New upstream version 2.1 (25d9555f) · Commits · Debian Med / relion

AUTHORS

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		This program is developed in the group of Sjors H.W. Scheres at the MRC Laboratory of Molecular Biology.
		This program is developed in the group of Sjors H.W. Scheres at the MRC Laboratory of Molecular Biology,

		- Sjors H.W. Scheres
		- Shaoda He
		- Takanori Nakane
		- Jasenko Zivanov
		- Liyi Dong

		and Erik Lindahl at Stockholm University.

		- Erik Lindahl
		- Björn O. Forsberg
		- Dari Kimanius

		However, it does also contain pieces of code from the following packages:
		XMIPP: http:/xmipp.cnb.csic.es

CMakeLists.txt

+2 −1

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		@@ -184,7 +184,7 @@ if(GUI)
		message(STATUS "X11 and FLTK were found")
		message(STATUS "FLTK_LIBRARIES: ${FLTK_LIBRARIES}")
		else()
		message(STATUS "FLTK was NOT found")
		message(STATUS "No FLTK installation was found")
		endif()
		endif(NOT FORCE_OWN_FLTK)

		@@ -210,6 +210,7 @@ if(NOT FORCE_OWN_FFTW)
		endif(NOT FORCE_OWN_FFTW)

		if(NOT FFTW_FOUND)
		message(STATUS "No FFTW installation was found")
		include(${CMAKE_SOURCE_DIR}/cmake/BuildFFTW.cmake)
		endif(NOT FFTW_FOUND)

README.md

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		#RELION
		RELION
		======


		RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer
		@@ -22,10 +21,10 @@ More extensive options and configurations are available
		but the outlines to clone and install relion for typical use are made easy
		through [cmake](https://en.wikipedia.org/wiki/CMake).

		On ubuntu machines, installing cmake is as easy as
		On ubuntu machines, installing cmake, the compiler, and additional dependencies (mpi, fftw) is as easy as:

		```
		sudo apt install cmake
		sudo apt install cmake build-essential mpi-default-bin mpi-default-dev libfftw3-dev
		```

		On other systems it is typically just as easy, you simply have to modify "apt" to
		@@ -46,9 +45,13 @@ cmake -DCMAKE_INSTALL_PREFIX=/where/to/install/ ..
		make -j4
		make install
		```
		(NOTES: "/where/to/install/.." is typically "/usr/local/relion".
		Make sure you create this directory beforehand.
		Installing to that location requires sudo, so in this case be sure to use
		"sudo make install" instead of "make install" in the last step.)

		These steps will download the source-code, create a build-directory,
		then configure and build relion, and lastely install it to be generally
		then configure and build relion, and lastly install it to be generally
		available on the system.


		@@ -59,9 +62,10 @@ RELION is intermittently updated, with both minor and major features.
		To update an existing installation, simply use the following commands

		```
		cd relion/build
		cd relion
		git pull
		cd build
		make -j4
		make
		make install # (or "sudo make install")

		```

cmake/BuildFFTW.cmake

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		message(STATUS "-------------------------------------------------")
		message(STATUS "------- WILL USE LOCALLY BUILT FFTW LIBS --------")
		message(STATUS "-------------------------------------------------")

		set(FFTW_EXTERNAL_PATH "${CMAKE_SOURCE_DIR}/external/fftw")

		if (NOT DEFINED TARGET_X86)
		@@ -32,9 +28,16 @@ find_library(FFTW_LIBRARIES NAMES ${libfft} PATHS ${FFTW_EXTERNAL_PATH}/li

		if(FFTW_INCLUDES AND FFTW_LIBRARIES)
		set(FFTW_FOUND TRUE)
		message( STATUS "Found previously built external (non-system) FFTW library")
		message(STATUS "Found previously built non-system FFTW libraries that will be used.")
		else()
		set(FFTW_FOUND FALSE)
		message(STATUS "--------------------------------------------------------")
		message(STATUS "-------- NO EXISTING FFTW LIBRARIES WHERE FOUND. -------")
		message(STATUS "-------------- FFTW WILL BE DOWNLOADED AND -------------")
		message(STATUS "--------------- BUILT DURING COMPILE-TIME. -------------")
		message(STATUS "--------------------------------------------------------")
		message(STATUS "---- A WORKING INTERNET CONNECTION WILL BE REQUIRED. ---")
		message(STATUS "--------------------------------------------------------")
		endif()

		## ----------------------------------------------------------------- NEW EXT LIBS? --

cmake/BuildFLTK.cmake

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		message(STATUS "-------------------------------------------------")
		message(STATUS "------- WILL USE LOCALLY BUILT FLTK LIBS --------")
		message(STATUS "-------------------------------------------------")


		set(FLTK_EXTERNAL_PATH "${CMAKE_SOURCE_DIR}/external/fltk")
		set(ext_conf_flags_fltk --enable-shared --prefix=${FLTK_EXTERNAL_PATH})
		@@ -13,10 +11,18 @@ find_path(FLTK_INCLUDES NAMES FL/Fl.H PATHS "${FLTK_EXTERNAL_PATH}/includ

		if(FLTK_INCLUDE_DIR AND FLTK_LIBRARIES)
		set(FLTK_FOUND TRUE)
		message( STATUS "Found previously built external (non-system) FLTK library")
		message(STATUS "Found previously built non-system FLTK libraries that will be used.")
		else()
		set(FLTK_FOUND FALSE)
		message(STATUS "--------------------------------------------------------")
		message(STATUS "-------- NO EXISTING FLTK LIBRARIES WHERE FOUND. -------")
		message(STATUS "-------------- FLTK WILL BE DOWNLOADED AND -------------")
		message(STATUS "--------------- BUILT DURING COMPILE-TIME. -------------")
		message(STATUS "--------------------------------------------------------")
		message(STATUS "---- A WORKING INTERNET CONNECTION WILL BE REQUIRED. ---")
		message(STATUS "--------------------------------------------------------")
		endif()

		## ----------------------------------------------------------------- NEW EXT LIBS? --

		if(NOT FLTK_FOUND)