diff options
author | vd <vd@FreeBSD.org> | 2006-01-26 01:34:35 +0800 |
---|---|---|
committer | vd <vd@FreeBSD.org> | 2006-01-26 01:34:35 +0800 |
commit | 3ea5bb77c41df61b80a2c4b90bbda04d694b2e86 (patch) | |
tree | 2aa83ed1cfd9161585bbc751bcbe744fdf973377 | |
parent | 9a3f6a309e558f326280ab2f90e4c95b96de94cb (diff) | |
download | freebsd-ports-gnome-3ea5bb77c41df61b80a2c4b90bbda04d694b2e86.tar.gz freebsd-ports-gnome-3ea5bb77c41df61b80a2c4b90bbda04d694b2e86.tar.zst freebsd-ports-gnome-3ea5bb77c41df61b80a2c4b90bbda04d694b2e86.zip |
Add new port science/afni
AFNI (Advanced Functional Neuro Imaging) is a tool for analyzing
3 dimensional images, especially functional MRI images used in
brain mapping research.
WWW: http://afni.nimh.nih.gov/
PR: ports/90752
Submitted by: Jason Bacon <bacon@smithers.neuro.mcw.edu>
Reviewed by: garga (mentor)
Approved by: garga (mentor)
-rw-r--r-- | science/Makefile | 1 | ||||
-rw-r--r-- | science/afni/Makefile | 128 | ||||
-rw-r--r-- | science/afni/distinfo | 18 | ||||
-rw-r--r-- | science/afni/files/pkg-message.in | 7 | ||||
-rw-r--r-- | science/afni/pkg-descr | 7 | ||||
-rw-r--r-- | science/afni/pkg-plist | 578 |
6 files changed, 739 insertions, 0 deletions
diff --git a/science/Makefile b/science/Makefile index 4934d6e0b590..d886f7a47da9 100644 --- a/science/Makefile +++ b/science/Makefile @@ -5,6 +5,7 @@ SUBDIR += 2dhf SUBDIR += abinit + SUBDIR += afni SUBDIR += at SUBDIR += bblimage SUBDIR += buddy diff --git a/science/afni/Makefile b/science/afni/Makefile new file mode 100644 index 000000000000..741ad1c928fc --- /dev/null +++ b/science/afni/Makefile @@ -0,0 +1,128 @@ +############################################################################ +# Ports collection Makefile for: afni +# Date created: 11 Jan 2005 +# Whom: bacon@smithers.neuro.mcw.edu +# +# $FreeBSD$ +# + +############################################################################ +# www.neuro.mcw.edu has the latest source distribution from which this port +# is built. It will be updated as time permits. +# +# afni.nimh.nih.gov is the ultimate source for AFNI, and will always +# contain the latest source release. If this port is not up to date, +# you can download the latest sources and build manually using +# Makefile.BSD, which is included in the source distribution. + +PORTNAME= afni +PORTVERSION= 2005.12.30.0934 +CATEGORIES= science biology graphics +MASTER_SITES= http://www.neuro.mcw.edu/~bacon/Ports/distfiles/AFNI/ +DISTFILES= afni_src.tgz afni_doc.tgz afni.1 \ + Makefile.FreeBSD_PORT TTatlas+tlrc.BRIK.gz TTatlas+tlrc.HEAD +DIST_SUBDIR= AFNI +EXTRACT_ONLY= afni_src.tgz afni_doc.tgz + +MAINTAINER= bacon@smithers.neuro.mcw.edu +COMMENT= Advanced Functional Neuro Imaging + +RUN_DEPENDS= cjpeg:${PORTSDIR}/graphics/jpeg \ + mpeg_encode:${PORTSDIR}/multimedia/mpeg_encode \ + whirlgif:${PORTSDIR}/graphics/whirlgif + +USE_GETTEXT= yes +USE_GMAKE= yes +USE_ICONV= yes +USE_MOTIF= yes +MAKE_ENV= CC="${CC}" + +WRKSRC= ${WRKDIR}/afni_src +MAKEFILE= Makefile.FreeBSD_PORT +ALL_TARGET= vastness suma + +SUB_FILES= pkg-message + +########################################################################### +# Install parameters + +MAN1= afni.1 + +# these need not to be stripped +SCRIPTS=\ + @2dwarper \ + @4Daverage \ + @AfniOrient2RAImap \ + @AfniOrientSign \ + @Align_Centers \ + @Center_Distance \ + @CheckForAfniDset \ + @CommandGlobb \ + @DTI_studio_reposition \ + @FromRAI \ + @GetAfniOrient \ + @GetAfniPrefix \ + @GetAfniView \ + @NoExt \ + @Purify_1D \ + @RenamePanga \ + @SUMA_AlignToExperiment \ + @SUMA_Make_Spec_FS \ + @SUMA_Make_Spec_SF \ + @ToRAI \ + @UpdateAfni \ + @VolCenter \ + @align_partial_oblique \ + @auto_align \ + @auto_tlrc \ + @clip_volume \ + @fix_FSsphere \ + @make_stim_file \ + @parse_afni_name \ + @parse_name \ + suma_change_spec \ + +PLIST_FILES+= ${SCRIPTS:S|^|bin/|} + +INSTALL_WRKSRC= ${WRKSRC}/BSD +INSTALL_TEMP= ${WRKSRC}/Backup.BSD + +post-extract: + ${CP} -f ${DISTDIR}/${DIST_SUBDIR}/Makefile.FreeBSD_PORT ${WRKSRC} + +do-install: + ${MKDIR} ${DATADIR} ${INSTALL_TEMP} + @${MV} ${INSTALL_WRKSRC}/libf2c.a ${INSTALL_TEMP} + ${INSTALL_DATA} ${INSTALL_WRKSRC}/*.so ${INSTALL_WRKSRC}/*.a \ + ${PREFIX}/lib + ${INSTALL_DATA} ${INSTALL_WRKSRC}/*.h \ + ${PREFIX}/include + ${INSTALL_DATA} ${INSTALL_WRKSRC}/*.jpg ${INSTALL_WRKSRC}/*.txt \ + ${DATADIR} + @${MV} ${INSTALL_WRKSRC}/*.so \ + ${INSTALL_WRKSRC}/*.a \ + ${INSTALL_WRKSRC}/*.h \ + ${INSTALL_WRKSRC}/*.jpg \ + ${INSTALL_WRKSRC}/*.txt \ + ${INSTALL_WRKSRC}/cjpeg \ + ${INSTALL_WRKSRC}/djpeg \ + ${INSTALL_WRKSRC}/mpeg_encode \ + ${INSTALL_WRKSRC}/whirlgif \ + ${INSTALL_TEMP} +.for f in ${SCRIPTS} + ${INSTALL_SCRIPT} ${INSTALL_WRKSRC}/${f} ${PREFIX}/bin + @${MV} ${INSTALL_WRKSRC}/${f} ${INSTALL_TEMP} +.endfor + ${INSTALL_PROGRAM} ${INSTALL_WRKSRC}/* ${PREFIX}/bin + ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/TTatlas* ${DATADIR} + ${INSTALL_MAN} ${DISTDIR}/${DIST_SUBDIR}/afni.1 ${PREFIX}/man/man1 + @${MV} ${INSTALL_TEMP}/* ${INSTALL_WRKSRC} +.if !defined(NOPORTDOCS) + ${MKDIR} ${DOCSDIR} + ${INSTALL_DATA} ${WRKDIR}/afni_doc/* ${DOCSDIR} +.endif + +post-install: + @${CAT} ${WRKDIR}/pkg-message + +.include <bsd.port.mk> diff --git a/science/afni/distinfo b/science/afni/distinfo new file mode 100644 index 000000000000..736740a02058 --- /dev/null +++ b/science/afni/distinfo @@ -0,0 +1,18 @@ +MD5 (AFNI/afni_src.tgz) = e6daf296ad9c5dd0284239e934ea701e +SHA256 (AFNI/afni_src.tgz) = 949a6960e89f2b140207e61fd45b265b03232c4956aaa57271779dcd492aff89 +SIZE (AFNI/afni_src.tgz) = 10512539 +MD5 (AFNI/afni_doc.tgz) = 3b085de85fc46908652ae287d1cceb38 +SHA256 (AFNI/afni_doc.tgz) = 28bfcb085d97f63a7e6b753d784908d7f90d9d3ba735d96b18c1e893af4d6cd1 +SIZE (AFNI/afni_doc.tgz) = 3267095 +MD5 (AFNI/afni.1) = 39c9a1a39b207cd957f0f0d5ec220e4e +SHA256 (AFNI/afni.1) = f14991934a8b78f2497cd1d0f48b849c1a6debef01c666eafd70993ba63c99da +SIZE (AFNI/afni.1) = 1103 +MD5 (AFNI/Makefile.FreeBSD_PORT) = 5a22ac13683686b6919415bef3784af1 +SHA256 (AFNI/Makefile.FreeBSD_PORT) = 0adbd36cedfc2dac76535fe621349a45e9812709eb5b2768427fffda9b42c628 +SIZE (AFNI/Makefile.FreeBSD_PORT) = 3002 +MD5 (AFNI/TTatlas+tlrc.BRIK.gz) = f5a107b049bc426af5342565f4e5beee +SHA256 (AFNI/TTatlas+tlrc.BRIK.gz) = 0b5b087006e07e05c5f0c8306acaade955924f744457cec0c00844cc2e9e67cd +SIZE (AFNI/TTatlas+tlrc.BRIK.gz) = 159912 +MD5 (AFNI/TTatlas+tlrc.HEAD) = a0ca787a2996d7e66548176808503ac5 +SHA256 (AFNI/TTatlas+tlrc.HEAD) = 51c3fb158990616f355fea56886fc7c85d80ac96779f5a65a8f69207c2a85919 +SIZE (AFNI/TTatlas+tlrc.HEAD) = 1750 diff --git a/science/afni/files/pkg-message.in b/science/afni/files/pkg-message.in new file mode 100644 index 000000000000..8c3b327015e3 --- /dev/null +++ b/science/afni/files/pkg-message.in @@ -0,0 +1,7 @@ +============================================================================= + +The environment variable AFNI_PLUGIN_PATH must contain +%%PREFIX%%/lib:%%PREFIX%%/share/afni +in order to run AFNI plugins and view splash images. + +============================================================================= diff --git a/science/afni/pkg-descr b/science/afni/pkg-descr new file mode 100644 index 000000000000..537fa54dae7b --- /dev/null +++ b/science/afni/pkg-descr @@ -0,0 +1,7 @@ +This is a port of AFNI, Advanced Functional Neuro Imaging. AFNI is +a tool for analyzing 3 dimensional images, especially functional MRI +images used in brain mapping research. + +WWW: http://afni.nimh.nih.gov/ + +-- Jason W. Bacon <bacon@smithers.neuro.mcw.edu> diff --git a/science/afni/pkg-plist b/science/afni/pkg-plist new file mode 100644 index 000000000000..79d7c557e25c --- /dev/null +++ b/science/afni/pkg-plist @@ -0,0 +1,578 @@ +bin/1dcat +bin/1ddot +bin/1deval +bin/1dfft +bin/1dgrayplot +bin/1dnorm +bin/1dplot +bin/1dsum +bin/1dsvd +bin/1dtranspose +bin/24swap +bin/2dImReg +bin/2swap +bin/3T_toafni +bin/3dAFNIto3D +bin/3dAFNItoANALYZE +bin/3dAFNItoMINC +bin/3dAFNItoNIFTI +bin/3dAFNItoNIML +bin/3dAFNItoRaw +bin/3dANALYZEtoAFNI +bin/3dANOVA +bin/3dANOVA2 +bin/3dANOVA3 +bin/3dAnatNudge +bin/3dAnhist +bin/3dAttribute +bin/3dAutoTcorrelate +bin/3dAutobox +bin/3dAutomask +bin/3dBRAIN_VOYAGERtoAFNI +bin/3dCM +bin/3dCRUISEtoAFNI +bin/3dClipLevel +bin/3dConvolve +bin/3dDTeig +bin/3dDWItoDT +bin/3dDeconvolve +bin/3dDeconvolve_f +bin/3dDespike +bin/3dDetrend +bin/3dEntropy +bin/3dExtrema +bin/3dFDR +bin/3dFWHM +bin/3dFourier +bin/3dFriedman +bin/3dIntracranial +bin/3dKruskalWallis +bin/3dLRflip +bin/3dLocalstat +bin/3dMINCtoAFNI +bin/3dMannWhitney +bin/3dMax +bin/3dMean +bin/3dMedianFilter +bin/3dNLfim +bin/3dNotes +bin/3dOverlap +bin/3dROIstats +bin/3dRegAna +bin/3dRowFillin +bin/3dSkullStrip +bin/3dSpatNorm +bin/3dStatClust +bin/3dSurf2Vol +bin/3dSurfMask +bin/3dTSgen +bin/3dTagalign +bin/3dTcat +bin/3dTcorrelate +bin/3dThreetoRGB +bin/3dToutcount +bin/3dTqual +bin/3dTshift +bin/3dTsmooth +bin/3dTstat +bin/3dUndump +bin/3dUniformize +bin/3dVol2Surf +bin/3dWarp +bin/3dWarpDrive +bin/3dWavelets +bin/3dWilcoxon +bin/3dWinsor +bin/3dZcat +bin/3dZcutup +bin/3dZeropad +bin/3dZregrid +bin/3danisosmooth +bin/3daxialize +bin/3dbuc2fim +bin/3dbucket +bin/3dcalc +bin/3dclust +bin/3dcopy +bin/3ddelay +bin/3ddot +bin/3ddup +bin/3dedge3 +bin/3dfim +bin/3dfim+ +bin/3dfractionize +bin/3dhistog +bin/3dinfo +bin/3dmaskave +bin/3dmaskdump +bin/3dmaxima +bin/3dmerge +bin/3dnewid +bin/3dnoise +bin/3dnvals +bin/3dpc +bin/3dproject +bin/3drefit +bin/3drename +bin/3dresample +bin/3dretroicor +bin/3drotate +bin/3dttest +bin/3dvolreg +bin/4swap +bin/AlphaSim +bin/CompareSurfaces +bin/ConvertDset +bin/ConvertSurface +bin/ConvexHull +bin/CreateIcosahedron +bin/DTIStudioFibertoSegments +bin/Dimon +bin/FD2 +bin/FSread_annot +bin/Ifile +bin/Imon +bin/IsoSurface +bin/MakeColorMap +bin/MapIcosahedron +bin/ROI2dataset +bin/ROIgrow +bin/RSFgen +bin/SUMA_glxdino +bin/SUMA_paperplane +bin/SUMA_pixmap2eps +bin/SampBias +bin/ScaleToMap +bin/SurfClust +bin/SurfMeasures +bin/SurfPatch +bin/SurfQual +bin/SurfSmooth +bin/SurfToSurf +bin/SurfaceMetrics +bin/Vecwarp +bin/Xphace +bin/abut +bin/adwarp +bin/afni +bin/afni_vcheck +bin/aiv +bin/byteorder +bin/cat_matvec +bin/ccalc +bin/cdf +bin/count +bin/dicom_hdr +bin/dicom_to_raw +bin/ent16 +bin/fftest +bin/file_tool +bin/fim2 +bin/float_scan +bin/from3d +bin/ftosh +bin/ge_header +bin/im2niml +bin/imand +bin/imaver +bin/imcalc +bin/imcutup +bin/imdump +bin/immask +bin/imreg +bin/imrotate +bin/imstack +bin/imstat +bin/imupsam +bin/inspec +bin/mayo_analyze +bin/mpegtoppm +bin/mritopgm +bin/myget +bin/nicat +bin/nifti1_test +bin/nifti_stats +bin/nifti_tool +bin/nsize +bin/p2t +bin/plugout_drive +bin/plugout_ijk +bin/plugout_tt +bin/plugout_tta +bin/qhull +bin/quickspec +bin/rmz +bin/rotcom +bin/rtfeedme +bin/serial_helper +bin/sfim +bin/siemens_vision +bin/sqwave +bin/strblast +bin/suma +bin/tfim +bin/to3d +bin/waver +bin/whereami +include/3ddata.h +include/afni_environ.h +include/afni_warp.h +include/cdflib.h +include/coxplot.h +include/cs.h +include/cs_sort_template.h +include/editvol.h +include/eispack.h +include/f2c.h +include/killer.h +include/machdep.h +include/mcw_glob.h +include/mcw_malloc.h +include/mrilib.h +include/multivector.h +include/niml.h +include/tagset.h +include/thd_compress.h +include/thd_iochan.h +include/thd_maker.h +include/vecmat.h +include/vol2surf.h +include/volpack.h +lib/libSUMA.a +lib/libcoxplot.a +lib/libmri.a +lib/libmrix.a +lib/libvolpack.a +lib/model_beta.so +lib/model_constant.so +lib/model_convgamma.so +lib/model_convgamma2a.so +lib/model_diffexp.so +lib/model_diffusion.so +lib/model_gammavar.so +lib/model_linear.so +lib/model_null.so +lib/model_quadratic.so +lib/model_sinewave_ap.so +lib/model_sinewave_apf.so +lib/model_squarewave_ap.so +lib/model_squarewave_apf.so +lib/model_trnglwave_ap.so +lib/model_trnglwave_apf.so +lib/plug_3Ddump_V2.so +lib/plug_3ddot.so +lib/plug_3ddup.so +lib/plug_4Ddump.so +lib/plug_L1fit.so +lib/plug_betafit.so +lib/plug_clust.so +lib/plug_compress.so +lib/plug_coorder.so +lib/plug_copy.so +lib/plug_crender.so +lib/plug_deconvolve.so +lib/plug_delay_V2.so +lib/plug_drawdset.so +lib/plug_edit.so +lib/plug_extract.so +lib/plug_fourier.so +lib/plug_hemisub.so +lib/plug_histog.so +lib/plug_imreg.so +lib/plug_lsqfit.so +lib/plug_maskave.so +lib/plug_maskcalc.so +lib/plug_maxima.so +lib/plug_nlfit.so +lib/plug_notes.so +lib/plug_nth_dataset.so +lib/plug_nudge.so +lib/plug_permtest.so +lib/plug_power.so +lib/plug_realtime.so +lib/plug_rename.so +lib/plug_render.so +lib/plug_reorder.so +lib/plug_retroicor.so +lib/plug_roiedit.so +lib/plug_roiplot.so +lib/plug_scatplot.so +lib/plug_second_dataset.so +lib/plug_stats.so +lib/plug_stavg.so +lib/plug_tag.so +lib/plug_threshold.so +lib/plug_ttget.so +lib/plug_vol2surf.so +lib/plug_volreg.so +lib/plug_wavelets.so +lib/plug_zeropad.so +%%DATADIR%%/TTatlas+tlrc.BRIK.gz +%%DATADIR%%/TTatlas+tlrc.HEAD +%%DATADIR%%/face_JimEliassen.jpg +%%DATADIR%%/face_JohannaBaas.jpg +%%DATADIR%%/face_SalloumJB.jpg +%%DATADIR%%/face_ZangYF.jpg +%%DATADIR%%/face_aclark.jpg +%%DATADIR%%/face_adij_mannheim.jpg +%%DATADIR%%/face_afniman.jpg +%%DATADIR%%/face_agoldman.jpg +%%DATADIR%%/face_ahammett.jpg +%%DATADIR%%/face_anewmanetal.jpg +%%DATADIR%%/face_anugent.jpg +%%DATADIR%%/face_asanders.jpg +%%DATADIR%%/face_ashackman.jpg +%%DATADIR%%/face_athomas.jpg +%%DATADIR%%/face_bandettini.jpg +%%DATADIR%%/face_barbaracd.jpg +%%DATADIR%%/face_bargall.jpg +%%DATADIR%%/face_bea.jpg +%%DATADIR%%/face_becky.jpg +%%DATADIR%%/face_bmcnamee.jpg +%%DATADIR%%/face_bodurka.jpg +%%DATADIR%%/face_bprogers.jpg +%%DATADIR%%/face_bridget.jpg +%%DATADIR%%/face_brodmann.jpg +%%DATADIR%%/face_browndyke.jpg +%%DATADIR%%/face_carol.jpg +%%DATADIR%%/face_cbikle.jpg +%%DATADIR%%/face_claudio.jpg +%%DATADIR%%/face_cmoritz.jpg +%%DATADIR%%/face_cmyers.jpg +%%DATADIR%%/face_csenior.jpg +%%DATADIR%%/face_cwettig.jpg +%%DATADIR%%/face_dglen.jpg +%%DATADIR%%/face_einstein.jpg +%%DATADIR%%/face_eli.jpg +%%DATADIR%%/face_ernv.jpg +%%DATADIR%%/face_eteoh.jpg +%%DATADIR%%/face_faustalui.jpg +%%DATADIR%%/face_ftam.jpg +%%DATADIR%%/face_gambero.jpg +%%DATADIR%%/face_gangchen.jpg +%%DATADIR%%/face_gganis.jpg +%%DATADIR%%/face_ggiulietti.jpg +%%DATADIR%%/face_glarkin.jpg +%%DATADIR%%/face_grant.jpg +%%DATADIR%%/face_hanlon.jpg +%%DATADIR%%/face_heekeren.jpg +%%DATADIR%%/face_hoffmangobbini.jpg +%%DATADIR%%/face_ibitter.jpg +%%DATADIR%%/face_ilevy.jpg +%%DATADIR%%/face_imukai.jpg +%%DATADIR%%/face_jbinder.jpg +%%DATADIR%%/face_jbjork.jpg +%%DATADIR%%/face_jchoi.jpg +%%DATADIR%%/face_jigokudani.jpg +%%DATADIR%%/face_jkurata.jpg +%%DATADIR%%/face_jskipper.jpg +%%DATADIR%%/face_jweisberg.jpg +%%DATADIR%%/face_kastnerlab.jpg +%%DATADIR%%/face_kebb.jpg +%%DATADIR%%/face_kkwong.jpg +%%DATADIR%%/face_kropella.jpg +%%DATADIR%%/face_kschreiber.jpg +%%DATADIR%%/face_kuba.jpg +%%DATADIR%%/face_lask.jpg +%%DATADIR%%/face_laura.jpg +%%DATADIR%%/face_lincoln1.jpg +%%DATADIR%%/face_lincoln2.jpg +%%DATADIR%%/face_lindachao.jpg +%%DATADIR%%/face_lizyoder.jpg +%%DATADIR%%/face_ljcox.jpg +%%DATADIR%%/face_llatour.jpg +%%DATADIR%%/face_lmccall.jpg +%%DATADIR%%/face_locikidsucsd.jpg +%%DATADIR%%/face_lukas.jpg +%%DATADIR%%/face_mamann.jpg +%%DATADIR%%/face_maxwell.jpg +%%DATADIR%%/face_mbeauchamp.jpg +%%DATADIR%%/face_mbelmonte.jpg +%%DATADIR%%/face_megcrew.jpg +%%DATADIR%%/face_mgarolera.jpg +%%DATADIR%%/face_mkenney.jpg +%%DATADIR%%/face_mmaieron.jpg +%%DATADIR%%/face_mmk.jpg +%%DATADIR%%/face_mpinsk.jpg +%%DATADIR%%/face_mruppe.jpg +%%DATADIR%%/face_mscohen.jpg +%%DATADIR%%/face_notspm.jpg +%%DATADIR%%/face_pchristidis.jpg +%%DATADIR%%/face_phoebechan.jpg +%%DATADIR%%/face_prowser.jpg +%%DATADIR%%/face_psfb.jpg +%%DATADIR%%/face_qiulin.jpg +%%DATADIR%%/face_rabeauchamp.jpg +%%DATADIR%%/face_rbirn.jpg +%%DATADIR%%/face_rhammett.jpg +%%DATADIR%%/face_rhenderson.jpg +%%DATADIR%%/face_rhoge.jpg +%%DATADIR%%/face_richd.jpg +%%DATADIR%%/face_rjsquirrel.jpg +%%DATADIR%%/face_rprost.jpg +%%DATADIR%%/face_rreynolds.jpg +%%DATADIR%%/face_rwcox.jpg +%%DATADIR%%/face_rwcox2.jpg +%%DATADIR%%/face_rwcox3.jpg +%%DATADIR%%/face_rwcox4.jpg +%%DATADIR%%/face_rwcox5.jpg +%%DATADIR%%/face_rwcox6.jpg +%%DATADIR%%/face_saccanch.jpg +%%DATADIR%%/face_sjapee.jpg +%%DATADIR%%/face_skammy.jpg +%%DATADIR%%/face_skapdoskar.jpg +%%DATADIR%%/face_smarrett.jpg +%%DATADIR%%/face_ssaad.jpg +%%DATADIR%%/face_ssmall.jpg +%%DATADIR%%/face_steverao.jpg +%%DATADIR%%/face_tieshan.jpg 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