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author | Felix Springer | 2018-10-24 00:32:51 +0200 |
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committer | Felix Springer | 2018-10-24 00:32:51 +0200 |
commit | 9ff7be51897bc50418c5070d27a234207aaa4988 (patch) | |
tree | 8246a63ab7348a45dbb3299c2efc179ebcd0da22 | |
download | aur-9ff7be51897bc50418c5070d27a234207aaa4988.tar.gz |
initial commit
-rw-r--r-- | .SRCINFO | 17 | ||||
-rw-r--r-- | COPYRIGHT | 122 | ||||
-rw-r--r-- | PKGBUILD | 44 | ||||
-rw-r--r-- | PROVIDES | 254 |
4 files changed, 437 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO new file mode 100644 index 000000000000..9cd1c9e30644 --- /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 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..b936a57c3c14 --- /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 000000000000..84527f2a2096 --- /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 |