Add Unipro UGENE, a free open-source crowss-platform bioinformatics software.

PR:		ports/173387
Submitted by:	Hannes Hauswedell

5 files changed, 1217 insertions, 0 deletions

diff --git a/biology/ugene/Makefile b/biology/ugene/Makefile
new file mode 100644
index 000000000000..9828a43a2a47
--- /dev/null
+++ b/biology/ugene/Makefile
@@ -0,0 +1,48 @@
+# Created by: Hannes Hauswedell <h2+fbsdports@fsfe.org>
+# $FreeBSD$
+
+PORTNAME=	ugene
+DISTVERSION=	1.11.4
+CATEGORIES=	biology
+MASTER_SITES=	http://ugene.unipro.ru/downloads/
+
+MAINTAINER=	h2+fbsdports@fsfe.org
+COMMENT=	Free, open-source, cross-platform bioinformatics toolkit
+
+LICENSE=	GPLv2
+
+LIB_DEPENDS=	execinfo:${PORTSDIR}/devel/libexecinfo
+RUN_DEPENDS=	bash:${PORTSDIR}/shells/bash
+
+USE_GL=		glu
+USE_QT4=	gui webkit xml svg linguist_build moc_build qmake_build \
+		qtestlib_build rcc_build uic_build imageformats_run
+USE_XORG=	xtst
+
+USE_LDCONFIG=	yes
+INSTALLS_ICONS=	yes
+MAKE_JOBS_SAFE=	yes
+
+MAN1=		${PORTNAME}.1
+MANCOMPRESSED=	yes
+
+.include <bsd.port.pre.mk>
+
+.if ${ARCH} == "amd64"
+# need to manually tell the build we are on x64
+CARCH=		CONFIG+=x64
+.endif
+
+# yes, bash is required, stuff will not execute with sh
+post-patch:
+	@${REINPLACE_CMD} -e 's|/bin/bash|/usr/bin/env bash|' \
+		${WRKSRC}/src/gen_bin_script.cmd \
+		${WRKSRC}/installer/_common_data/ugene
+
+do-configure:
+	@cd ${CONFIGURE_WRKSRC} && ${SETENV} ${CONFIGURE_ENV} ${QMAKE} \
+		PREFIX=${PREFIX} INSTALL_PREFIX=${PREFIX} \
+		INSTALL_MANDIR=${MAN1PREFIX}/man ${CARCH} \
+		UGENE_INSTALL_DATA=${DATADIR} -r ${PORTNAME}.pro
+
+.include <bsd.port.post.mk>
diff --git a/biology/ugene/distinfo b/biology/ugene/distinfo
new file mode 100644
index 000000000000..23b6433eef20
--- /dev/null
+++ b/biology/ugene/distinfo
@@ -0,0 +1,2 @@
+SHA256 (ugene-1.11.4.tar.gz) = 5b9b914e7ef5a3d3658f3346cccdb5cd6583b03db3b7bed7e163cb5cfd5663fa
+SIZE (ugene-1.11.4.tar.gz) = 14761290
diff --git a/biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp b/biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp
new file mode 100644
index 000000000000..42a782ad317b
--- /dev/null
+++ b/biology/ugene/files/patch-src-corelibs-U2Private-src-CrashHandler.cpp
@@ -0,0 +1,20 @@
+--- ./src/corelibs/U2Private/src/CrashHandler.cpp.old	2012-10-30 15:36:22.000000000 +0100
++++ ./src/corelibs/U2Private/src/CrashHandler.cpp	2012-10-30 15:47:47.000000000 +0100
+@@ -253,7 +253,7 @@
+     }
+     //handler = AddVectoredExceptionHandler(1, CrashHandlerFunc);
+     
+-#elif defined( Q_OS_MAC)
++#elif defined( Q_OS_MAC ) || defined ( Q_OS_FREEBSD )
+     return; //TODO: implement crash hander for MAC OS
+ #else
+     stack_t sigstk;
+@@ -284,7 +284,7 @@
+ void CrashHandler::runMonitorProcess(const QString &exceptionType) {
+     QString path = QCoreApplication::applicationDirPath() + "/ugenem";
+ 
+-#ifndef Q_OS_WIN
++#if !defined ( Q_OS_WIN ) && !defined ( Q_OS_FREEBSD )
+     char pid_buf[30];
+     sprintf(pid_buf, "%d", getpid());
+     char name_buf[512];
diff --git a/biology/ugene/pkg-descr b/biology/ugene/pkg-descr
new file mode 100644
index 000000000000..9ac1f2d9ce6d
--- /dev/null
+++ b/biology/ugene/pkg-descr
@@ -0,0 +1,12 @@
+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.
+
+WWW: http://ugene.unipro.ru/
diff --git a/biology/ugene/pkg-plist b/biology/ugene/pkg-plist
new file mode 100644
index 000000000000..86d67cf6f169
--- /dev/null
+++ b/biology/ugene/pkg-plist
@@ -0,0 +1,1135 @@
+bin/ugene
+lib/ugene/libU2Algorithm.so
+lib/ugene/libU2Core.so
+lib/ugene/libU2Designer.so
+lib/ugene/libU2Formats.so
+lib/ugene/libU2Gui.so
+lib/ugene/libU2Lang.so
+lib/ugene/libU2Private.so
+lib/ugene/libU2Remote.so
+lib/ugene/libU2Test.so
+lib/ugene/libU2View.so
+lib/ugene/libgtest.so
+lib/ugene/libugenedb.so
+lib/ugene/plugins/CoreTests.license
+lib/ugene/plugins/CoreTests.plugin
+lib/ugene/plugins/GUITestBase.license
+lib/ugene/plugins/GUITestBase.plugin
+lib/ugene/plugins/annotator.license
+lib/ugene/plugins/annotator.plugin
+lib/ugene/plugins/api_tests.license
+lib/ugene/plugins/api_tests.plugin
+lib/ugene/plugins/ball.license
+lib/ugene/plugins/ball.plugin
+lib/ugene/plugins/biostruct3d_view.license
+lib/ugene/plugins/biostruct3d_view.plugin
+lib/ugene/plugins/chroma_view.license
+lib/ugene/plugins/chroma_view.plugin
+lib/ugene/plugins/circular_view.license
+lib/ugene/plugins/circular_view.plugin
+lib/ugene/plugins/dbi_bam.license
+lib/ugene/plugins/dbi_bam.plugin
+lib/ugene/plugins/dna_export.license
+lib/ugene/plugins/dna_export.plugin
+lib/ugene/plugins/dna_flexibility.license
+lib/ugene/plugins/dna_flexibility.plugin
+lib/ugene/plugins/dna_graphpack.license
+lib/ugene/plugins/dna_graphpack.plugin
+lib/ugene/plugins/dna_stat.license
+lib/ugene/plugins/dna_stat.plugin
+lib/ugene/plugins/dotplot.license
+lib/ugene/plugins/dotplot.plugin
+lib/ugene/plugins/enzymes.license
+lib/ugene/plugins/enzymes.plugin
+lib/ugene/plugins/expert_discovery.license
+lib/ugene/plugins/expert_discovery.plugin
+lib/ugene/plugins/external_tool_support.license
+lib/ugene/plugins/external_tool_support.plugin
+lib/ugene/plugins/genome_aligner.license
+lib/ugene/plugins/genome_aligner.plugin
+lib/ugene/plugins/gor4.license
+lib/ugene/plugins/gor4.plugin
+lib/ugene/plugins/hmm2.license
+lib/ugene/plugins/hmm2.plugin
+lib/ugene/plugins/kalign.license
+lib/ugene/plugins/kalign.plugin
+lib/ugene/plugins/libCoreTests.so
+lib/ugene/plugins/libGUITestBase.so
+lib/ugene/plugins/libannotator.so
+lib/ugene/plugins/libapi_tests.so
+lib/ugene/plugins/libball.so
+lib/ugene/plugins/libbiostruct3d_view.so
+lib/ugene/plugins/libchroma_view.so
+lib/ugene/plugins/libcircular_view.so
+lib/ugene/plugins/libdbi_bam.so
+lib/ugene/plugins/libdna_export.so
+lib/ugene/plugins/libdna_flexibility.so
+lib/ugene/plugins/libdna_graphpack.so
+lib/ugene/plugins/libdna_stat.so
+lib/ugene/plugins/libdotplot.so
+lib/ugene/plugins/libenzymes.so
+lib/ugene/plugins/libexpert_discovery.so
+lib/ugene/plugins/libexternal_tool_support.so
+lib/ugene/plugins/libgenome_aligner.so
+lib/ugene/plugins/libgor4.so
+lib/ugene/plugins/libhmm2.so
+lib/ugene/plugins/libkalign.so
+lib/ugene/plugins/libopencl_support.so
+lib/ugene/plugins/liborf_marker.so
+lib/ugene/plugins/libperf_monitor.so
+lib/ugene/plugins/libphylip.so
+lib/ugene/plugins/libprimer3.so
+lib/ugene/plugins/libpsipred.so
+lib/ugene/plugins/libptools.so
+lib/ugene/plugins/libquery_designer.so
+lib/ugene/plugins/libremote_blast.so
+lib/ugene/plugins/libremote_service.so
+lib/ugene/plugins/librepeat_finder.so
+lib/ugene/plugins/libsitecon.so
+lib/ugene/plugins/libsmith_waterman.so
+lib/ugene/plugins/libtest_runner.so
+lib/ugene/plugins/libweight_matrix.so
+lib/ugene/plugins/libworkflow_designer.so
+lib/ugene/plugins/opencl_support.license
+lib/ugene/plugins/opencl_support.plugin
+lib/ugene/plugins/orf_marker.license
+lib/ugene/plugins/orf_marker.plugin
+lib/ugene/plugins/perf_monitor.license
+lib/ugene/plugins/perf_monitor.plugin
+lib/ugene/plugins/phylip.license
+lib/ugene/plugins/phylip.plugin
+lib/ugene/plugins/primer3.license
+lib/ugene/plugins/primer3.plugin
+lib/ugene/plugins/psipred.license
+lib/ugene/plugins/psipred.plugin
+lib/ugene/plugins/ptools.license
+lib/ugene/plugins/ptools.plugin
+lib/ugene/plugins/query_designer.license
+lib/ugene/plugins/query_designer.plugin
+lib/ugene/plugins/remote_blast.license
+lib/ugene/plugins/remote_blast.plugin
+lib/ugene/plugins/remote_service.license
+lib/ugene/plugins/remote_service.plugin
+lib/ugene/plugins/repeat_finder.license
+lib/ugene/plugins/repeat_finder.plugin
+lib/ugene/plugins/sitecon.license
+lib/ugene/plugins/sitecon.plugin
+lib/ugene/plugins/smith_waterman.license
+lib/ugene/plugins/smith_waterman.plugin
+lib/ugene/plugins/test_runner.license
+lib/ugene/plugins/test_runner.plugin
+lib/ugene/plugins/weight_matrix.license
+lib/ugene/plugins/weight_matrix.plugin
+lib/ugene/plugins/workflow_designer.license
+lib/ugene/plugins/workflow_designer.plugin
+lib/ugene/transl_cs.qm
+lib/ugene/transl_en.qm
+lib/ugene/transl_ru.qm
+lib/ugene/transl_zh.qm
+lib/ugene/ugene
+lib/ugene/ugenecl
+lib/ugene/ugenem
+lib/ugene/ugeneui
+share/applications/ugene.desktop
+share/pixmaps/ugene.png
+share/pixmaps/ugene.xpm
+%%DATADIR%%/DBXRefRegistry.txt
+%%DATADIR%%/back_translation/Bacteria/Arthrobacter_aurescens_TC1.cut
+%%DATADIR%%/back_translation/Bacteria/Bacillus_subtilis.cut
+%%DATADIR%%/back_translation/Bacteria/Escherichia_coli.cut
+%%DATADIR%%/back_translation/Bacteria/Haemophilus_influenzae.cut
+%%DATADIR%%/back_translation/Bacteria/Helicobacter_pylori.cut
+%%DATADIR%%/back_translation/Bacteria/Listeria_monocytogenes.cut
+%%DATADIR%%/back_translation/Bacteria/Neisseria_meningitidis.cut
+%%DATADIR%%/back_translation/Bacteria/Salmonella_typhimurium_LT2.cut
+%%DATADIR%%/back_translation/Bacteria/Streptomyces_coelicolor_A3(2).cut
+%%DATADIR%%/back_translation/Bacteria/Sulfolobus_solfataricus_P2.cut
+%%DATADIR%%/back_translation/Invertebrates/Apis_mellifera_(honey_bee).cut
+%%DATADIR%%/back_translation/Invertebrates/Caenorhabditis_elegans.cut
+%%DATADIR%%/back_translation/Invertebrates/Drosophila_melanogaster_(fruit_fly).cut
+%%DATADIR%%/back_translation/Invertebrates/Plasmodium_falciparum_(malaria_parasite_P._falciparum).cut
+%%DATADIR%%/back_translation/Invertebrates/mitochondrion_Caenorhabditis_elegans.cut
+%%DATADIR%%/back_translation/Invertebrates/mitochondrion_Drosophila_melanogaster_(fruit_fly).cut
+%%DATADIR%%/back_translation/Mammalia/Bos_taurus_(cow).cut
+%%DATADIR%%/back_translation/Mammalia/Canis_familiaris_(dog).cut
+%%DATADIR%%/back_translation/Mammalia/Sus_scrofa_(pig).cut
+%%DATADIR%%/back_translation/Mammalia/mitochondrion_Bos_taurus_(cow).cut
+%%DATADIR%%/back_translation/Mammalia/mitochondrion_Sus_scrofa_(pig).cut
+%%DATADIR%%/back_translation/Plants/Arabidopsis_thaliana_(thale_cress).cut
+%%DATADIR%%/back_translation/Plants/Oryza_sativa.cut
+%%DATADIR%%/back_translation/Plants/Zea_mays.cut
+%%DATADIR%%/back_translation/Primates/Homo_sapiens_(human).cut
+%%DATADIR%%/back_translation/Primates/Pan_troglodytes_(chimpanzee).cut
+%%DATADIR%%/back_translation/Primates/mitochondrion_Homo_sapiens_(human).cut
+%%DATADIR%%/back_translation/Primates/mitochondrion_Pan_troglodytes_(chimpanzee).cut
+%%DATADIR%%/back_translation/Rodents/Mus_musculus_(house_mouse).cut
+%%DATADIR%%/back_translation/Rodents/Rattus_norvegicus_(Norway_rat).cut
+%%DATADIR%%/back_translation/Vertebrates/Gallus_gallus_(chicken).cut
+%%DATADIR%%/back_translation/Vertebrates/Takifugu_rubripes_(Fugu_rubripes).cut
+%%DATADIR%%/back_translation/Vertebrates/Xenopus_laevis_(African_clawed_frog).cut
+%%DATADIR%%/back_translation/Vertebrates/mitochondrion_Gallus_gallus_(chicken).cut
+%%DATADIR%%/back_translation/Vertebrates/mitochondrion_Takifugu_rubripes_(Fugu_rubripes).cut
+%%DATADIR%%/back_translation/Viruses/Human_immunodeficiency_virus_1_(HIV-1).cut
+%%DATADIR%%/back_translation/Viruses/Influenza_A_virus.cut
+%%DATADIR%%/back_translation/Yeast/Saccharomyces_cerevisiae_(baker's_yeast).cut
+%%DATADIR%%/back_translation/tables.xml
+%%DATADIR%%/biostruct3d_plugin/BioStruct3DLinks.txt
+%%DATADIR%%/cmdline/align-clustalw.uwl
+%%DATADIR%%/cmdline/align-kalign.uwl
+%%DATADIR%%/cmdline/align-mafft.uwl
+%%DATADIR%%/cmdline/align-tcoffee.uwl
+%%DATADIR%%/cmdline/align.uwl
+%%DATADIR%%/cmdline/bowtie-build.uwl
+%%DATADIR%%/cmdline/bowtie.uwl
+%%DATADIR%%/cmdline/convert-msa.uwl
+%%DATADIR%%/cmdline/convert-seq.uwl
+%%DATADIR%%/cmdline/extract-sequence.uwl
+%%DATADIR%%/cmdline/fetch-sequence.uwl
+%%DATADIR%%/cmdline/fetch.uwl
+%%DATADIR%%/cmdline/find-orfs.uwl
+%%DATADIR%%/cmdline/find-repeats.uwl
+%%DATADIR%%/cmdline/find-sw.uwl
+%%DATADIR%%/cmdline/generate-dna.uwl
+%%DATADIR%%/cmdline/hmm2-build.uwl
+%%DATADIR%%/cmdline/hmm2-search.uwl
+%%DATADIR%%/cmdline/join-quality.uwl
+%%DATADIR%%/cmdline/local-blast+.uwl
+%%DATADIR%%/cmdline/local-blast.uwl
+%%DATADIR%%/cmdline/pfm-build.uwl
+%%DATADIR%%/cmdline/pfm-search.uwl
+%%DATADIR%%/cmdline/pwm-build.uwl
+%%DATADIR%%/cmdline/pwm-search.uwl
+%%DATADIR%%/cmdline/query.uwl
+%%DATADIR%%/cmdline/remote-request.uwl
+%%DATADIR%%/cmdline/revcompl.uwl
+%%DATADIR%%/cmdline/sitecon-build.uwl
+%%DATADIR%%/cmdline/sitecon-search.uwl
+%%DATADIR%%/enzymes/rebase_v003_all.bairoch.gz
+%%DATADIR%%/enzymes/rebase_v003_t2_com.bairoch.gz
+%%DATADIR%%/license
+%%DATADIR%%/position_weight_matrix/JASPAR/all_jaspar.csv
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+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Cphx_3484.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Crx_3485.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Cutl1_3494.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Cutl1_3494.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dbx1_3486.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dbx2_3487.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dlx1_1741.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dlx2_2273.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dlx3_1030.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dlx4_3488.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dlx5_3419.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dmbx1_2277.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dobox4_3956.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Dobox5_3493.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Duxl_1286.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Emx2_3420.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/En1_3123.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/En2_0952.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Esx1_3124.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Evx1_3952.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Evx2_2645.3.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Gbx1_2883.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Gbx2_3110.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Gsc_2327.3.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Gsh2_3990.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hdx_3845.3.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hlx1_2350.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hlxb9_3422.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hmbox1_2674.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hmx1_3423.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hmx2_3424.3.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hmx3_3490.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Homez_1063.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa10_2318.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa11_2218.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa13_3126.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa1_3425.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa2_3079.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa3_2783.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa4_3426.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa5_3415.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa6_1040.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa7_2668.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa7_3750.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxa9_2622.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb13_3479.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb3_1720.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb4_2627.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb5_3122.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb6_3428.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb7_3953.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb8_3780.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxb9_3413.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc10_2779.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc11_3718.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc12_3480.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc13_3127.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc4_3491.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc5_2630.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc6_3954.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc8_3429.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxc9_2367.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd10_2368.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd11_3873.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd12_3481.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd13_2356.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd1_3448.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd3_1742.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Hoxd8_2644.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Ipf1_3815.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx2_0900.3.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx3_0920.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx3_2226.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx4_2242.3.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx5_2385.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Irx6_2623.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Isl2_3430.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Isx_3445.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lbx2_3869.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx1_2240.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx2_0953.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx3_3431.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx4_1719.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx5_2279.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx6_2272.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx6_3432.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx8_2247.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lhx9_3492.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lmx1a_2238.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Lmx1b_3433.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Meis1_2335.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Meox1_2310.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Mrg1_2246.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Mrg2_2302.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Msx1_3031.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Msx2_3449.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Msx3_3206.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx1-1_3856.3.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx1-2_3214.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-2_2823.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-3_3435.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-4_3074.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-5_3436.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-6_3437.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx2-9_3082.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx3-1_2923.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx6-1_2825.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx6-1_2825.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Nkx6-3_3446.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox1_3970.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox2_3438.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox3_3439.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox5_2284.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox5_3963.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Obox6_3440.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Og2x_3719.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Otp_3496.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Otx1_2325.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Otx2_3441.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pax4_3989.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pax6_3838.3.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pax7_3783.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pbx1_3203.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Phox2a_3947.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Phox2b_3948.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pitx1_2312.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pitx2_2274.3.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pitx3_3497.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pknox1_2364.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pknox2_3077.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou1f1_3818.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou2f1_3081.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou2f2_3748.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou2f3_3986.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou3f1_3819.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou3f2_2824.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou3f3_3235.2.pwm
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+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Pou4f3_2791.1.pwm
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+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Prrx1_3442.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Prrx2_3072.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Rax_3443.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Rhox11_1765.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Rhox11_2205.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Rhox6_4251.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Shox2_2641.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six1_0935.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six2_2307.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six3_1732.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six4_2860.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six6_2267.4.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Six6_2267.5.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tcf1_2666.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tcf2_0913.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tgif1_2342.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tgif2_3451.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Titf1_1722.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Tlx2_3498.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Uncx4.1_2281.2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Vax1_3499.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Vax2_3500.1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/Cell08/Vsx1_1728.1.pwm
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+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Aro80.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Asg1.pwm
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+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Cbf1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Cep3.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Cha4.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Cup9.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ecm22.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Fhl1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Fkh1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Fkh2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gal4.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gat1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gat3.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gat4.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gcn4.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gln3.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gsm1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Gzf3.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Hal9.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Leu3.pwm
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+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Matalpha2.pwm
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+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Met32.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mga1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mig1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mig2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Mig3.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ndt80.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Nhp6a.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Nhp6b.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Nrg1.pwm
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+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pbf1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pbf2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pdr1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Phd1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pho2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Pho4.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Put3.pwm
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+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rdr1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rds1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rds2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rgt1.pwm
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+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rsc3.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rsc30.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Rtg3.pwm
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+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Sfp1.pwm
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+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Skn7.pwm
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+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Srd1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Stb3.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Stp2.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Stp4.pwm
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+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tea1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Tec1.pwm
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+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ume6.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Usv1.pwm
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+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yap1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yap6.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ybr239c.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ydr520c.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yer130c.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ygr067c.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ykl222c.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yll054c.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yml081w.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ynr063w.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yox1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ypr013c.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ypr015c.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Ypr196w.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yrm1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/GR09/Yrr1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/NBT06/Cbf1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/NBT06/Ceh-22.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/NBT06/Oct-1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/NBT06/Rap1.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/NBT06/Zif268.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/PNAS08/Cgd2_3490.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/PNAS08/PF14_0633.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/PNAS08/PFF0200c.pwm
+%%DATADIR%%/position_weight_matrix/UniPROBE/all_uniprobe.csv
+%%DATADIR%%/primer3/drosophila.w.transposons.txt
+%%DATADIR%%/primer3/humrep_and_simple.txt
+%%DATADIR%%/primer3/rodent_ref.txt
+%%DATADIR%%/primer3/rodrep_and_simple.txt
+%%DATADIR%%/query_samples/RepeatsWithORF.uql
+%%DATADIR%%/query_samples/SimpleGene.uql
+%%DATADIR%%/samples/ABIF/A01.abi
+%%DATADIR%%/samples/ACE/BL060C3.ace
+%%DATADIR%%/samples/ACE/K26.ace
+%%DATADIR%%/samples/Assembly/chrM.fa
+%%DATADIR%%/samples/Assembly/chrM.sam
+%%DATADIR%%/samples/Assembly/chrM.sorted.bam
+%%DATADIR%%/samples/CLUSTALW/COI.aln
+%%DATADIR%%/samples/CLUSTALW/HIV-1.aln
+%%DATADIR%%/samples/CLUSTALW/ty3.aln.gz
+%%DATADIR%%/samples/EMBL/AF177870.emb
+%%DATADIR%%/samples/EMBL/AL000263.emb
+%%DATADIR%%/samples/FASTA/human_T1.fa
+%%DATADIR%%/samples/FASTQ/eas.fastq
+%%DATADIR%%/samples/GFF/5prime_utr_intron_A20.gff
+%%DATADIR%%/samples/GFF/5prime_utr_intron_A21.gff
+%%DATADIR%%/samples/Genbank/CVU55762.gb
+%%DATADIR%%/samples/Genbank/NC_014267.1.gb
+%%DATADIR%%/samples/Genbank/PBR322.gb
+%%DATADIR%%/samples/Genbank/murine.gb
+%%DATADIR%%/samples/Genbank/sars.gb
+%%DATADIR%%/samples/HMM/aligment15900.hmm
+%%DATADIR%%/samples/MMDB/1CRN.prt
+%%DATADIR%%/samples/MMDB/2JQS.prt
+%%DATADIR%%/samples/MSF/HMA.msf
+%%DATADIR%%/samples/MSF/lipid8.msf
+%%DATADIR%%/samples/MSF/pla2_20.msf
+%%DATADIR%%/samples/Newick/COI.nwk
+%%DATADIR%%/samples/PDB/1CF7.PDB
+%%DATADIR%%/samples/PDB/1CRN.PDB
+%%DATADIR%%/samples/PDB/3INS.PDB
+%%DATADIR%%/samples/Raw/raw.seq
+%%DATADIR%%/samples/SCF/90-JRI-07.scf
+%%DATADIR%%/samples/Stockholm/CBS.sto
+%%DATADIR%%/samples/Stockholm/UPSK.sto
+%%DATADIR%%/samples/Swiss-Prot/D0VTW9.txt
+%%DATADIR%%/samples/Swiss-Prot/P01375.txt
+%%DATADIR%%/samples/Swiss-Prot/P16152.txt
+%%DATADIR%%/sitecon_models/eukaryotic/CEBP_a.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/CEBPall.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/CLOCK.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/CRE.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/E2F1.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/E2F1DP1sel1.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/EGR1.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/Eklf.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/GATA1.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/GATA_ALL.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/Gata2.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/Gata3.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/HMG1.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/HNF1.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/HNF3_4.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/HNF4.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/MYOGsel3.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/MyoD.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/NF1.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/NFATp.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/NFkB_all.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/NFkB_hetero.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/NFkB_homo.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/Nf_e2.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/Nrf2.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/Oct1.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/Oct_all.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/PPRE.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/Pu1.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/SRE_can.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/STAT.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/STAT1.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/TTF1.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/USF.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/cMyc_can.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/er2.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/irf.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/isre.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/nfy.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/p53.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/setCREB.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/setCREBzag.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/srf_all.sitecon.gz
+%%DATADIR%%/sitecon_models/eukaryotic/yy1.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/AgaR.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/AraC.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/ArcA.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/ArgR.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/CpxR.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/Crp.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/CysB.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/CytR.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/DeoR.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/DnaA.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/FUR.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/FadR.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/FlhDC.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/Fnr.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/Frur.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/GALR.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/GALS.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/GLPR.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/GNTR.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/HNS.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/ICLR.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/IHF.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/ISCR1.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/ISCR3.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/LEXA.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/Lrp.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/MALT.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/MARA.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/MELR.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/MLC.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/MODE.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/MetJ.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/MetR1.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/NAC.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/NAGC_new2.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/NANR.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/NARL2.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/NARP.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/NTRC.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/NarL.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/OmpR.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/OxyR.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/PHOB.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/PHOP.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/PurR.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/ROB.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/RcsB_1core.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/RcsB_2core.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/Rob2.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/TORR.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/TRPR.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/TyrR.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/fis_new1.sitecon.gz
+%%DATADIR%%/sitecon_models/prokaryotic/soxS.sitecon.gz
+%%DATADIR%%/translations.txt
+%%DATADIR%%/weight_matrix/blosum100.txt
+%%DATADIR%%/weight_matrix/blosum30.txt
+%%DATADIR%%/weight_matrix/blosum35.txt
+%%DATADIR%%/weight_matrix/blosum40.txt
+%%DATADIR%%/weight_matrix/blosum45.txt
+%%DATADIR%%/weight_matrix/blosum50.txt
+%%DATADIR%%/weight_matrix/blosum55.txt
+%%DATADIR%%/weight_matrix/blosum60.txt
+%%DATADIR%%/weight_matrix/blosum62.txt
+%%DATADIR%%/weight_matrix/blosum65.txt
+%%DATADIR%%/weight_matrix/blosum70.txt
+%%DATADIR%%/weight_matrix/blosum75.txt
+%%DATADIR%%/weight_matrix/blosum80.txt
+%%DATADIR%%/weight_matrix/blosum85.txt
+%%DATADIR%%/weight_matrix/blosum90.txt
+%%DATADIR%%/weight_matrix/blosumn.txt
+%%DATADIR%%/weight_matrix/dayhoff.txt
+%%DATADIR%%/weight_matrix/dna.txt
+%%DATADIR%%/weight_matrix/gonnet.txt
+%%DATADIR%%/weight_matrix/identity.txt
+%%DATADIR%%/weight_matrix/match.txt
+%%DATADIR%%/weight_matrix/md_10.txt
+%%DATADIR%%/weight_matrix/md_20.txt
+%%DATADIR%%/weight_matrix/md_40.txt
+%%DATADIR%%/weight_matrix/nuc.4.4.txt
+%%DATADIR%%/weight_matrix/pam10.txt
+%%DATADIR%%/weight_matrix/pam100.txt
+%%DATADIR%%/weight_matrix/pam110.txt
+%%DATADIR%%/weight_matrix/pam120.cdi.txt
+%%DATADIR%%/weight_matrix/pam120.txt
+%%DATADIR%%/weight_matrix/pam130.txt
+%%DATADIR%%/weight_matrix/pam140.txt
+%%DATADIR%%/weight_matrix/pam150.txt
+%%DATADIR%%/weight_matrix/pam160.cdi.txt
+%%DATADIR%%/weight_matrix/pam160.txt
+%%DATADIR%%/weight_matrix/pam170.txt
+%%DATADIR%%/weight_matrix/pam180.txt
+%%DATADIR%%/weight_matrix/pam190.txt
+%%DATADIR%%/weight_matrix/pam20.txt
+%%DATADIR%%/weight_matrix/pam200.cdi.txt
+%%DATADIR%%/weight_matrix/pam200.txt
+%%DATADIR%%/weight_matrix/pam210.txt
+%%DATADIR%%/weight_matrix/pam220.txt
+%%DATADIR%%/weight_matrix/pam230.txt
+%%DATADIR%%/weight_matrix/pam240.txt
+%%DATADIR%%/weight_matrix/pam250.cdi.txt
+%%DATADIR%%/weight_matrix/pam250.txt
+%%DATADIR%%/weight_matrix/pam260.txt
+%%DATADIR%%/weight_matrix/pam270.txt
+%%DATADIR%%/weight_matrix/pam280.txt
+%%DATADIR%%/weight_matrix/pam290.txt
+%%DATADIR%%/weight_matrix/pam30.txt
+%%DATADIR%%/weight_matrix/pam300.txt
+%%DATADIR%%/weight_matrix/pam310.txt
+%%DATADIR%%/weight_matrix/pam320.txt
+%%DATADIR%%/weight_matrix/pam330.txt
+%%DATADIR%%/weight_matrix/pam340.txt
+%%DATADIR%%/weight_matrix/pam350.txt
+%%DATADIR%%/weight_matrix/pam360.txt
+%%DATADIR%%/weight_matrix/pam370.txt
+%%DATADIR%%/weight_matrix/pam380.txt
+%%DATADIR%%/weight_matrix/pam390.txt
+%%DATADIR%%/weight_matrix/pam40.cdi.txt
+%%DATADIR%%/weight_matrix/pam40.txt
+%%DATADIR%%/weight_matrix/pam400.txt
+%%DATADIR%%/weight_matrix/pam410.txt
+%%DATADIR%%/weight_matrix/pam420.txt
+%%DATADIR%%/weight_matrix/pam430.txt
+%%DATADIR%%/weight_matrix/pam440.txt
+%%DATADIR%%/weight_matrix/pam450.txt
+%%DATADIR%%/weight_matrix/pam460.txt
+%%DATADIR%%/weight_matrix/pam470.txt
+%%DATADIR%%/weight_matrix/pam480.txt
+%%DATADIR%%/weight_matrix/pam490.txt
+%%DATADIR%%/weight_matrix/pam50.txt
+%%DATADIR%%/weight_matrix/pam500.txt
+%%DATADIR%%/weight_matrix/pam60.txt
+%%DATADIR%%/weight_matrix/pam70.txt
+%%DATADIR%%/weight_matrix/pam80.cdi.txt
+%%DATADIR%%/weight_matrix/pam80.txt
+%%DATADIR%%/weight_matrix/pam90.txt
+%%DATADIR%%/weight_matrix/rna.txt
+%%DATADIR%%/weight_matrix/vtml160.txt
+%%DATADIR%%/weight_matrix/vtml200.txt
+%%DATADIR%%/workflow_samples/Alignment/basic_align.uwl
+%%DATADIR%%/workflow_samples/Conversions/faqual2fastq.uwl
+%%DATADIR%%/workflow_samples/Conversions/msa2clustal.uwl
+%%DATADIR%%/workflow_samples/Conversions/query2alignment.uwl
+%%DATADIR%%/workflow_samples/Conversions/seq2gen.uwl
+%%DATADIR%%/workflow_samples/Custom elements/script-dump-sequence-info.uwl
+%%DATADIR%%/workflow_samples/Custom elements/script-quality-filter.uwl
+%%DATADIR%%/workflow_samples/Data marking/annotation_marker.uwl
+%%DATADIR%%/workflow_samples/Data marking/length_marker.uwl
+%%DATADIR%%/workflow_samples/Data merging/find-substrings.uwl
+%%DATADIR%%/workflow_samples/Data merging/merge-sequence.uwl
+%%DATADIR%%/workflow_samples/Data merging/tfbs.uwl
+%%DATADIR%%/workflow_samples/HMMER/build-test-HMM.uwl
+%%DATADIR%%/workflow_samples/HMMER/searchHMM.uwl
+%%DATADIR%%/workflow_samples/Transcriptomics/SearchTFBS.uwl
+%%DATADIR%%/workflow_samples/users/CreateAlignment.usa
+%%DATADIR%%/workflow_samples/users/Dump sequence info.usa
+%%DATADIR%%/workflow_samples/users/QualityFilter.usa
+@dirrm %%DATADIR%%/workflow_samples/users
+@dirrm %%DATADIR%%/workflow_samples/Transcriptomics
+@dirrm %%DATADIR%%/workflow_samples/HMMER
+@dirrm %%DATADIR%%/workflow_samples/Data merging
+@dirrm %%DATADIR%%/workflow_samples/Data marking
+@dirrm %%DATADIR%%/workflow_samples/Custom elements
+@dirrm %%DATADIR%%/workflow_samples/Conversions
+@dirrm %%DATADIR%%/workflow_samples/Alignment
+@dirrm %%DATADIR%%/workflow_samples
+@dirrm %%DATADIR%%/weight_matrix
+@dirrm %%DATADIR%%/sitecon_models/prokaryotic
+@dirrm %%DATADIR%%/sitecon_models/eukaryotic
+@dirrm %%DATADIR%%/sitecon_models
+@dirrm %%DATADIR%%/samples/Swiss-Prot
+@dirrm %%DATADIR%%/samples/Stockholm
+@dirrm %%DATADIR%%/samples/SCF
+@dirrm %%DATADIR%%/samples/Raw
+@dirrm %%DATADIR%%/samples/PDB
+@dirrm %%DATADIR%%/samples/Newick
+@dirrm %%DATADIR%%/samples/MSF
+@dirrm %%DATADIR%%/samples/MMDB
+@dirrm %%DATADIR%%/samples/HMM
+@dirrm %%DATADIR%%/samples/Genbank
+@dirrm %%DATADIR%%/samples/GFF
+@dirrm %%DATADIR%%/samples/FASTQ
+@dirrm %%DATADIR%%/samples/FASTA
+@dirrm %%DATADIR%%/samples/EMBL
+@dirrm %%DATADIR%%/samples/CLUSTALW
+@dirrm %%DATADIR%%/samples/Assembly
+@dirrm %%DATADIR%%/samples/ACE
+@dirrm %%DATADIR%%/samples/ABIF
+@dirrm %%DATADIR%%/samples
+@dirrm %%DATADIR%%/query_samples
+@dirrm %%DATADIR%%/primer3
+@dirrm %%DATADIR%%/position_weight_matrix/UniPROBE/PNAS08
+@dirrm %%DATADIR%%/position_weight_matrix/UniPROBE/NBT06
+@dirrm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09
+@dirrm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08
+@dirrm %%DATADIR%%/position_weight_matrix/UniPROBE
+@dirrm %%DATADIR%%/position_weight_matrix/JASPAR/vertebrates
+@dirrm %%DATADIR%%/position_weight_matrix/JASPAR/urochordates
+@dirrm %%DATADIR%%/position_weight_matrix/JASPAR/plants
+@dirrm %%DATADIR%%/position_weight_matrix/JASPAR/nematodes
+@dirrm %%DATADIR%%/position_weight_matrix/JASPAR/insects
+@dirrm %%DATADIR%%/position_weight_matrix/JASPAR/fungi
+@dirrm %%DATADIR%%/position_weight_matrix/JASPAR
+@dirrm %%DATADIR%%/position_weight_matrix
+@dirrm %%DATADIR%%/manuals
+@dirrm %%DATADIR%%/enzymes
+@dirrm %%DATADIR%%/cmdline
+@dirrm %%DATADIR%%/biostruct3d_plugin
+@dirrm %%DATADIR%%/back_translation/Yeast
+@dirrm %%DATADIR%%/back_translation/Viruses
+@dirrm %%DATADIR%%/back_translation/Vertebrates
+@dirrm %%DATADIR%%/back_translation/Rodents
+@dirrm %%DATADIR%%/back_translation/Primates
+@dirrm %%DATADIR%%/back_translation/Plants
+@dirrm %%DATADIR%%/back_translation/Mammalia
+@dirrm %%DATADIR%%/back_translation/Invertebrates
+@dirrm %%DATADIR%%/back_translation/Bacteria
+@dirrm %%DATADIR%%/back_translation
+@dirrm %%DATADIR%%
+@dirrmtry share/applications
+@dirrm lib/ugene/plugins
+@dirrm lib/ugene