diff options
| -rw-r--r-- | .SRCINFO | 259 | ||||
| -rw-r--r-- | PKGBUILD | 28 | ||||
| -rw-r--r-- | PROVIDES | 254 | ||||
| -rwxr-xr-x | imod.sh | 55 |
4 files changed, 324 insertions, 272 deletions
@@ -1,7 +1,7 @@ pkgbase = imod-binary - pkgdesc = image processing, modeling and display programs for tomography and 3D reconstruction + pkgdesc = Image-Processing, Modeling and Display Programs for Tomography and 3D Reconstruction pkgver = 4.9.10 - pkgrel = 1 + pkgrel = 2 url = http://bio3d.colorado.edu/imod/ arch = x86_64 license = GPL @@ -9,9 +9,264 @@ pkgbase = imod-binary depends = python optdepends = cuda>=8.0.0: for library bindings 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/imod/AMD64-RHEL5/imod_4.9.10_RHEL7-64_CUDA8.0.sh + source = imod.sh md5sums = 09dea781cbefa60f1b8360ed622ab709 + md5sums = 5994f7008e2b3ffd7e37339b14abb0da pkgname = imod-binary @@ -1,26 +1,20 @@ # 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" +pkgrel=2 +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') +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' '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') +source=('https://bio3d.colorado.edu/imod/AMD64-RHEL5/imod_4.9.10_RHEL7-64_CUDA8.0.sh' + 'imod.sh') +md5sums=('09dea781cbefa60f1b8360ed622ab709' + '17e904b7f7c168e45793dc00d8a6aa57') pkgver() { echo "$pkgver" @@ -36,9 +30,11 @@ build() { package() { mkdir -p "$pkgdir/opt" - mkdir -p "$pkgdir/usr/bin/" - cp -r "$srcdir/IMODtempDir/imod_$pkgver/" "$pkgdir/opt" - ln -s "/opt/imod_$pkgver" "$pkgdir/opt/IMOD" + 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/" } # vim:set ts=2 sw=2 et: diff --git a/PROVIDES b/PROVIDES deleted file mode 100644 index 84527f2a2096..000000000000 --- 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 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 $* & } |