FreeBSD Bugzilla – Attachment 129408 Details for
Bug 173387
[new port] biology/ugene
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file.shar
file.shar (text/plain), 81.22 KB, created by
Hannes Hauswedell
on 2012-11-05 13:10:01 UTC
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hide
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Description:
file.shar
Filename:
MIME Type:
Creator:
Hannes Hauswedell
Created:
2012-11-05 13:10:01 UTC
Size:
81.22 KB
patch
obsolete
># This is a shell archive. Save it in a file, remove anything before ># this line, and then unpack it by entering "sh file". Note, it may ># create directories; files and directories will be owned by you and ># have default permissions. ># ># This archive contains: ># ># ugene ># ugene/files ># ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp ># ugene/pkg-plist ># ugene/pkg-descr ># ugene/distinfo ># ugene/Makefile ># >echo c - ugene >mkdir -p ugene > /dev/null 2>&1 >echo c - ugene/files >mkdir -p ugene/files > /dev/null 2>&1 >echo x - ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp >sed 's/^X//' >ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp << '0b3ccc567ca0de5a1b14a2de4497b4f6' >X--- ./src/corelibs/U2Private/src/CrashHandler.cpp.old 2012-10-30 15:36:22.000000000 +0100 >X+++ ./src/corelibs/U2Private/src/CrashHandler.cpp 2012-10-30 15:47:47.000000000 +0100 >X@@ -253,7 +253,7 @@ >X } >X //handler = AddVectoredExceptionHandler(1, CrashHandlerFunc); >X >X-#elif defined( Q_OS_MAC) >X+#elif defined( Q_OS_MAC ) || defined ( Q_OS_FREEBSD ) >X return; //TODO: implement crash hander for MAC OS >X #else >X stack_t sigstk; >X@@ -284,7 +284,7 @@ >X void CrashHandler::runMonitorProcess(const QString &exceptionType) { >X QString path = QCoreApplication::applicationDirPath() + "/ugenem"; >X >X-#ifndef Q_OS_WIN >X+#if !defined ( Q_OS_WIN ) && !defined (Q_OS_FREEBSD) >X char pid_buf[30]; >X sprintf(pid_buf, "%d", getpid()); >X char name_buf[512]; >0b3ccc567ca0de5a1b14a2de4497b4f6 >echo x - ugene/pkg-plist >sed 's/^X//' >ugene/pkg-plist << '905ed5b1d190579fce073589acbfd494' >Xbin/ugene >Xlib/ugene/libU2Algorithm.so >Xlib/ugene/libU2Core.so >Xlib/ugene/libU2Designer.so >Xlib/ugene/libU2Formats.so >Xlib/ugene/libU2Gui.so >Xlib/ugene/libU2Lang.so >Xlib/ugene/libU2Private.so >Xlib/ugene/libU2Remote.so >Xlib/ugene/libU2Test.so >Xlib/ugene/libU2View.so >Xlib/ugene/libgtest.so >Xlib/ugene/libugenedb.so >Xlib/ugene/plugins/CoreTests.plugin >Xlib/ugene/plugins/GUITestBase.plugin >Xlib/ugene/plugins/annotator.plugin >Xlib/ugene/plugins/api_tests.plugin >Xlib/ugene/plugins/ball.plugin >Xlib/ugene/plugins/biostruct3d_view.plugin >Xlib/ugene/plugins/chroma_view.plugin >Xlib/ugene/plugins/circular_view.plugin >Xlib/ugene/plugins/dbi_bam.plugin >Xlib/ugene/plugins/dna_export.plugin >Xlib/ugene/plugins/dna_flexibility.plugin >Xlib/ugene/plugins/dna_graphpack.plugin >Xlib/ugene/plugins/dna_stat.plugin >Xlib/ugene/plugins/dotplot.plugin >Xlib/ugene/plugins/enzymes.plugin >Xlib/ugene/plugins/expert_discovery.plugin >Xlib/ugene/plugins/external_tool_support.plugin >Xlib/ugene/plugins/genome_aligner.plugin >Xlib/ugene/plugins/gor4.plugin >Xlib/ugene/plugins/hmm2.plugin >Xlib/ugene/plugins/kalign.plugin >Xlib/ugene/plugins/libCoreTests.so >Xlib/ugene/plugins/libGUITestBase.so >Xlib/ugene/plugins/libannotator.so >Xlib/ugene/plugins/libapi_tests.so >Xlib/ugene/plugins/libball.so >Xlib/ugene/plugins/libbiostruct3d_view.so >Xlib/ugene/plugins/libchroma_view.so >Xlib/ugene/plugins/libcircular_view.so >Xlib/ugene/plugins/libdbi_bam.so >Xlib/ugene/plugins/libdna_export.so >Xlib/ugene/plugins/libdna_flexibility.so >Xlib/ugene/plugins/libdna_graphpack.so >Xlib/ugene/plugins/libdna_stat.so >Xlib/ugene/plugins/libdotplot.so >Xlib/ugene/plugins/libenzymes.so >Xlib/ugene/plugins/libexpert_discovery.so >Xlib/ugene/plugins/libexternal_tool_support.so >Xlib/ugene/plugins/libgenome_aligner.so >Xlib/ugene/plugins/libgor4.so >Xlib/ugene/plugins/libhmm2.so >Xlib/ugene/plugins/libkalign.so >Xlib/ugene/plugins/libopencl_support.so >Xlib/ugene/plugins/liborf_marker.so >Xlib/ugene/plugins/libperf_monitor.so >Xlib/ugene/plugins/libphylip.so >Xlib/ugene/plugins/libprimer3.so >Xlib/ugene/plugins/libpsipred.so >Xlib/ugene/plugins/libptools.so >Xlib/ugene/plugins/libquery_designer.so >Xlib/ugene/plugins/libremote_blast.so >Xlib/ugene/plugins/libremote_service.so >Xlib/ugene/plugins/librepeat_finder.so >Xlib/ugene/plugins/libsitecon.so >Xlib/ugene/plugins/libsmith_waterman.so >Xlib/ugene/plugins/libtest_runner.so >Xlib/ugene/plugins/libweight_matrix.so >Xlib/ugene/plugins/libworkflow_designer.so >Xlib/ugene/plugins/opencl_support.plugin >Xlib/ugene/plugins/orf_marker.plugin >Xlib/ugene/plugins/perf_monitor.plugin >Xlib/ugene/plugins/phylip.plugin >Xlib/ugene/plugins/primer3.plugin >Xlib/ugene/plugins/psipred.plugin >Xlib/ugene/plugins/ptools.plugin >Xlib/ugene/plugins/query_designer.plugin >Xlib/ugene/plugins/remote_blast.plugin >Xlib/ugene/plugins/remote_service.plugin >Xlib/ugene/plugins/repeat_finder.plugin >Xlib/ugene/plugins/sitecon.plugin >Xlib/ugene/plugins/smith_waterman.plugin >Xlib/ugene/plugins/test_runner.plugin >Xlib/ugene/plugins/weight_matrix.plugin >Xlib/ugene/plugins/workflow_designer.plugin >Xlib/ugene/transl_cs.qm >Xlib/ugene/transl_en.qm >Xlib/ugene/transl_ru.qm >Xlib/ugene/transl_zh.qm >Xlib/ugene/ugene >Xlib/ugene/ugenecl >Xlib/ugene/ugenem >Xlib/ugene/ugeneui >Xshare/applications/ugene.desktop >Xshare/man/man1/ugene.1.gz >Xshare/pixmaps/ugene.png >Xshare/pixmaps/ugene.xpm >Xshare/ugene/data/DBXRefRegistry.txt >Xshare/ugene/data/back_translation/Bacteria/Arthrobacter_aurescens_TC1.cut >Xshare/ugene/data/back_translation/Bacteria/Bacillus_subtilis.cut >Xshare/ugene/data/back_translation/Bacteria/Escherichia_coli.cut >Xshare/ugene/data/back_translation/Bacteria/Haemophilus_influenzae.cut >Xshare/ugene/data/back_translation/Bacteria/Helicobacter_pylori.cut >Xshare/ugene/data/back_translation/Bacteria/Listeria_monocytogenes.cut >Xshare/ugene/data/back_translation/Bacteria/Neisseria_meningitidis.cut >Xshare/ugene/data/back_translation/Bacteria/Salmonella_typhimurium_LT2.cut >Xshare/ugene/data/back_translation/Bacteria/Streptomyces_coelicolor_A3(2).cut >Xshare/ugene/data/back_translation/Bacteria/Sulfolobus_solfataricus_P2.cut >Xshare/ugene/data/back_translation/Invertebrates/Apis_mellifera_(honey_bee).cut >Xshare/ugene/data/back_translation/Invertebrates/Caenorhabditis_elegans.cut >Xshare/ugene/data/back_translation/Invertebrates/Drosophila_melanogaster_(fruit_fly).cut >Xshare/ugene/data/back_translation/Invertebrates/Plasmodium_falciparum_(malaria_parasite_P._falciparum).cut >Xshare/ugene/data/back_translation/Invertebrates/mitochondrion_Caenorhabditis_elegans.cut >Xshare/ugene/data/back_translation/Invertebrates/mitochondrion_Drosophila_melanogaster_(fruit_fly).cut >Xshare/ugene/data/back_translation/Mammalia/Bos_taurus_(cow).cut >Xshare/ugene/data/back_translation/Mammalia/Canis_familiaris_(dog).cut >Xshare/ugene/data/back_translation/Mammalia/Sus_scrofa_(pig).cut >Xshare/ugene/data/back_translation/Mammalia/mitochondrion_Bos_taurus_(cow).cut >Xshare/ugene/data/back_translation/Mammalia/mitochondrion_Sus_scrofa_(pig).cut >Xshare/ugene/data/back_translation/Plants/Arabidopsis_thaliana_(thale_cress).cut >Xshare/ugene/data/back_translation/Plants/Oryza_sativa.cut >Xshare/ugene/data/back_translation/Plants/Zea_mays.cut >Xshare/ugene/data/back_translation/Primates/Homo_sapiens_(human).cut >Xshare/ugene/data/back_translation/Primates/Pan_troglodytes_(chimpanzee).cut >Xshare/ugene/data/back_translation/Primates/mitochondrion_Homo_sapiens_(human).cut >Xshare/ugene/data/back_translation/Primates/mitochondrion_Pan_troglodytes_(chimpanzee).cut >Xshare/ugene/data/back_translation/Rodents/Mus_musculus_(house_mouse).cut >Xshare/ugene/data/back_translation/Rodents/Rattus_norvegicus_(Norway_rat).cut >Xshare/ugene/data/back_translation/Vertebrates/Gallus_gallus_(chicken).cut >Xshare/ugene/data/back_translation/Vertebrates/Takifugu_rubripes_(Fugu_rubripes).cut >Xshare/ugene/data/back_translation/Vertebrates/Xenopus_laevis_(African_clawed_frog).cut >Xshare/ugene/data/back_translation/Vertebrates/mitochondrion_Gallus_gallus_(chicken).cut >Xshare/ugene/data/back_translation/Vertebrates/mitochondrion_Takifugu_rubripes_(Fugu_rubripes).cut >Xshare/ugene/data/back_translation/Viruses/Human_immunodeficiency_virus_1_(HIV-1).cut >Xshare/ugene/data/back_translation/Viruses/Influenza_A_virus.cut >Xshare/ugene/data/back_translation/Yeast/Saccharomyces_cerevisiae_(baker's_yeast).cut >Xshare/ugene/data/back_translation/tables.xml >Xshare/ugene/data/biostruct3d_plugin/BioStruct3DLinks.txt >Xshare/ugene/data/cmdline/align-clustalw.uwl >Xshare/ugene/data/cmdline/align-kalign.uwl >Xshare/ugene/data/cmdline/align-mafft.uwl >Xshare/ugene/data/cmdline/align-tcoffee.uwl >Xshare/ugene/data/cmdline/align.uwl >Xshare/ugene/data/cmdline/bowtie-build.uwl >Xshare/ugene/data/cmdline/bowtie.uwl >Xshare/ugene/data/cmdline/convert-msa.uwl >Xshare/ugene/data/cmdline/convert-seq.uwl >Xshare/ugene/data/cmdline/extract-sequence.uwl >Xshare/ugene/data/cmdline/fetch-sequence.uwl >Xshare/ugene/data/cmdline/fetch.uwl >Xshare/ugene/data/cmdline/find-orfs.uwl >Xshare/ugene/data/cmdline/find-repeats.uwl >Xshare/ugene/data/cmdline/find-sw.uwl >Xshare/ugene/data/cmdline/generate-dna.uwl >Xshare/ugene/data/cmdline/hmm2-build.uwl >Xshare/ugene/data/cmdline/hmm2-search.uwl >Xshare/ugene/data/cmdline/join-quality.uwl >Xshare/ugene/data/cmdline/local-blast+.uwl >Xshare/ugene/data/cmdline/local-blast.uwl >Xshare/ugene/data/cmdline/pfm-build.uwl >Xshare/ugene/data/cmdline/pfm-search.uwl >Xshare/ugene/data/cmdline/pwm-build.uwl >Xshare/ugene/data/cmdline/pwm-search.uwl >Xshare/ugene/data/cmdline/query.uwl >Xshare/ugene/data/cmdline/remote-request.uwl >Xshare/ugene/data/cmdline/revcompl.uwl >Xshare/ugene/data/cmdline/sitecon-build.uwl >Xshare/ugene/data/cmdline/sitecon-search.uwl >Xshare/ugene/data/enzymes/rebase_v003_all.bairoch.gz >Xshare/ugene/data/enzymes/rebase_v003_t2_com.bairoch.gz >Xshare/ugene/data/license >Xshare/ugene/data/position_weight_matrix/JASPAR/all_jaspar.csv >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0265.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0266.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0267.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0268.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0269.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0270.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0271.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0272.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0273.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0274.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0275.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0276.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0277.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0278.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0279.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0280.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0281.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0282.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0283.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0284.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0285.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0286.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0287.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0288.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0289.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0290.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0291.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0292.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0293.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0294.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0295.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0296.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0297.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0298.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0299.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0300.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0301.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0302.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0303.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0304.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0305.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0306.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0307.1.pfm >Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0308.1.pfm 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>Xshare/ugene/data/position_weight_matrix/UniPROBE/GR09/Ypr015c.pwm >Xshare/ugene/data/position_weight_matrix/UniPROBE/GR09/Ypr196w.pwm >Xshare/ugene/data/position_weight_matrix/UniPROBE/GR09/Yrm1.pwm >Xshare/ugene/data/position_weight_matrix/UniPROBE/GR09/Yrr1.pwm >Xshare/ugene/data/position_weight_matrix/UniPROBE/NBT06/Cbf1.pwm >Xshare/ugene/data/position_weight_matrix/UniPROBE/NBT06/Ceh-22.pwm >Xshare/ugene/data/position_weight_matrix/UniPROBE/NBT06/Oct-1.pwm >Xshare/ugene/data/position_weight_matrix/UniPROBE/NBT06/Rap1.pwm >Xshare/ugene/data/position_weight_matrix/UniPROBE/NBT06/Zif268.pwm >Xshare/ugene/data/position_weight_matrix/UniPROBE/PNAS08/Cgd2_3490.pwm >Xshare/ugene/data/position_weight_matrix/UniPROBE/PNAS08/PF14_0633.pwm >Xshare/ugene/data/position_weight_matrix/UniPROBE/PNAS08/PFF0200c.pwm >Xshare/ugene/data/position_weight_matrix/UniPROBE/all_uniprobe.csv >Xshare/ugene/data/primer3/drosophila.w.transposons.txt >Xshare/ugene/data/primer3/humrep_and_simple.txt >Xshare/ugene/data/primer3/rodent_ref.txt >Xshare/ugene/data/primer3/rodrep_and_simple.txt >Xshare/ugene/data/query_samples/RepeatsWithORF.uql >Xshare/ugene/data/query_samples/SimpleGene.uql >Xshare/ugene/data/samples/ABIF/A01.abi >Xshare/ugene/data/samples/ACE/BL060C3.ace >Xshare/ugene/data/samples/ACE/K26.ace >Xshare/ugene/data/samples/Assembly/chrM.fa >Xshare/ugene/data/samples/Assembly/chrM.sam >Xshare/ugene/data/samples/Assembly/chrM.sorted.bam >Xshare/ugene/data/samples/CLUSTALW/COI.aln >Xshare/ugene/data/samples/CLUSTALW/HIV-1.aln >Xshare/ugene/data/samples/CLUSTALW/ty3.aln.gz >Xshare/ugene/data/samples/EMBL/AF177870.emb >Xshare/ugene/data/samples/EMBL/AL000263.emb >Xshare/ugene/data/samples/FASTA/human_T1.fa >Xshare/ugene/data/samples/FASTQ/eas.fastq >Xshare/ugene/data/samples/GFF/5prime_utr_intron_A20.gff >Xshare/ugene/data/samples/GFF/5prime_utr_intron_A21.gff >Xshare/ugene/data/samples/Genbank/CVU55762.gb >Xshare/ugene/data/samples/Genbank/NC_014267.1.gb >Xshare/ugene/data/samples/Genbank/PBR322.gb >Xshare/ugene/data/samples/Genbank/murine.gb >Xshare/ugene/data/samples/Genbank/sars.gb >Xshare/ugene/data/samples/HMM/aligment15900.hmm >Xshare/ugene/data/samples/MMDB/1CRN.prt >Xshare/ugene/data/samples/MMDB/2JQS.prt >Xshare/ugene/data/samples/MSF/HMA.msf >Xshare/ugene/data/samples/MSF/lipid8.msf >Xshare/ugene/data/samples/MSF/pla2_20.msf >Xshare/ugene/data/samples/Newick/COI.nwk >Xshare/ugene/data/samples/PDB/1CF7.PDB >Xshare/ugene/data/samples/PDB/1CRN.PDB >Xshare/ugene/data/samples/PDB/3INS.PDB >Xshare/ugene/data/samples/Raw/raw.seq >Xshare/ugene/data/samples/SCF/90-JRI-07.scf >Xshare/ugene/data/samples/Stockholm/CBS.sto >Xshare/ugene/data/samples/Stockholm/UPSK.sto >Xshare/ugene/data/samples/Swiss-Prot/D0VTW9.txt >Xshare/ugene/data/samples/Swiss-Prot/P01375.txt >Xshare/ugene/data/samples/Swiss-Prot/P16152.txt >Xshare/ugene/data/sitecon_models/eukaryotic/CEBP_a.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/CEBPall.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/CLOCK.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/CRE.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/E2F1.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/E2F1DP1sel1.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/EGR1.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/Eklf.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/GATA1.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/GATA_ALL.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/Gata2.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/Gata3.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/HMG1.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/HNF1.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/HNF3_4.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/HNF4.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/MYOGsel3.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/MyoD.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/NF1.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/NFATp.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/NFkB_all.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/NFkB_hetero.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/NFkB_homo.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/Nf_e2.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/Nrf2.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/Oct1.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/Oct_all.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/PPRE.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/Pu1.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/SRE_can.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/STAT.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/STAT1.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/TTF1.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/USF.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/cMyc_can.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/er2.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/irf.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/isre.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/nfy.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/p53.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/setCREB.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/setCREBzag.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/srf_all.sitecon.gz >Xshare/ugene/data/sitecon_models/eukaryotic/yy1.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/AgaR.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/AraC.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/ArcA.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/ArgR.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/CpxR.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/Crp.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/CysB.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/CytR.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/DeoR.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/DnaA.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/FUR.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/FadR.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/FlhDC.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/Fnr.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/Frur.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/GALR.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/GALS.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/GLPR.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/GNTR.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/HNS.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/ICLR.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/IHF.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/ISCR1.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/ISCR3.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/LEXA.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/Lrp.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/MALT.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/MARA.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/MELR.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/MLC.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/MODE.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/MetJ.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/MetR1.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/NAC.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/NAGC_new2.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/NANR.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/NARL2.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/NARP.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/NTRC.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/NarL.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/OmpR.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/OxyR.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/PHOB.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/PHOP.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/PurR.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/ROB.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/RcsB_1core.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/RcsB_2core.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/Rob2.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/TORR.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/TRPR.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/TyrR.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/fis_new1.sitecon.gz >Xshare/ugene/data/sitecon_models/prokaryotic/soxS.sitecon.gz >Xshare/ugene/data/translations.txt >Xshare/ugene/data/weight_matrix/blosum100.txt >Xshare/ugene/data/weight_matrix/blosum30.txt >Xshare/ugene/data/weight_matrix/blosum35.txt >Xshare/ugene/data/weight_matrix/blosum40.txt >Xshare/ugene/data/weight_matrix/blosum45.txt >Xshare/ugene/data/weight_matrix/blosum50.txt >Xshare/ugene/data/weight_matrix/blosum55.txt >Xshare/ugene/data/weight_matrix/blosum60.txt >Xshare/ugene/data/weight_matrix/blosum62.txt >Xshare/ugene/data/weight_matrix/blosum65.txt >Xshare/ugene/data/weight_matrix/blosum70.txt >Xshare/ugene/data/weight_matrix/blosum75.txt >Xshare/ugene/data/weight_matrix/blosum80.txt >Xshare/ugene/data/weight_matrix/blosum85.txt >Xshare/ugene/data/weight_matrix/blosum90.txt >Xshare/ugene/data/weight_matrix/blosumn.txt >Xshare/ugene/data/weight_matrix/dayhoff.txt >Xshare/ugene/data/weight_matrix/dna.txt >Xshare/ugene/data/weight_matrix/gonnet.txt >Xshare/ugene/data/weight_matrix/identity.txt >Xshare/ugene/data/weight_matrix/match.txt >Xshare/ugene/data/weight_matrix/md_10.txt >Xshare/ugene/data/weight_matrix/md_20.txt >Xshare/ugene/data/weight_matrix/md_40.txt >Xshare/ugene/data/weight_matrix/nuc.4.4.txt >Xshare/ugene/data/weight_matrix/pam10.txt >Xshare/ugene/data/weight_matrix/pam100.txt >Xshare/ugene/data/weight_matrix/pam110.txt >Xshare/ugene/data/weight_matrix/pam120.cdi.txt >Xshare/ugene/data/weight_matrix/pam120.txt >Xshare/ugene/data/weight_matrix/pam130.txt >Xshare/ugene/data/weight_matrix/pam140.txt >Xshare/ugene/data/weight_matrix/pam150.txt >Xshare/ugene/data/weight_matrix/pam160.cdi.txt >Xshare/ugene/data/weight_matrix/pam160.txt >Xshare/ugene/data/weight_matrix/pam170.txt >Xshare/ugene/data/weight_matrix/pam180.txt >Xshare/ugene/data/weight_matrix/pam190.txt >Xshare/ugene/data/weight_matrix/pam20.txt >Xshare/ugene/data/weight_matrix/pam200.cdi.txt >Xshare/ugene/data/weight_matrix/pam200.txt >Xshare/ugene/data/weight_matrix/pam210.txt >Xshare/ugene/data/weight_matrix/pam220.txt >Xshare/ugene/data/weight_matrix/pam230.txt >Xshare/ugene/data/weight_matrix/pam240.txt >Xshare/ugene/data/weight_matrix/pam250.cdi.txt >Xshare/ugene/data/weight_matrix/pam250.txt >Xshare/ugene/data/weight_matrix/pam260.txt >Xshare/ugene/data/weight_matrix/pam270.txt >Xshare/ugene/data/weight_matrix/pam280.txt >Xshare/ugene/data/weight_matrix/pam290.txt >Xshare/ugene/data/weight_matrix/pam30.txt >Xshare/ugene/data/weight_matrix/pam300.txt >Xshare/ugene/data/weight_matrix/pam310.txt >Xshare/ugene/data/weight_matrix/pam320.txt >Xshare/ugene/data/weight_matrix/pam330.txt >Xshare/ugene/data/weight_matrix/pam340.txt >Xshare/ugene/data/weight_matrix/pam350.txt >Xshare/ugene/data/weight_matrix/pam360.txt >Xshare/ugene/data/weight_matrix/pam370.txt >Xshare/ugene/data/weight_matrix/pam380.txt >Xshare/ugene/data/weight_matrix/pam390.txt >Xshare/ugene/data/weight_matrix/pam40.cdi.txt >Xshare/ugene/data/weight_matrix/pam40.txt >Xshare/ugene/data/weight_matrix/pam400.txt >Xshare/ugene/data/weight_matrix/pam410.txt >Xshare/ugene/data/weight_matrix/pam420.txt >Xshare/ugene/data/weight_matrix/pam430.txt >Xshare/ugene/data/weight_matrix/pam440.txt >Xshare/ugene/data/weight_matrix/pam450.txt >Xshare/ugene/data/weight_matrix/pam460.txt >Xshare/ugene/data/weight_matrix/pam470.txt >Xshare/ugene/data/weight_matrix/pam480.txt >Xshare/ugene/data/weight_matrix/pam490.txt >Xshare/ugene/data/weight_matrix/pam50.txt >Xshare/ugene/data/weight_matrix/pam500.txt >Xshare/ugene/data/weight_matrix/pam60.txt >Xshare/ugene/data/weight_matrix/pam70.txt >Xshare/ugene/data/weight_matrix/pam80.cdi.txt >Xshare/ugene/data/weight_matrix/pam80.txt >Xshare/ugene/data/weight_matrix/pam90.txt >Xshare/ugene/data/weight_matrix/rna.txt >Xshare/ugene/data/weight_matrix/vtml160.txt >Xshare/ugene/data/weight_matrix/vtml200.txt >Xshare/ugene/data/workflow_samples/Alignment/basic_align.uwl >Xshare/ugene/data/workflow_samples/Conversions/faqual2fastq.uwl >Xshare/ugene/data/workflow_samples/Conversions/msa2clustal.uwl >Xshare/ugene/data/workflow_samples/Conversions/query2alignment.uwl >Xshare/ugene/data/workflow_samples/Conversions/seq2gen.uwl >Xshare/ugene/data/workflow_samples/Custom elements/script-dump-sequence-info.uwl >Xshare/ugene/data/workflow_samples/Custom elements/script-quality-filter.uwl >Xshare/ugene/data/workflow_samples/Data marking/annotation_marker.uwl >Xshare/ugene/data/workflow_samples/Data marking/length_marker.uwl >Xshare/ugene/data/workflow_samples/Data merging/find-substrings.uwl >Xshare/ugene/data/workflow_samples/Data merging/merge-sequence.uwl >Xshare/ugene/data/workflow_samples/Data merging/tfbs.uwl >Xshare/ugene/data/workflow_samples/HMMER/build-test-HMM.uwl >Xshare/ugene/data/workflow_samples/HMMER/searchHMM.uwl >Xshare/ugene/data/workflow_samples/Transcriptomics/SearchTFBS.uwl >Xshare/ugene/data/workflow_samples/users/CreateAlignment.usa >Xshare/ugene/data/workflow_samples/users/Dump sequence info.usa >Xshare/ugene/data/workflow_samples/users/QualityFilter.usa >X@dirrm share/ugene/data/workflow_samples/users >X@dirrm share/ugene/data/workflow_samples/Transcriptomics >X@dirrm share/ugene/data/workflow_samples/HMMER >X@dirrm share/ugene/data/workflow_samples/Data merging >X@dirrm share/ugene/data/workflow_samples/Data marking >X@dirrm share/ugene/data/workflow_samples/Custom elements >X@dirrm share/ugene/data/workflow_samples/Conversions >X@dirrm share/ugene/data/workflow_samples/Alignment >X@dirrm share/ugene/data/workflow_samples >X@dirrm share/ugene/data/weight_matrix >X@dirrm share/ugene/data/sitecon_models/prokaryotic >X@dirrm share/ugene/data/sitecon_models/eukaryotic >X@dirrm share/ugene/data/sitecon_models >X@dirrm share/ugene/data/samples/Swiss-Prot >X@dirrm share/ugene/data/samples/Stockholm >X@dirrm share/ugene/data/samples/SCF >X@dirrm share/ugene/data/samples/Raw >X@dirrm share/ugene/data/samples/PDB >X@dirrm share/ugene/data/samples/Newick >X@dirrm share/ugene/data/samples/MSF >X@dirrm share/ugene/data/samples/MMDB >X@dirrm share/ugene/data/samples/HMM >X@dirrm share/ugene/data/samples/Genbank >X@dirrm share/ugene/data/samples/GFF >X@dirrm share/ugene/data/samples/FASTQ >X@dirrm share/ugene/data/samples/FASTA >X@dirrm share/ugene/data/samples/EMBL >X@dirrm share/ugene/data/samples/CLUSTALW >X@dirrm share/ugene/data/samples/Assembly >X@dirrm share/ugene/data/samples/ACE >X@dirrm share/ugene/data/samples/ABIF >X@dirrm share/ugene/data/samples >X@dirrm share/ugene/data/query_samples >X@dirrm share/ugene/data/primer3 >X@dirrm share/ugene/data/position_weight_matrix/UniPROBE/PNAS08 >X@dirrm share/ugene/data/position_weight_matrix/UniPROBE/NBT06 >X@dirrm share/ugene/data/position_weight_matrix/UniPROBE/GR09 >X@dirrm share/ugene/data/position_weight_matrix/UniPROBE/Cell08 >X@dirrm share/ugene/data/position_weight_matrix/UniPROBE >X@dirrm share/ugene/data/position_weight_matrix/JASPAR/vertebrates >X@dirrm share/ugene/data/position_weight_matrix/JASPAR/urochordates >X@dirrm share/ugene/data/position_weight_matrix/JASPAR/plants >X@dirrm share/ugene/data/position_weight_matrix/JASPAR/nematodes >X@dirrm share/ugene/data/position_weight_matrix/JASPAR/insects >X@dirrm share/ugene/data/position_weight_matrix/JASPAR/fungi >X@dirrm share/ugene/data/position_weight_matrix/JASPAR >X@dirrm share/ugene/data/position_weight_matrix >X@dirrm share/ugene/data/manuals >X@dirrm share/ugene/data/enzymes >X@dirrm share/ugene/data/cmdline >X@dirrm share/ugene/data/biostruct3d_plugin >X@dirrm share/ugene/data/back_translation/Yeast >X@dirrm share/ugene/data/back_translation/Viruses >X@dirrm share/ugene/data/back_translation/Vertebrates >X@dirrm share/ugene/data/back_translation/Rodents >X@dirrm share/ugene/data/back_translation/Primates >X@dirrm share/ugene/data/back_translation/Plants >X@dirrm share/ugene/data/back_translation/Mammalia >X@dirrm share/ugene/data/back_translation/Invertebrates >X@dirrm share/ugene/data/back_translation/Bacteria >X@dirrm share/ugene/data/back_translation >X@dirrm share/ugene/data >X@dirrm share/ugene >X@dirrm share/man/man1 >X@dirrm share/man >X@dirrm share/applications >X@dirrm lib/ugene/plugins >X@dirrm lib/ugene >905ed5b1d190579fce073589acbfd494 >echo x - ugene/pkg-descr >sed 's/^X//' >ugene/pkg-descr << 'c6440c1edeef66071366f9d15fecebe6' >XUnipro UGENE is a multiplatform open-source software with the main goal >Xof assisting molecular biologists without much expertise in >Xbioinformatics to manage, analyze and visualize their data. UGENE >Xintegrates widely used bioinformatics tools within a common user >Xinterface. >X >XThe toolkit supports multiple biological data formats and allows the >Xretrieval of data from remote data sources. It provides visualization >Xmodules for biological objects such as annotated genome sequences, Next >XGeneration Sequencing (NGS) assembly data, multiple sequence alignments, >Xphylogenetic trees and 3D structures. >X >XWWW: http://ugene.unipro.ru/ >c6440c1edeef66071366f9d15fecebe6 >echo x - ugene/distinfo >sed 's/^X//' >ugene/distinfo << '3a74f8abc95a360614b3f632fe178e08' >XSHA256 (ugene-1.11.3.tar.gz) = c445b27e1d690c99869bef2ac0684be6ac012ba80f0c6801915a04506e95930e >XSIZE (ugene-1.11.3.tar.gz) = 14510331 >3a74f8abc95a360614b3f632fe178e08 >echo x - ugene/Makefile >sed 's/^X//' >ugene/Makefile << '127dc6e291f7ddd39199aa214dd377b1' >X# New ports collection makefile for: biology/ugene >X# Date created: 05 Nov 2012 >X# Whom: Hannes Hauswedell <h2+fbsdports@fsfe.org> >X# >X# $FreeBSD foo$ >X# >X >XPORTNAME= ugene >XDISTVERSION= 1.11.3 >XCATEGORIES= biology >XMASTER_SITES= http://ugene.unipro.ru/downloads/ >X >XMAINTAINER= h2+fbsdports@fsfe.org >XCOMMENT= UGENE is a free open-source cross-platform bioinformatics toolkit >X >XLICENSE= GPLv2 >X >XRUN_DEPENDS= ${LOCALBASE}/bin/bash:${PORTSDIR}/shells/bash >X >XUSE_GZIP= yes >XUSE_QT4= gui webkit xml linguist_build moc_build svg qmake_build \ >X rcc_build uic_build imageformats_run >X >XINSTALLS_ICONS= yes >XMAKE_JOBS_SAFE= yes >X >XHAS_CONFIGURE= yes >X >X.include <bsd.port.pre.mk> >X >XCARCH= >X.if ${ARCH} == "amd64" >X# need to manually tell the build we are on 64bit >XCARCH= CONFIG+=x64 >X.endif >X >X# yes, bash is required, stuff will not execute with sh >Xpost-patch: >X @${REINPLACE_CMD} -e 's|/bin/bash|'${LOCALBASE}'/bin/bash|' \ >X ${WRKSRC}/src/gen_bin_script.cmd \ >X ${WRKSRC}/installer/_common_data/ugene >X >Xdo-configure: >X @cd ${WRKSRC} && ${SETENV} ${CONFIGURE_ENV} ${QMAKE} \ >X PREFIX=${PREFIX} INSTALL_PREFIX=${PREFIX} \ >X ${CARCH} -r ${PORTNAME}.pro >X >X.include <bsd.port.post.mk> >127dc6e291f7ddd39199aa214dd377b1 >exit
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