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-rw-r--r--.SRCINFO269
-rw-r--r--PKGBUILD53
-rw-r--r--PROVIDES254
-rwxr-xr-ximod.sh55
4 files changed, 339 insertions, 292 deletions
diff --git a/.SRCINFO b/.SRCINFO
index 9cd1c9e3064..88930ffb086 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,17 +1,272 @@
pkgbase = imod-binary
- pkgdesc = image processing, modeling and display programs for tomography and 3D reconstruction
- pkgver = 4.9.10
+ pkgdesc = Image-Processing, Modeling and Display Programs for Tomography and 3D Reconstruction
+ pkgver = 4.12.27
pkgrel = 1
- url = http://bio3d.colorado.edu/imod/
+ url = https://bio3d.colorado.edu/imod/
arch = x86_64
license = GPL
depends = libjpeg6-turbo
depends = python
- optdepends = cuda>=8.0.0: for library bindings
+ 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
- source = https://bio3d.colorado.edu/imod/AMD64-RHEL5/imod_4.9.10_RHEL7-64_CUDA8.0.sh
- md5sums = 09dea781cbefa60f1b8360ed622ab709
+ 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-binary
-
diff --git a/PKGBUILD b/PKGBUILD
index b936a57c3c1..217a6956198 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,44 +1,35 @@
-# 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'
+# Maintainer: Charles Vejnar <first name [dot] last name [at] gmail [dot] com>
+# Contributor: Felix Springer <felixspringer149@gmail.com>
pkgname=imod-binary
-pkgver=4.9.10
+pkgver=4.12.27
pkgrel=1
-pkgdesc="image processing, modeling and display programs for tomography and 3D reconstruction"
+pkgdesc="Image-Processing, Modeling and Display Programs for Tomography and 3D Reconstruction"
arch=('x86_64')
-url="http://bio3d.colorado.edu/imod/"
+url="https://bio3d.colorado.edu/imod/"
license=('GPL')
-provides=('imod')
+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>=8.0.0: for library bindings'
+optdepends=('cuda>=10.1: for library bindings'
+ 'java-runtime: for Etomo'
'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 "$pkgver"
-}
+source=("https://bio3d.colorado.edu/ftp/latestIMOD/RHEL7-64_CUDA10.1/imod_${pkgver}_RHEL7-64_CUDA10.1.sh"
+ 'imod.sh')
+sha1sums=('8ac7b7708204b216c9d87ac95ffa436365b05046'
+ 'd9748aa6447b3d880df50b3507e7d5108106d80d')
build() {
- sh imod_4.9.10_RHEL7-64_CUDA8.0.sh -extract
-
- cd "IMODtempDir/"
- tar xvzf "imod_${pkgver}_RHEL7-64_CUDA8.0.tar.gz"
-}
+ sh imod_${pkgver}_RHEL7-64_CUDA10.1.sh -extract
+ cd "IMODtempDir/"
+ tar xvzf "imod_${pkgver}_RHEL7-64_CUDA10.1.tar.gz"
+}
package() {
- mkdir -p "$pkgdir/opt"
- mkdir -p "$pkgdir/usr/bin/"
- cp -r "$srcdir/IMODtempDir/imod_$pkgver/" "$pkgdir/opt"
- ln -s "/opt/imod_$pkgver" "$pkgdir/opt/IMOD"
-}
+ mkdir -p "$pkgdir/opt"
+ cp -r "$srcdir/IMODtempDir/imod_$pkgver/" "$pkgdir/opt/"
+ mv "$pkgdir/opt/imod_$pkgver" "$pkgdir/opt/imod"
-# vim:set ts=2 sw=2 et:
+ mkdir -p "$pkgdir/etc/profile.d/"
+ cp "imod.sh" "$pkgdir/etc/profile.d/"
+}
diff --git a/PROVIDES b/PROVIDES
deleted file mode 100644
index 84527f2a209..00000000000
--- a/PROVIDES
+++ /dev/null
@@ -1,254 +0,0 @@
-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
diff --git a/imod.sh b/imod.sh
new file mode 100755
index 00000000000..981f48d1f04
--- /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 $* & }