diff options
| -rw-r--r-- | .SRCINFO | 272 | ||||
| -rw-r--r-- | COPYRIGHT | 122 | ||||
| -rw-r--r-- | PKGBUILD | 35 | ||||
| -rwxr-xr-x | imod.sh | 55 |
4 files changed, 484 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO new file mode 100644 index 000000000000..934c6c651de1 --- /dev/null +++ b/.SRCINFO @@ -0,0 +1,272 @@ +pkgbase = imod-bin + pkgdesc = Image-Processing, Modeling and Display Programs for Tomography and 3D Reconstruction + pkgver = 4.12.27 + pkgrel = 1 + url = https://bio3d.colorado.edu/imod/ + arch = x86_64 + license = GPL + depends = libjpeg6-turbo + depends = python + optdepends = cuda>=10.1: for library bindings + optdepends = java-runtime: for Etomo + optdepends = tcsh: for only a few very specializied scripts + provides = 3dmod + provides = 3dmodv + provides = addtostack + provides = adocxmlconv + provides = alignframes + provides = alignlog + provides = alterheader + provides = archiveorig + provides = assemblevol + provides = autofidseed + provides = autopatchfit + provides = avganova + provides = avgstack + provides = avgstatplot + provides = b3dcatfiles + provides = b3dcopy + provides = b3dhostname + provides = b3dremove + provides = b3dtouch + provides = b3dwinps + provides = batchruntomo + provides = beadtrack + provides = binvol + provides = blendmont + provides = boxavg + provides = boxstartend + provides = calc + provides = ccderaser + provides = checkmtmod + provides = checkxforms + provides = chunksetup + provides = clip + provides = clipmodel + provides = clonemodel + provides = clonevolume + provides = collectmmm + provides = colornewst + provides = combinefft + provides = contourmod + provides = convertmod + provides = copyheader + provides = copytomocoms + provides = corrsearch3d + provides = cryoposition + provides = ctfphaseflip + provides = ctfplotter + provides = densmatch + provides = densnorm + provides = dm2mrc + provides = dm3props + provides = dualvolmatch + provides = echo2 + provides = edgeeraser + provides = edgemtf + provides = edgepatches + provides = edmont + provides = edpiecepoint + provides = endmodel + provides = enhance + provides = eraser + provides = etomo + provides = etomo.jar + provides = etomoPluginDemo + provides = excise + provides = excludeviews + provides = expandargs + provides = extposition + provides = extractmagrad + provides = extractpieces + provides = extracttilts + provides = extstack + provides = fenestra + provides = fftrans + provides = fiberpitch + provides = filltomo + provides = filterplot + provides = findbeads3d + provides = findcontrast + provides = finddistort + provides = findgradient + provides = findhotpixels + provides = findsection + provides = findsirtdiffs + provides = findwarp + provides = finishjoin + provides = fitpatches + provides = fixboundaries + provides = fixmont + provides = flattenwarp + provides = framewatcher + provides = genhstplt + provides = goodframe + provides = gpumonitor + provides = gputilttest + provides = header + provides = howflared + provides = idfprocess + provides = imavgstat + provides = imod + provides = imod2meta + provides = imod2obj + provides = imod2patch + provides = imod2rib + provides = imod2vrml + provides = imod2vrml2 + provides = imodauto + provides = imodchopconts + provides = imodcpuload + provides = imodcurvature + provides = imod-dist + provides = imodexplode + provides = imodextract + provides = imodfillin + provides = imodfindbeads + provides = imodhelp + provides = imodinfo + provides = imodjoin + provides = imodkillgroup + provides = imodmesh + provides = imodmop + provides = imodpsview + provides = imodqtassist + provides = imodsendevent + provides = imodsetvalues + provides = imodsortsurf + provides = imodtrans + provides = imoduntar + provides = imodv + provides = joinmodel + provides = joinwarp2model + provides = makecomfile + provides = makegradtable + provides = makejoincom + provides = makepyramid + provides = MarkersCorrespond + provides = matchorwarp + provides = matchrotpairs + provides = matchshifts + provides = matchvol + provides = maxjoinsize + provides = midas + provides = model2point + provides = montagesize + provides = mrc2tif + provides = mrcbyte + provides = mrctaper + provides = mrcx + provides = mtdetect + provides = mtffilter + provides = mtk + provides = mtlengths + provides = mtmodel + provides = mtoverlap + provides = mtpairing + provides = mtrotlong + provides = mtsmooth + provides = mtteach + provides = nad_eed_3d + provides = nda + provides = newstack + provides = numericdiff + provides = onegenplot + provides = onepatchcorr + provides = patch2imod + provides = patchcorr3d + provides = patchcrawl3d + provides = pickbestseed + provides = point2model + provides = preNAD + provides = preNID + provides = processchunks + provides = prochunks.csh + provides = queuechunk + provides = RAPTOR + provides = raw2mrc + provides = rawtiltcoords + provides = realscalemod + provides = rec2imod + provides = recombine + provides = reducecont + provides = reducemont + provides = reducemtmod + provides = refinematch + provides = remapmodel + provides = repackseed + provides = resamplemod + provides = restrictalign + provides = rotatevol + provides = rotmont + provides = runimodqtapp + provides = runraptor + provides = sampletilt + provides = scalemodel + provides = sda + provides = selfalign + provides = setlibpath + provides = settmpdir + provides = setupcombine + provides = setupcoms + provides = setuplong + provides = setupstitch + provides = sirtsetup + provides = slashfindspheres + provides = slashmasksort + provides = slurmCleanup.sh + provides = slurmInit.sh + provides = smoothsurf + provides = solvematch + provides = sortbeadsurfs + provides = splitblend + provides = splitcombine + provides = splitcorrection + provides = splitmrc + provides = splittilt + provides = squeezevol + provides = startprocess + provides = stitchalign + provides = subimage + provides = subimanova + provides = subimstat + provides = subm + provides = submfg + provides = subtomosetup + provides = subtractcurves + provides = sumdensity + provides = taperoutvol + provides = tapervoledge + provides = tif2mrc + provides = tilt + provides = tiltalign + provides = tiltxcorr + provides = tomodataplots + provides = tomopieces + provides = tomopitch + provides = tomosnapshot + provides = tomostitch + provides = transferfid + provides = trimvol + provides = vmstocsh + provides = vmstopy + provides = warpvol + provides = wmod2imod + provides = xcorrstack + provides = xf2rotmagstr + provides = xfalign + provides = xfforfidless + provides = xfinterstack + provides = xfinverse + provides = xfjointomo + provides = xfmodel + provides = xfproduct + provides = xfsimplex + provides = xftoxg + provides = xyzproj + source = https://bio3d.colorado.edu/ftp/latestIMOD/RHEL7-64_CUDA10.1/imod_4.12.27_RHEL7-64_CUDA10.1.sh + source = imod.sh + sha1sums = 8ac7b7708204b216c9d87ac95ffa436365b05046 + sha1sums = d9748aa6447b3d880df50b3507e7d5108106d80d + +pkgname = imod-bin diff --git a/COPYRIGHT b/COPYRIGHT new file mode 100644 index 000000000000..8bc2fdcfdc9a --- /dev/null +++ b/COPYRIGHT @@ -0,0 +1,122 @@ +IMOD Version 4.9.0 Copyright Notice and Credits +-------------------------------------------------------------------------- +Except as noted, ALL SOFTWARE LISTED IS Copyright (C) 1994-2017 +the Regents of the University of Colorado. + +All portions of IMOD, except as noted below, are open source under the +General Public License (GPL) version 2.0. A copy of this license is in the +file GPL.txt. (All license files referred to here are in the directory +'licenses' in the binary distribution or 'dist' in the source code.) The +libraries written entirely in C/C++ are released under the Lesser GPL (see +LGPL.txt). Software may be modified and redistributed under the terms of +these licenses. The source can be found at +http://bio3d.colorado.edu/imod/nightlyBuild +and +http://bio3d.colorado.edu/imod/openSource + +THIS SOFTWARE AND/OR DOCUMENTATION IS PROVIDED WITH NO WARRANTY, +EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTY OF +MERCHANTABILITY AND WARRANTY OF FITNESS FOR A PARTICULAR PURPOSE. + +Arch User Repository (AUR) package is maintaned by Felix Springer. + +Programs were written by David Mastronarde, James Kremer, Rick +Gaudette, Sue Held, Quanren Xiong, and John Heumann at the University +of Colorado, some based on work and libraries from the MRC. We thank David +Agard and Hans Chen for the original MRC source code, Wah Chiu for a Unix +version of low-level MRC file routines used in the FORTRAN parts, and Chuck +Robertson for much work on the port to Linux. + +The program nad_eed_3d by Achilleas Frangakis and Reiner Hegerl is +copyright Max-Planck-Institut for Biochemistry, Martinsried, Germany. + +The LSQR routine by Michael Saunders is used in some programs. IMOD uses a +C version of LSQR and some BLAS routines from the BCLS package of Michael +Friedlander, which are covered by the Lesser GPL (see LGPL.txt). + +IMOD uses a subset of the LAPACK routines developed at Univ. of Tennessee, +Univ. of California Berkeley, NAG Ltd., Courant Institute, Argonne National +Lab, and Rice University. They are copyrighted by the University of +Tennessee and covered by a BSD-style license (see LAPACK.txt). IMOD also +uses a subset of the BLAS routines, developed by: Jack Dongarra, Argonne +National Lab; Jeremy Du Croz, NAG Ltd.; Iain Duff, AERE Harwell; Richard +Hanson, Sandia National Labs; and Sven Hammarling, NAG Ltd. + +The program imodwincpu was adapted from code obtained from +www.codeproject.com and written by Dudi Abramov. It is excluded from the +GPL license and is covered exclusively by the Code Project Open License (see +CPOL.html). + +Routines for computing some statistical functions were adapted from +S. J. Zhang and J. M. Jin, Computation of Special Functions. New York: John +Wiley & Sons, 1996 and are copyrighted by the authors and publisher. + +Andrew Noske (originally at the University of Queensland, Australia, then at +the University of California, San Diego) contributed the beadhelper, +drawingtools, interpolator, namewizard, and stereology plugins. See the help +displayed by those plugins for acknowledgements of funding for his work. + +Jane Ding at California Institute of Technology contributed the Grab with Note +plugin. + +The isosurface display in 3dmod uses contouring and surface smoothing +modules from Chimera, developed at the Resource for Biocomputing, +Visualization, and Informatics at the University of California, San +Francisco, supported by NIH/NCRR grant P41-RR01081. + +RAPTOR was developed by Fernando Amat, Farshid Moussavi, and Mark Horowitz +at Stanford University and is copyrighted by them. It is covered by the +license in RAPTORlicense.txt. It uses three libraries, parts of which are +included in the IMOD source code distribution: +OpenCV (http://sourceforge.net/projects/opencvlibrary/), +covered by the license in OpenCV.txt, +SuiteSparse (http://www.cise.ufl.edu/research/sparse/SuiteSparse/), +covered by the licenses in CSparse.txt and LGPL.txt, and +Stair Vision Library (http://sourceforge.net/projects/stairvision/), +covered by the license in StairVision.txt. + +The warping library uses modules from Pavel Sakov's 'nn' package, which are +copyrighted by Sakov and CSIRO, and covered by the license in nn.txt. The +library also uses code from Ken Clarkson's 'hull' program, which is +copyrighted by AT&T and covered by the license in hull.txt. + +Routines for solving 3x3 eigenvectors are copyrighted by Joachim Kopp and +covered by the LGPL license. + +Mauro Maiorca, at the Biochemistry & Molecular Biology Department, Bio21 +Institute, University of Melbourne, Australia, contributed the preNAD and +preNID programs. His work was supported by funding from the Australian +Research Council and the National Health and Medical Research Council. preNAD +and preNID use recursive line filter routines from Gregoire Malandain, covered +by version 3 of the GPL (see GPL-3.0.txt). + +IMOD uses TIFF libraries which are Copyright (c) 1988-1997 Sam Leffler +and Copyright (c) 1991-1997 Silicon Graphics, Inc. (see TIFF.txt). + +Because IMOD uses the libjpeg library, this software is based in part on the +work of the Independent JPEG Group. IMOD also uses the zlib library, which is +Copyright 1995-2010 by Jean-loup Gailly and Mark Adler. + +IMOD use FFTW libraries which are Copyright (c) 1997--1999 Massachusetts +Institute of Technology, written by Matteo Frigo and Steven G. Johnson, and +covered by version 2 of the GPL. + +IMOD uses HDF5 libraries which are Copyright 1998-2006 by the Board of +Trustees of the University of Illinois and Copyright 2006-2014 by The HDF +Group and covered by the license in HDF5.txt. + +The module gcvspl.c is based on an f2c translation of gcvspl.f, which was +obtained from http://www.netlib.org. gcvspl.f was written by H.J. Woltring +based on routines in Lyche et al. (1983) and other sources as documented in +gcvspl.c. + +IMOD includes a copy of the Mini-XML library which is Copyright 2003-2016 by +Michael R. Sweet and is covered by the modified Library GPL in Mini-XML.txt + +This work was supported in the past by NIH P41 grants from NCRR and NIGMS to +J. Richard McIntosh and Andreas Hoenger; and by NIBIB grant EB005027 to +David Mastronarde. + +Contact: mast at colorado dot edu + www: http://bio3d.colorado.edu/imod/index.html + University of Colorado, Dept. of MCD Biology, 347 UCB, Boulder, CO 80309 diff --git a/PKGBUILD b/PKGBUILD new file mode 100644 index 000000000000..d7493487073d --- /dev/null +++ b/PKGBUILD @@ -0,0 +1,35 @@ +# Maintainer: Charles Vejnar <first name [dot] last name [at] gmail [dot] com> +# Contributor: Felix Springer <felixspringer149@gmail.com> + +pkgname=imod-bin +pkgver=4.12.27 +pkgrel=1 +pkgdesc="Image-Processing, Modeling and Display Programs for Tomography and 3D Reconstruction" +arch=('x86_64') +url="https://bio3d.colorado.edu/imod/" +license=('GPL') +provides=('3dmod' '3dmodv' 'addtostack' 'adocxmlconv' 'alignframes' 'alignlog' 'alterheader' 'archiveorig' 'assemblevol' 'autofidseed' 'autopatchfit' 'avganova' 'avgstack' 'avgstatplot' 'b3dcatfiles' 'b3dcopy' 'b3dhostname' 'b3dremove' 'b3dtouch' 'b3dwinps' 'batchruntomo' 'beadtrack' 'binvol' 'blendmont' 'boxavg' 'boxstartend' 'calc' 'ccderaser' 'checkmtmod' 'checkxforms' 'chunksetup' 'clip' 'clipmodel' 'clonemodel' 'clonevolume' 'collectmmm' 'colornewst' 'combinefft' 'contourmod' 'convertmod' 'copyheader' 'copytomocoms' 'corrsearch3d' 'cryoposition' 'ctfphaseflip' 'ctfplotter' 'densmatch' 'densnorm' 'dm2mrc' 'dm3props' 'dualvolmatch' 'echo2' 'edgeeraser' 'edgemtf' 'edgepatches' 'edmont' 'edpiecepoint' 'endmodel' 'enhance' 'eraser' 'etomo' 'etomo.jar' 'etomoPluginDemo' 'excise' 'excludeviews' 'expandargs' 'extposition' 'extractmagrad' 'extractpieces' 'extracttilts' 'extstack' 'fenestra' 'fftrans' 'fiberpitch' 'filltomo' 'filterplot' 'findbeads3d' 'findcontrast' 'finddistort' 'findgradient' 'findhotpixels' 'findsection' 'findsirtdiffs' 'findwarp' 'finishjoin' 'fitpatches' 'fixboundaries' 'fixmont' 'flattenwarp' 'framewatcher' 'genhstplt' 'goodframe' 'gpumonitor' 'gputilttest' 'header' 'howflared' 'idfprocess' 'imavgstat' 'imod' 'imod2meta' 'imod2obj' 'imod2patch' 'imod2rib' 'imod2vrml' 'imod2vrml2' 'imodauto' 'imodchopconts' 'imodcpuload' 'imodcurvature' 'imod-dist' 'imodexplode' 'imodextract' 'imodfillin' 'imodfindbeads' 'imodhelp' 'imodinfo' 'imodjoin' 'imodkillgroup' 'imodmesh' 'imodmop' 'imodpsview' 'imodqtassist' 'imodsendevent' 'imodsetvalues' 'imodsortsurf' 'imodtrans' 'imoduntar' 'imodv' 'joinmodel' 'joinwarp2model' 'makecomfile' 'makegradtable' 'makejoincom' 'makepyramid' 'MarkersCorrespond' 'matchorwarp' 'matchrotpairs' 'matchshifts' 'matchvol' 'maxjoinsize' 'midas' 'model2point' 'montagesize' 'mrc2tif' 'mrcbyte' 'mrctaper' 'mrcx' 'mtdetect' 'mtffilter' 'mtk' 'mtlengths' 'mtmodel' 'mtoverlap' 'mtpairing' 'mtrotlong' 'mtsmooth' 'mtteach' 'nad_eed_3d' 'nda' 'newstack' 'numericdiff' 'onegenplot' 'onepatchcorr' 'patch2imod' 'patchcorr3d' 'patchcrawl3d' 'pickbestseed' 'point2model' 'preNAD' 'preNID' 'processchunks' 'prochunks.csh' 'queuechunk' 'RAPTOR' 'raw2mrc' 'rawtiltcoords' 'realscalemod' 'rec2imod' 'recombine' 'reducecont' 'reducemont' 'reducemtmod' 'refinematch' 'remapmodel' 'repackseed' 'resamplemod' 'restrictalign' 'rotatevol' 'rotmont' 'runimodqtapp' 'runraptor' 'sampletilt' 'scalemodel' 'sda' 'selfalign' 'setlibpath' 'settmpdir' 'setupcombine' 'setupcoms' 'setuplong' 'setupstitch' 'sirtsetup' 'slashfindspheres' 'slashmasksort' 'slurmCleanup.sh' 'slurmInit.sh' 'smoothsurf' 'solvematch' 'sortbeadsurfs' 'splitblend' 'splitcombine' 'splitcorrection' 'splitmrc' 'splittilt' 'squeezevol' 'startprocess' 'stitchalign' 'subimage' 'subimanova' 'subimstat' 'subm' 'submfg' 'subtomosetup' 'subtractcurves' 'sumdensity' 'taperoutvol' 'tapervoledge' 'tif2mrc' 'tilt' 'tiltalign' 'tiltxcorr' 'tomodataplots' 'tomopieces' 'tomopitch' 'tomosnapshot' 'tomostitch' 'transferfid' 'trimvol' 'vmstocsh' 'vmstopy' 'warpvol' 'wmod2imod' 'xcorrstack' 'xf2rotmagstr' 'xfalign' 'xfforfidless' 'xfinterstack' 'xfinverse' 'xfjointomo' 'xfmodel' 'xfproduct' 'xfsimplex' 'xftoxg' 'xyzproj') +depends=('libjpeg6-turbo' 'python') +optdepends=('cuda>=10.1: for library bindings' + 'java-runtime: for Etomo' + 'tcsh: for only a few very specializied scripts') +source=("https://bio3d.colorado.edu/ftp/latestIMOD/RHEL7-64_CUDA10.1/imod_${pkgver}_RHEL7-64_CUDA10.1.sh" + 'imod.sh') +sha1sums=('8ac7b7708204b216c9d87ac95ffa436365b05046' + 'd9748aa6447b3d880df50b3507e7d5108106d80d') + +build() { + sh imod_${pkgver}_RHEL7-64_CUDA10.1.sh -extract + + cd "IMODtempDir/" + tar xvzf "imod_${pkgver}_RHEL7-64_CUDA10.1.tar.gz" +} + +package() { + mkdir -p "$pkgdir/opt" + cp -r "$srcdir/IMODtempDir/imod_$pkgver/" "$pkgdir/opt/" + mv "$pkgdir/opt/imod_$pkgver" "$pkgdir/opt/imod" + + mkdir -p "$pkgdir/etc/profile.d/" + cp "imod.sh" "$pkgdir/etc/profile.d/" +} diff --git a/imod.sh b/imod.sh new file mode 100755 index 000000000000..981f48d1f045 --- /dev/null +++ b/imod.sh @@ -0,0 +1,55 @@ +#!/usr/bin/bash + +# Set IMOD_DIR if it is not set already +# +export IMOD_DIR=${IMOD_DIR:=/opt/imod} + +# Set IMOD_JAVADIR if it is not set already +# +if [ -f "/usr/bin/archlinux-java" ] +then + export IMOD_JAVADIR=${IMOD_JAVADIR:=/usr/lib/jvm/`/usr/bin/archlinux-java get`} +fi + +# Put the IMOD programs on the path +# +if ! echo ${PATH} | /bin/grep -q "$IMOD_DIR/bin" ; then + export PATH=$IMOD_DIR/bin:$PATH +fi + +# Set variable with location of the IMOD plugins +# +export IMOD_PLUGIN_DIR=$IMOD_DIR/lib/imodplug + +# Tell the system where the IMOD libraries are located. +# +export LD_LIBRARY_PATH=$IMOD_DIR/lib:$LD_LIBRARY_PATH + +# Put the man pages on the man path only if it exists +# +if [ ! -z "$MANPATH" ] ; then + export MANPATH=$IMOD_DIR/man:$MANPATH +fi + +# Set a variable with the location of configuration/calibration/data files +# +export IMOD_CALIB_DIR=${IMOD_CALIB_DIR:=/opt/IMOD/ImodCalib} + +# Source local startup file in ImodCalib if it exists +# +if [ -r $IMOD_CALIB_DIR/IMOD.sh ] ; then + . $IMOD_CALIB_DIR/IMOD.sh +fi + +# Disable alarming stack traces from Intel Fortran +# +export FOR_DISABLE_STACK_TRACE=1 + +# Set a variable to indicate where our copy of Qt library is +# +export IMOD_QTLIBDIR="$IMOD_DIR/qtlib" + +# A subm function to run command files in the background with submfg +# +if [ -z "$BASH" ] ; then return 0 ; fi +function subm () { submfg $* & } |