOUND)
- message("Build system will fetch and build Jellyfish")
- message("==================================================================")
- ExternalProject_Add(libjellyfish
--    DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--    DOWNLOAD_COMMAND curl -k -L https://github.com/gmarcais/Jellyfish/releases/download/v2.2.5/jellyfish-2.2.5.tar.gz -o jellyfish-2.2.5.tgz &&
--    	rm -fr jellyfish-2.2.5 &&
--     	tar -xzvf jellyfish-2.2.5.tgz
-     SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.5
-     INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-     CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.5/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS}
-@@ -335,11 +328,7 @@ if ("${TBB_COMPILER}" STREQUAL "gcc")
- endif()
- 
- ExternalProject_Add(libtbb
--	DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--    URL http://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb43_20140724oss_src.tgz
--    DOWNLOAD_COMMAND curl -k -L  http://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb43_20140724oss_src.tgz -o tbb_20140724oss_src.tgz &&
--                     tar -xzvf tbb_20140724oss_src.tgz
--    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb43_20140724oss
-+	SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb43_20140724oss
-     INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-     PATCH_COMMAND "${TBB_PATCH_STEP}"
-     CONFIGURE_COMMAND ""
-@@ -407,11 +396,6 @@ message("TBB_LIBRARIES = ${TBB_LIBRARIES}")
- message("Build system will compile libgff")
- message("==================================================================")
- ExternalProject_Add(libgff
--    DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--    DOWNLOAD_COMMAND curl -k -L https://github.com/Kingsford-Group/libgff/archive/v1.0.tar.gz -o libgff.tgz &&
--    	tar -xzvf libgff.tgz &&
--        rm -fr libgff &&
--	    mv libgff-1.0 libgff
-     SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff
-     UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
-     INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-@@ -445,9 +429,6 @@ if (NOT HAVE_FAST_MALLOC)
-     message("Build system will fetch and use JEMalloc")
-     message("==================================================================")
-     ExternalProject_Add(libjemalloc
--        DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--        DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/jemalloc/archive/3.6.0.tar.gz -o jemalloc-3.6.0.tar.gz &&
--        tar -xzf jemalloc-3.6.0.tar.gz
-         SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jemalloc-3.6.0
-         BUILD_IN_SOURCE TRUE
-         INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-@@ -465,9 +446,6 @@ endif ()
- message("Build system will fetch and build SparseHash")
- message("==================================================================")
- ExternalProject_Add(libsparsehash
--    DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--    DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/sparsehash/archive/sparsehash-2.0.2.tar.gz -o sparsehash-2.0.2.tar.gz &&
--        tar -xzf sparsehash-2.0.2.tar.gz
-     SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/sparsehash-sparsehash-2.0.2
-     BUILD_IN_SOURCE TRUE
-     INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-@@ -487,7 +465,6 @@ ExternalProject_Add(libsparsehash
- #
- ####
- if(NOT FETCHED_RAPMAP)
--  exec_program(${CMAKE_CURRENT_SOURCE_DIR}/scripts/fetchRapMap.sh)
-   set(FETCHED_RAPMAP TRUE CACHE BOOL "Has RapMap been fetched?" FORCE)
- endif()
- 
-diff --git a/scripts/fetchRapMap.sh b/scripts/fetchRapMap.sh
-deleted file mode 100755
-index cab05a1..0000000
---- a/scripts/fetchRapMap.sh
-+++ /dev/null
-@@ -1,37 +0,0 @@
--#!/bin/bash
--
--CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
--EXTERNAL_DIR=${CURR_DIR}/../external
--INSTALL_DIR=${CURR_DIR}/../external/install
--
--if [ -d ${EXTERNAL_DIR}/RapMap ] ; then
--    rm -fr ${EXTERNAL_DIR}/RapMap
--fi
--
--if [ -d ${INSTALL_DIR}/include/rapmap ] ; then
--    rm -fr ${INSTALL_DIR}/include/rapmap
--fi
--
--if [ -d ${INSTALL_DIR}/src/rapmap ] ; then
--    rm -fr ${INSTALL_DIR}/src/rapmap
--fi
--
--mkdir -p ${EXTERNAL_DIR}
--curl -k -L https://github.com/COMBINE-lab/RapMap/archive/quasi-mph.zip -o ${EXTERNAL_DIR}/rapmap.zip
--rm -fr ${EXTERNAL_DIR}/RapMap
--unzip ${EXTERNAL_DIR}/rapmap.zip -d ${EXTERNAL_DIR}
--mv ${EXTERNAL_DIR}/RapMap-quasi-mph ${EXTERNAL_DIR}/RapMap
--
--mkdir -p ${INSTALL_DIR}/include/rapmap
--mkdir -p ${INSTALL_DIR}/src/rapmap
--
--rm ${EXTERNAL_DIR}/RapMap/src/xxhash.c
--rm ${EXTERNAL_DIR}/RapMap/include/xxhash.h
--
--cp -r ${EXTERNAL_DIR}/RapMap/external/libdivsufsort.zip ${EXTERNAL_DIR}
--cp -r ${EXTERNAL_DIR}/RapMap/src/*.c ${INSTALL_DIR}/src/rapmap
--cp -r ${EXTERNAL_DIR}/RapMap/src/*.cpp ${INSTALL_DIR}/src/rapmap
--cp -r ${EXTERNAL_DIR}/RapMap/include/tclap ${INSTALL_DIR}/include/rapmap
--cp -r ${EXTERNAL_DIR}/RapMap/include/*.h ${INSTALL_DIR}/include/rapmap
--cp -r ${EXTERNAL_DIR}/RapMap/include/*.hpp ${INSTALL_DIR}/include/rapmap
--cp -r ${EXTERNAL_DIR}/RapMap/include/emphf ${INSTALL_DIR}/include/rapmap