add finddqe build folder

This commit is contained in:
Assmann Greta Marie
2023-10-30 17:01:11 +01:00
parent 134774a01d
commit 892dbbdc45
5 changed files with 91 additions and 0 deletions

2
EM/finddqe/README Normal file
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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.

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EM/finddqe/build Executable file
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#!/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"
}

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EM/finddqe/files/Makefile Normal file
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#
# ------ 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

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finddqe/1.6 unstable b:intel/22.2

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EM/finddqe/modulefile Normal file
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#%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 <greta.assmann@psi.ch>"
module-help "Ruskin RS Yu Z Grigorieff N 2013 Quantitative characterization of electron detectors for transmission electron microscopy J Struct Biol 184 385-393 "