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-rw-r--r--.SRCINFO17
-rw-r--r--COPYRIGHT122
-rw-r--r--PKGBUILD44
-rw-r--r--PROVIDES254
4 files changed, 437 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 00000000000..9cd1c9e3064
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,17 @@
+pkgbase = imod-binary
+ pkgdesc = image processing, modeling and display programs for tomography and 3D reconstruction
+ pkgver = 4.9.10
+ pkgrel = 1
+ url = http://bio3d.colorado.edu/imod/
+ arch = x86_64
+ license = GPL
+ depends = libjpeg6-turbo
+ depends = python
+ optdepends = cuda>=8.0.0: for library bindings
+ optdepends = tcsh: for only a few very specializied scripts
+ provides = imod
+ source = https://bio3d.colorado.edu/imod/AMD64-RHEL5/imod_4.9.10_RHEL7-64_CUDA8.0.sh
+ md5sums = 09dea781cbefa60f1b8360ed622ab709
+
+pkgname = imod-binary
+
diff --git a/COPYRIGHT b/COPYRIGHT
new file mode 100644
index 00000000000..8bc2fdcfdc9
--- /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 00000000000..b936a57c3c1
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,44 @@
+# Maintainer: Felix Springer <felixspringer149@gmail.com>
+
+# alias imod-env="IMOD_DIR='/opt/IMOD/'; source '/opt/IMOD/IMOD-linux.sh'"
+#
+# use this alias to access imod from bash!
+# the programs are only after execution of the alias 'imod-env' added to your PATH
+# execute the alias 'imod-env' in your '~/.bash_profile' or your shell-profile to be able to access the programs anytime without invoking 'imod-env' first
+
+# the provided programs are listed in 'PROVIDES'
+
+pkgname=imod-binary
+pkgver=4.9.10
+pkgrel=1
+pkgdesc="image processing, modeling and display programs for tomography and 3D reconstruction"
+arch=('x86_64')
+url="http://bio3d.colorado.edu/imod/"
+license=('GPL')
+provides=('imod')
+depends=('libjpeg6-turbo' 'python')
+optdepends=('cuda>=8.0.0: for library bindings'
+ 'tcsh: for only a few very specializied scripts')
+source=('https://bio3d.colorado.edu/imod/AMD64-RHEL5/imod_4.9.10_RHEL7-64_CUDA8.0.sh')
+md5sums=('09dea781cbefa60f1b8360ed622ab709')
+
+pkgver() {
+ echo "$pkgver"
+}
+
+build() {
+ sh imod_4.9.10_RHEL7-64_CUDA8.0.sh -extract
+
+ cd "IMODtempDir/"
+ tar xvzf "imod_${pkgver}_RHEL7-64_CUDA8.0.tar.gz"
+}
+
+
+package() {
+ mkdir -p "$pkgdir/opt"
+ mkdir -p "$pkgdir/usr/bin/"
+ cp -r "$srcdir/IMODtempDir/imod_$pkgver/" "$pkgdir/opt"
+ ln -s "/opt/imod_$pkgver" "$pkgdir/opt/IMOD"
+}
+
+# vim:set ts=2 sw=2 et:
diff --git a/PROVIDES b/PROVIDES
new file mode 100644
index 00000000000..84527f2a209
--- /dev/null
+++ b/PROVIDES
@@ -0,0 +1,254 @@
+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