FreeBSD Mail Archives

Date:      Mon, 5 Nov 2012 13:07:30 GMT
From:      Hannes Hauswedell <h2+fbsdports@fsfe.org>
To:        freebsd-gnats-submit@FreeBSD.org
Subject:   ports/173387: [new port] biology/ugene
Message-ID:  <201211051307.qA5D7UBd083322@red.freebsd.org>
Resent-Message-ID: <201211051310.qA5DA3jI011768@freefall.freebsd.org>

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>Number:         173387
>Category:       ports
>Synopsis:       [new port] biology/ugene
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Mon Nov 05 13:10:01 UTC 2012
>Closed-Date:
>Last-Modified:
>Originator:     Hannes Hauswedell
>Release:        9.0 Release
>Organization:
FSFE
>Environment:
FreeBSD fbsdmain 9.0-RELEASE FreeBSD 9.0-RELEASE #0: Tue Jan  3 07:46:30 UTC 2012     root@farrell.cse.buffalo.edu:/usr/obj/usr/src/sys/GENERIC  amd64
>Description:
new port, 
pkg-descr:


Unipro UGENE is a multiplatform open-source software with the main goal
of assisting molecular biologists without much expertise in 
bioinformatics to manage, analyze and visualize their data. UGENE 
integrates widely used bioinformatics tools within a common user 
interface. 

The toolkit supports multiple biological data formats and allows the 
retrieval of data from remote data sources. It provides visualization
modules for biological objects such as annotated genome sequences, Next
Generation Sequencing (NGS) assembly data, multiple sequence alignments,
phylogenetic trees and 3D structures.


btw. send-pr.html still doesn't recognize .shar, because it says its x-shar ...
>How-To-Repeat:

>Fix:
commit the port ;)

Patch attached with submission follows:

# 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
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0309.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0310.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0311.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0312.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0313.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0314.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0315.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0316.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0317.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0318.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0319.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0320.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0321.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0322.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0323.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0324.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0325.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0326.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0327.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0328.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0329.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0330.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0331.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0332.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0333.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0334.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0335.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0336.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0337.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0338.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0339.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0340.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0341.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0342.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0343.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0344.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0345.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0346.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0347.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0348.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0349.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0350.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0351.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0352.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0353.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0354.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0355.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0356.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0357.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0358.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0359.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0360.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0361.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0362.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0363.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0364.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0365.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0366.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0367.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0368.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0369.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0370.1.pfm
Xshare/ugene/data/position_weight_matrix/JASPAR/fungi/MA0371.1.pfm
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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



>Release-Note:
>Audit-Trail:
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