fixed problems with $PATH

4 files changed, 324 insertions, 272 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 9cd1c9e3064..984eeda2150 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -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
 
diff --git a/PKGBUILD b/PKGBUILD
index b936a57c3c1..da7afd6f9de 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -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 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 $* & }