diff --git a/EM/finddqe/README b/EM/finddqe/README new file mode 100644 index 0000000..c21a410 --- /dev/null +++ b/EM/finddqe/README @@ -0,0 +1,2 @@ +Installation information: +The Makefile_linux_amd64_gnu that is given with the tar file is not sufficient for installation. Requires two small changes, adding of two flags to the Makefile. This is done with the pbuild::configure step , where the corrected Makefile is copied into the src folder. diff --git a/EM/finddqe/build b/EM/finddqe/build new file mode 100755 index 0000000..abc6d96 --- /dev/null +++ b/EM/finddqe/build @@ -0,0 +1,28 @@ +#!/usr/bin/env modbuild + +# Binary distribution with manual installation. See README.md + +pbuild::add_to_group 'EM' + +pbuild::set_download_url "https://grigoriefflab.umassmed.edu/system/tdf?path=FindDQE_150706.tar.gz&file=1&type=node&id=4220" "$P-$V_PKG.tar.gz" + +pbuild::configure() { + cp "$BUILDBLOCK_DIR/files/Makefile" "$SRC_DIR/src" +} + +pbuild::compile() { + cd "$SRC_DIR/src" + make +} + +pbuild::install() { + mkdir -p "$PREFIX/bin" + cp "$SRC_DIR/bin/finddqe.exe" "$PREFIX/bin/finddqe" +} + + + + + + + diff --git a/EM/finddqe/files/Makefile b/EM/finddqe/files/Makefile new file mode 100644 index 0000000..589e95f --- /dev/null +++ b/EM/finddqe/files/Makefile @@ -0,0 +1,51 @@ +# +# ------ MAKEFILE FILE FOR Linux FREALIGN ----------- +# +# Using: gnu compiler +# +# Thanks to: Shixin Yang & Dr Edward Egelman at University of Virginia +# for providing this file +# +# Notes: To create executable: make -f Makefile_linux_amd64_gnu +# + +SHELL = /bin/sh + +FFLAGS = -m64 -O3 -s -fomit-frame-pointer -Wall -falign-functions=4 \ + -funroll-loops -fexpensive-optimizations -fschedule-insns2 \ + -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE \ + -cpp -w -c + +CFLAGS = -m64 -O3 -DPROTOTYPE -D_FILE_OFFSET_BITS=64 \ + -D_LARGEFILE_SOURCE -cpp -w -c + +COMP = gfortran + +CC = gcc + +ifeq ($(MKLROOT),"") + LF = -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE +else + LF = -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wl,--start-group $(MKLROOT)/lib/intel64/libmkl_intel_lp64.a $(MKLROOT)/lib/intel64/libmkl_core.a $(MKLROOT)/lib/intel64/libmkl_sequential.a -Wl,--end-group -ldl -lpthread +endif + +PGM = finddqe + +LIB = $(PGM).a + +.PRECIOUS : $(PGM) $(LIB) + +include Makefile.inc + +ioc.o : ioc.c + $(CC) $(CFLAGS) -o ioc.o ioc.c + $(AR) r $(LIB) ioc.o + @\rm ioc.o + +$(LIB) : ioc.o $(ELEMENTS) + @echo all object files placed in library + +.f.a: + $(COMP) $(FFLAGS) $< + $(AR) r $(LIB) $*.o + @\rm $*.o diff --git a/EM/finddqe/files/variants b/EM/finddqe/files/variants new file mode 100644 index 0000000..880f337 --- /dev/null +++ b/EM/finddqe/files/variants @@ -0,0 +1 @@ +finddqe/1.6 unstable b:intel/22.2 diff --git a/EM/finddqe/modulefile b/EM/finddqe/modulefile new file mode 100644 index 0000000..724a0e5 --- /dev/null +++ b/EM/finddqe/modulefile @@ -0,0 +1,9 @@ +#%Module1.0 + +module-whatis "FindDQE determines the detective quantum efficiency (DQE) of a detector." +module-url "https://grigoriefflab.umassmed.edu/finddqe" +module-license "The Janelia Research Campus Software License 1.2 http://license.janelia.org/license/janelia_license_1_2.html" +module-maintainer "Greta Assmann " + +module-help "Ruskin RS Yu Z Grigorieff N 2013 Quantitative characterization of electron detectors for transmission electron microscopy J Struct Biol 184 385-393 " +