Index: head/science/massxpert/Makefile =================================================================== --- head/science/massxpert/Makefile (revision 309043) +++ head/science/massxpert/Makefile (revision 309044) @@ -1,26 +1,34 @@ -# New ports collection makefile for: massxpert -# Date created: 2010-05-14 -# Whom: Gvozdikov Veniamin -# +# Created by: Gvozdikov Veniamin # $FreeBSD$ -# PORTNAME= massxpert -PORTVERSION= 3.1.0 -PORTREVISION= 1 +PORTVERSION= 3.3.0 CATEGORIES= science MASTER_SITES= http://download.tuxfamily.org/massxpert/source/ MAINTAINER= g.veniamin@googlemail.com COMMENT= The massXpert software for (bio)chemists +LIB_DEPENDS= pthread-stubs:${PORTSDIR}/devel/libpthread-stubs \ + pcre:${PORTSDIR}/devel/pcre \ + png15:${PORTSDIR}/graphics/png \ + freetype:${PORTSDIR}/print/freetype2 \ + expat:${PORTSDIR}/textproc/expat2 \ + fontconfig:${PORTSDIR}/x11-fonts/fontconfig \ + xcb:${PORTSDIR}/x11/libxcb + LICENSE= GPLv3 USE_CMAKE= yes -USE_LDCONFIG= yes -USE_QT4= gui xml rcc_build qmake_build uic_build moc_build \ +USE_GETTEXT= yes +USE_ICONV= yes +USE_XORG= ice sm x11 xau xdmcp xext xrender +USE_GNOME= glib20 +USE_QT4= corelib gui xml rcc_build qmake_build uic_build moc_build \ svg +USE_LDCONFIG= yes +MAKE_JOBS_UNSAFE= yes MAN7= massxpert-data.7 MAN1= massxpert.1 .include Index: head/science/massxpert/distinfo =================================================================== --- head/science/massxpert/distinfo (revision 309043) +++ head/science/massxpert/distinfo (revision 309044) @@ -1,2 +1,2 @@ -SHA256 (massxpert-3.1.0.tar.gz) = b9b60b19b71362e2907cd92c220021061c8b912ba8965e88379ffb552411c5bb -SIZE (massxpert-3.1.0.tar.gz) = 14827138 +SHA256 (massxpert-3.3.0.tar.gz) = eed640a43825ab58dc47cad93831a767c574c93f9ee3aa37e621beb2a999177f +SIZE (massxpert-3.3.0.tar.gz) = 16853069 Index: head/science/massxpert/pkg-descr =================================================================== --- head/science/massxpert/pkg-descr (revision 309043) +++ head/science/massxpert/pkg-descr (revision 309044) @@ -1,20 +1,20 @@ The massXpert project aims at providing (bio)chemists with a software package allowing the following: * User-specific atom definitions and polymer chemistry definitions; * Powerful sequence editing with user-defined glyphs for each monomer and monomer chemical modification. Multi-region selections; * Polymer sequence chemical/enzymatic cleavage; * Intramolecular cross-linking, like disulfide bonds with total resolution of the peptides generated upon enzymatic cleavage; * Gas-phase fragmentation of oligomers; * Mass-to-charge ratio calculations with inline change of ionization agent; * Calculation of net electrical charge and of isoelectric point (even by taking into account monomer modifications if polymer is a protein); * Simulation of isotopic patterns for any chemical formula and z charge; * A number of plugins allow 1) translation of the sequence from one format to another (using a dictionary, like between the 1-letter code and the 3-letter code of proteins) 2) conversion of number format according to any localized number format 3) sort mass lists. -WWW: http://massxpert.org/ +WWW: http://massxpert.org/ Index: head/science/massxpert/pkg-plist =================================================================== --- head/science/massxpert/pkg-plist (revision 309043) +++ head/science/massxpert/pkg-plist (revision 309044) @@ -1,222 +1,223 @@ bin/massxpert lib/massxpert/plugins/libmassListSorterPlugin.so lib/massxpert/plugins/libseqToolsPlugin.so lib/massxpert/plugins/libnumeralsLocaleConverterPlugin.so %%DOCSDIR%%/COPYING share/applications/massxpert.desktop %%DATADIR%%/locales/massxpert_fr.qm %%DATADIR%%/pol-chem-defs/dna/adenine.svg %%DATADIR%%/pol-chem-defs/dna/biotlink.svg %%DATADIR%%/pol-chem-defs/dna/chem_pad.conf %%DATADIR%%/pol-chem-defs/dna/cross_linker_dictionary %%DATADIR%%/pol-chem-defs/dna/cursor.svg %%DATADIR%%/pol-chem-defs/dna/cytosine.svg %%DATADIR%%/pol-chem-defs/dna/default-cross-link-vignette.svg %%DATADIR%%/pol-chem-defs/dna/default-modif-vignette.svg %%DATADIR%%/pol-chem-defs/dna/diphospho.svg %%DATADIR%%/pol-chem-defs/dna/dna.xml %%DATADIR%%/pol-chem-defs/dna/guanine.svg %%DATADIR%%/pol-chem-defs/dna/methyl.svg %%DATADIR%%/pol-chem-defs/dna/modification_dictionary %%DATADIR%%/pol-chem-defs/dna/monomer_dictionary %%DATADIR%%/pol-chem-defs/dna/oxidation.svg %%DATADIR%%/pol-chem-defs/dna/phospho.svg %%DATADIR%%/pol-chem-defs/dna/ps-adenine.svg %%DATADIR%%/pol-chem-defs/dna/ps-cytosine.svg %%DATADIR%%/pol-chem-defs/dna/ps-guanine.svg %%DATADIR%%/pol-chem-defs/dna/ps-thymine.svg %%DATADIR%%/pol-chem-defs/dna/thymine-dimer.svg %%DATADIR%%/pol-chem-defs/dna/thymine.svg %%DATADIR%%/pol-chem-defs/dna/uracile.svg %%DATADIR%%/pol-chem-defs/massxpert-pol-chem-defs-cat %%DATADIR%%/pol-chem-defs/nucac/biotlink.svg %%DATADIR%%/pol-chem-defs/nucac/chem_pad.conf %%DATADIR%%/pol-chem-defs/nucac/cross_linker_dictionary %%DATADIR%%/pol-chem-defs/nucac/cursor.svg %%DATADIR%%/pol-chem-defs/nucac/dadenine.svg %%DATADIR%%/pol-chem-defs/nucac/dcytosine.svg %%DATADIR%%/pol-chem-defs/nucac/default-cross-link-vignette.svg %%DATADIR%%/pol-chem-defs/nucac/default-modif-vignette.svg %%DATADIR%%/pol-chem-defs/nucac/dguanine.svg %%DATADIR%%/pol-chem-defs/nucac/diphospho.svg %%DATADIR%%/pol-chem-defs/nucac/dthymine.svg %%DATADIR%%/pol-chem-defs/nucac/methyl.svg %%DATADIR%%/pol-chem-defs/nucac/modification_dictionary %%DATADIR%%/pol-chem-defs/nucac/monomer_dictionary %%DATADIR%%/pol-chem-defs/nucac/nucac.xml %%DATADIR%%/pol-chem-defs/nucac/oxidation.svg %%DATADIR%%/pol-chem-defs/nucac/phospho.svg %%DATADIR%%/pol-chem-defs/nucac/ps-dadenine.svg %%DATADIR%%/pol-chem-defs/nucac/ps-dguanine.svg %%DATADIR%%/pol-chem-defs/nucac/ps-dcytosine.svg %%DATADIR%%/pol-chem-defs/nucac/ps-dthymine.svg %%DATADIR%%/pol-chem-defs/nucac/ps-radenine.svg %%DATADIR%%/pol-chem-defs/nucac/ps-rcytosine.svg %%DATADIR%%/pol-chem-defs/nucac/ps-rguanine.svg %%DATADIR%%/pol-chem-defs/nucac/ps-ruracile.svg %%DATADIR%%/pol-chem-defs/nucac/radenine.svg %%DATADIR%%/pol-chem-defs/nucac/rcytosine.svg %%DATADIR%%/pol-chem-defs/nucac/rguanine.svg %%DATADIR%%/pol-chem-defs/nucac/ruracile.svg %%DATADIR%%/pol-chem-defs/nucac/thymine-dimer.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/acetyl.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/alanine.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/arginine.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/asparagine.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/aspartate.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/cfp-chromophore.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/chem_pad.conf %%DATADIR%%/pol-chem-defs/protein-1-letter/cross_linker_dictionary %%DATADIR%%/pol-chem-defs/protein-1-letter/cursor.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/cysteine.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/default-cross-link-vignette.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/default-modif-vignette.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/disulfidebond-cross-link.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/glutamate.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/glutamine.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/glycine.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/histidine.svg +%%DATADIR%%/pol-chem-defs/protein-1-letter/hydroxylation.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/isoleucine.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/leucine.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/lysine.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/methionine.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/modification_dictionary %%DATADIR%%/pol-chem-defs/protein-1-letter/monomer_dictionary %%DATADIR%%/pol-chem-defs/protein-1-letter/oxidation.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/pdb-code-conversion.dic %%DATADIR%%/pol-chem-defs/protein-1-letter/phenylalanine.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/phospho.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/pka_ph_pi.xml %%DATADIR%%/pol-chem-defs/protein-1-letter/proline.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/protein-1-letter.xml %%DATADIR%%/pol-chem-defs/protein-1-letter/protonloss.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/serine.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/sulfbond.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/sulpho.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/threonine.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/tryptophan.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/tyrosine.svg %%DATADIR%%/pol-chem-defs/protein-1-letter/valine.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/acetyl.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/alanine.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/arginine.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/asparagine.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/aspartate.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/chem_pad.conf %%DATADIR%%/pol-chem-defs/protein-3-letters/cross_linker_dictionary %%DATADIR%%/pol-chem-defs/protein-3-letters/cursor.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/cysteine.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/default-cross-link-vignette.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/default-modif-vignette.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/glutamate.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/glutamine.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/glycine.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/histidine.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/isoleucine.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/leucine.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/lysine.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/methionine.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/phospho.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/modification_dictionary %%DATADIR%%/pol-chem-defs/protein-3-letters/monomer_dictionary %%DATADIR%%/pol-chem-defs/protein-3-letters/oxidation.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/pdb-code-conversion.dic %%DATADIR%%/pol-chem-defs/protein-3-letters/phenylalanine.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/proline.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/protein-3-letters.xml %%DATADIR%%/pol-chem-defs/protein-3-letters/protonloss.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/serine.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/sulfbond.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/sulpho.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/threonine.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/tryptophan.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/tyrosine.svg %%DATADIR%%/pol-chem-defs/protein-3-letters/valine.svg %%DATADIR%%/pol-chem-defs/saccharide/allose-text.svg %%DATADIR%%/pol-chem-defs/saccharide/allose.svg %%DATADIR%%/pol-chem-defs/saccharide/altrose-text.svg %%DATADIR%%/pol-chem-defs/saccharide/altrose.svg %%DATADIR%%/pol-chem-defs/saccharide/arabinose-text.svg %%DATADIR%%/pol-chem-defs/saccharide/arabinose.svg %%DATADIR%%/pol-chem-defs/saccharide/chem_pad.conf %%DATADIR%%/pol-chem-defs/saccharide/cross_linker_dictionary %%DATADIR%%/pol-chem-defs/saccharide/cursor.svg %%DATADIR%%/pol-chem-defs/saccharide/default-cross-link-vignette.svg %%DATADIR%%/pol-chem-defs/saccharide/default-modif-vignette.svg %%DATADIR%%/pol-chem-defs/saccharide/erythrose-text.svg %%DATADIR%%/pol-chem-defs/saccharide/erythrose.svg %%DATADIR%%/pol-chem-defs/saccharide/erythrulose-text.svg %%DATADIR%%/pol-chem-defs/saccharide/erythrulose.svg %%DATADIR%%/pol-chem-defs/saccharide/fructose-text.svg %%DATADIR%%/pol-chem-defs/saccharide/fructose.svg %%DATADIR%%/pol-chem-defs/saccharide/galactose-text.svg %%DATADIR%%/pol-chem-defs/saccharide/galactose.svg %%DATADIR%%/pol-chem-defs/saccharide/glucose-text.svg %%DATADIR%%/pol-chem-defs/saccharide/glucose.svg %%DATADIR%%/pol-chem-defs/saccharide/gulose-text.svg %%DATADIR%%/pol-chem-defs/saccharide/gulose.svg %%DATADIR%%/pol-chem-defs/saccharide/idose-text.svg %%DATADIR%%/pol-chem-defs/saccharide/idose.svg %%DATADIR%%/pol-chem-defs/saccharide/lyxose-text.svg %%DATADIR%%/pol-chem-defs/saccharide/lyxose.svg %%DATADIR%%/pol-chem-defs/saccharide/mannose-text.svg %%DATADIR%%/pol-chem-defs/saccharide/mannose.svg %%DATADIR%%/pol-chem-defs/saccharide/methyl.svg %%DATADIR%%/pol-chem-defs/saccharide/modification_dictionary %%DATADIR%%/pol-chem-defs/saccharide/monomer_dictionary %%DATADIR%%/pol-chem-defs/saccharide/psicose-text.svg %%DATADIR%%/pol-chem-defs/saccharide/psicose.svg %%DATADIR%%/pol-chem-defs/saccharide/ribose-text.svg %%DATADIR%%/pol-chem-defs/saccharide/ribose.svg %%DATADIR%%/pol-chem-defs/saccharide/ribulose-text.svg %%DATADIR%%/pol-chem-defs/saccharide/ribulose.svg %%DATADIR%%/pol-chem-defs/saccharide/saccharide.xml %%DATADIR%%/pol-chem-defs/saccharide/sorbose-text.svg %%DATADIR%%/pol-chem-defs/saccharide/sorbose.svg %%DATADIR%%/pol-chem-defs/saccharide/tagatose-text.svg %%DATADIR%%/pol-chem-defs/saccharide/tagatose.svg %%DATADIR%%/pol-chem-defs/saccharide/talose-text.svg %%DATADIR%%/pol-chem-defs/saccharide/talose.svg %%DATADIR%%/pol-chem-defs/saccharide/template-text.svg %%DATADIR%%/pol-chem-defs/saccharide/threose-text.svg %%DATADIR%%/pol-chem-defs/saccharide/threose.svg %%DATADIR%%/pol-chem-defs/saccharide/xylose-text.svg %%DATADIR%%/pol-chem-defs/saccharide/xylose.svg %%DATADIR%%/pol-chem-defs/saccharide/xylulose-text.svg %%DATADIR%%/pol-chem-defs/saccharide/xylulose.svg %%DATADIR%%/pol-seqs/17-mer-ps-po-dna-chimera.mxp %%DATADIR%%/pol-seqs/centrin-2-human.mxp %%DATADIR%%/pol-seqs/cerulean-histag.mxp %%DATADIR%%/pol-seqs/chicken-telokin.mxp %%DATADIR%%/pol-seqs/citrin-fluorescent-protein.mxp %%DATADIR%%/pol-seqs/cyan-fluorescent-protein-h148d-histag.mxp %%DATADIR%%/pol-seqs/cyan-fluorescent-protein.mxp %%DATADIR%%/pol-seqs/horse-myoglobin.mxp %%DATADIR%%/pol-seqs/kunitz-inhibitor-human.mxp %%DATADIR%%/pol-seqs/leu-enkephalin.mxp %%DATADIR%%/pol-seqs/protein-1-letter.mxp %%DATADIR%%/pol-seqs/protein-3-letters.mxp %%DATADIR%%/pol-seqs/tev-protease-his-tag.mxp %%DATADIR%%/pol-seqs/yellow-fluorescent-protein.mxp %%DATADIR%%/pol-seqs/insulin-a-ox.mxp %%DATADIR%%/pol-seqs/insulin-b-ox.mxp %%DATADIR%%/dictionaries/codon-to-protein-1.dic %%DATADIR%%/dictionaries/codon-to-protein-3.dic %%DATADIR%%/dictionaries/pdb-protein-to-mxp.dic %%DATADIR%%/dictionaries/protein-1-to-3.dic %%DATADIR%%/dictionaries/protein-3-to-1.dic %%DATADIR%%/chem_pad.conf @dirrmtry %%DATADIR%%/pol-seqs @dirrmtry %%DATADIR%%/pol-chem-defs/saccharide @dirrmtry %%DATADIR%%/pol-chem-defs/protein-3-letters @dirrmtry %%DATADIR%%/pol-chem-defs/protein-1-letter @dirrmtry %%DATADIR%%/pol-chem-defs/nucac @dirrmtry %%DATADIR%%/pol-chem-defs/dna @dirrmtry %%DATADIR%%/pol-chem-defs @dirrmtry %%DATADIR%%/locales @dirrmtry %%DATADIR%%/dictionaries @dirrmtry share/applications @dirrmtry %%DATADIR%% @dirrm %%DOCSDIR%% @dirrm lib/massxpert/plugins @dirrm lib/massxpert