diff options
Diffstat (limited to 'sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch')
| -rw-r--r-- | sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch | 200 |
1 files changed, 0 insertions, 200 deletions
diff --git a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch deleted file mode 100644 index 438763960..000000000 --- a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch +++ /dev/null @@ -1,200 +0,0 @@ ---- salmon-0.10.2/CMakeLists.txt 2018-06-25 13:12:49.275828719 +0200 -+++ salmon-0.10.2/CMakeLists.txt 2018-06-25 13:12:38.945565690 +0200 -@@ -235,31 +235,7 @@ - - find_package (LibLZMA) - if (NOT LIBLZMA_FOUND) -- message ("Will attempt to fetch and build liblzma") -- message ("=======================================") --ExternalProject_Add(liblzma -- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- ## -- DOWNLOAD_COMMAND curl -k -L http://tukaani.org/xz/xz-5.2.2.tar.gz -o xz-5.2.2.tar.gz && -- ${SHASUM} 73df4d5d34f0468bd57d09f2d8af363e95ed6cc3a4a86129d2f2c366259902a2 xz-5.2.2.tar.gz && -- tar -xzvf xz-5.2.2.tar.gz -- #URL http://tukaani.org/xz/xz-5.2.2.tar.gz -- #URL_HASH SHA1=14663612422ab61386673be78fbb2556f50a1f08 -- ## -- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2 -- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install -- BUILD_IN_SOURCE TRUE -- CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} CPPFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} LDFLAGS=${EXTRA_CMAKE_LIBRARY_FLAGS} -- BUILD_COMMAND make ${QUIET_MAKE} -- INSTALL_COMMAND make ${QUIET_MAKE} install --) -- --# Tell cmake that the external project generated a library so we can --# add dependencies here instead of later --set (LIBLZMA_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/liblzma.a) --set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib") --set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include") --set (FETCHED_LIBLZMA TRUE) -+ message (FATAL_ERROR "liblzma must be installed before configuration & building can proceed") - else() - message("Found liblzma library: ${LIBLZMA_LIBRARIES}") - message("===========================================") -@@ -267,28 +243,7 @@ - - find_package (BZip2) - if (NOT BZIP2_FOUND) -- message ("Will attempt to fetch and build libbz2") -- message ("=======================================") --ExternalProject_Add(libbz2 -- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz -o bzip2-1.0.6.tar.gz && -- ${SHASUM} a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd bzip2-1.0.6.tar.gz && -- tar -xzvf bzip2-1.0.6.tar.gz -- #URL http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz -- #URL_HASH SHA1=3f89f861209ce81a6bab1fd1998c0ef311712002 -- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bzip2-1.0.6 -- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install -- BUILD_IN_SOURCE TRUE -- CONFIGURE_COMMAND "" -- BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} -- INSTALL_COMMAND make ${QUIET_MAKE} install PREFIX=<INSTALL_DIR> --) --# Tell cmake that the external project generated a library so we can --# add dependencies here instead of later --set (BZIP2_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/libbz2.a) --set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib -I${GAT_SOURCE_DIR}/external/install/include") --set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include") --set (FETCHED_LIBBZ2 TRUE) -+ message (FATAL_ERROR "libbz2 must be installed before configuration & building can proceed") - else() - message("Found libbz2 library: ${BZIP2_LIBRARIES}") - message("===========================================") -@@ -333,61 +288,15 @@ - # Either inform the user of how to obtain Boost, or, if they passed in the FETCH_BOOST - # option, go and grab it for them. - ## --if ((NOT Boost_FOUND) AND (NOT FETCH_BOOST)) -+if (NOT Boost_FOUND) - message(FATAL_ERROR - "Salmon cannot be compiled without Boost.\n" - "It is recommended to visit http://www.boost.org/ and install Boost according to those instructions.\n" - "This build system can also download and install a local version of boost for you (this takes a lot of time).\n" - "To fetch and build boost locally, call cmake with -DFETCH_BOOST=TRUE" - ) --elseif(FETCH_BOOST) -- ## Let the rest of the build process know we're going to be fetching boost -- set (BOOST_LIB_SUBSET --with-iostreams --with-atomic --with-chrono --with-container --with-date_time --with-exception -- --with-filesystem --with-graph --with-graph_parallel --with-math -- --with-program_options --with-system --with-thread -- --with-timer) -- set (BOOST_WILL_RECONFIGURE TRUE) -- set (FETCH_BOOST FALSE) -- 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/1.66.0/boost_1_66_0.tar.gz -o boost_1_66_0.tar.gz && -- ${SHASUM} bd0df411efd9a585e5a2212275f8762079fed8842264954675a4fddc46cfcf60 boost_1_66_0.tar.gz && -- tar xzf boost_1_66_0.tar.gz -- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0 -- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install -- #PATCH_COMMAND patch -p2 < ${CMAKE_CURRENT_SOURCE_DIR}/external/boost156.patch -- CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/bootstrap.sh ${BOOST_CONFIGURE_TOOLSET} ${BOOST_BUILD_LIBS} --prefix=<INSTALL_DIR> -- BUILD_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/b2 -d0 -j2 ${BOOST_LIB_SUBSET} toolset=${BOOST_TOOLSET} ${BOOST_EXTRA_FLAGS} cxxflags=${BOOST_CXX_FLAGS} link=static install -- BUILD_IN_SOURCE 1 -- INSTALL_COMMAND "" -- ) -- -- ## -- # After we've installed boost, -- ## -- SET( RECONFIG_FLAGS ${RECONFIG_FLAGS} -DBOOST_WILL_RECONFIGURE=FALSE -DBOOST_RECONFIGURE=TRUE -DFETCH_BOOST=FALSE) -- ExternalProject_Add_Step(libboost reconfigure -- COMMAND ${CMAKE_COMMAND} ${CMAKE_CURRENT_SOURCE_DIR} ${RECONFIG_FLAGS} -- DEPENDEES install -- ) -- set (FETCHED_BOOST TRUE) - endif() - --## --# If we're fetching boost and we need to have dummy paths for these variables --# so that CMake won't complain --## --if (BOOST_WILL_RECONFIGURE) -- message("Setting Temporary Boost paths") -- set(Boost_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include) -- set(Boost_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include) -- set(Boost_LIBRARY_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib) -- set(Boost_FOUND TRUE) --endif() -- -- - message("BOOST INCLUDE DIR = ${Boost_INCLUDE_DIR}") - message("BOOST INCLUDE DIRS = ${Boost_INCLUDE_DIRS}") - message("BOOST LIB DIR = ${Boost_LIBRARY_DIRS}") -@@ -422,9 +331,9 @@ - include(ExternalProject) - ExternalProject_Add(libcereal - DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -o cereal-v1.2.2.tar.gz && -- ${SHASUM} 1921f26d2e1daf9132da3c432e2fd02093ecaedf846e65d7679ddf868c7289c4 cereal-v1.2.2.tar.gz && -- tar -xzvf cereal-v1.2.2.tar.gz -+ DOWNLOAD_COMMAND cp ../../../distdir/cereal-1.2.2.tar.gz . && -+ ${SHASUM} 1921f26d2e1daf9132da3c432e2fd02093ecaedf846e65d7679ddf868c7289c4 cereal-1.2.2.tar.gz && -+ tar -xzvf cereal-1.2.2.tar.gz - - ## - #URL https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -@@ -455,12 +364,12 @@ - ExternalProject_Add(libbwa - DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external - #URL https://github.com/COMBINE-lab/bwa/archive/0.7.12.3.tar.gz -- #DOWNLOAD_NAME bwa-master.tar.gz -- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -o bwa-master.tar.gz && -- ${SHASUM} 1ac5661d9e12e9017a47f0264201a75d9128f28dbd9a26952925f7745ddf6036 bwa-master.tar.gz && -- mkdir -p bwa-master && -- tar -xzvf bwa-master.tar.gz --strip-components=1 -C bwa-master -- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-master -+ #DOWNLOAD_NAME bwa-0.7.12.5.tar.gz -+ DOWNLOAD_COMMAND cp ../../../distdir/bwa-0.7.12.5.tar.gz . && -+ ${SHASUM} 1ac5661d9e12e9017a47f0264201a75d9128f28dbd9a26952925f7745ddf6036 bwa-0.7.12.5.tar.gz && -+ mkdir -p bwa-0.7.12.5 && -+ tar -xzvf bwa-0.7.12.5.tar.gz --strip-components=1 -C bwa-0.7.12.5 -+ SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-0.7.12.5 - INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install - CONFIGURE_COMMAND "" - BUILD_COMMAND sh -c "make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}" -@@ -562,9 +471,9 @@ - message("==================================================================") - ExternalProject_Add(libgff - DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -o libgff.tgz && -- ${SHASUM} 34597ecd3718e6d6e7a1dd4350220664be2c1cd992070d1218564a20d7aa5697 libgff.tgz && -- tar -xzvf libgff.tgz -+ DOWNLOAD_COMMAND cp ../../../distdir/libgff-1.1.tgz . && -+ ${SHASUM} 34597ecd3718e6d6e7a1dd4350220664be2c1cd992070d1218564a20d7aa5697 libgff-1.1.tgz && -+ tar -xzvf libgff-1.1.tgz - ## - #URL https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz - #DOWNLOAD_NAME libff.tgz -@@ -600,10 +509,10 @@ - message("==================================================================") - ExternalProject_Add(libstadenio - DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -o staden-io_lib-v1.14.8.tar.gz && -- ${SHASUM} f6f30eefa478cfb708f3109a35fb6ffa0e24951d9d971985df2cef5919dd0bc3 staden-io_lib-v1.14.8.tar.gz && -+ DOWNLOAD_COMMAND cp ../../../distdir/staden-io_lib-1.14.8.tar.gz . && -+ ${SHASUM} f6f30eefa478cfb708f3109a35fb6ffa0e24951d9d971985df2cef5919dd0bc3 staden-io_lib-1.14.8.tar.gz && - mkdir -p staden-io_lib-1.14.8 && -- tar -xzf staden-io_lib-v1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 && -+ tar -xzf staden-io_lib-1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 && - rm -fr staden-io_lib && - mv -f staden-io_lib-1.14.8 staden-io_lib - SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/staden-io_lib -@@ -620,9 +529,9 @@ - message("==================================================================") - ExternalProject_Add(libspdlog - DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -o spdlog-v0.16.1.tar.gz && -- ${SHASUM} 733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae spdlog-v0.16.1.tar.gz && -- tar -xzf spdlog-v0.16.1.tar.gz -+ DOWNLOAD_COMMAND cp ../../../distdir/spdlog-0.16.1.tar.gz . && -+ ${SHASUM} 733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae spdlog-0.16.1.tar.gz && -+ tar -xzf spdlog-0.16.1.tar.gz - ## - #URL https://github.com/COMBINE-lab/spdlog/archive/v0.12.0.tar.gz - #DOWNLOAD_NAME spdlog-v0.12.0.tar.gz |