git: 8b43ef57fd38 - main - biology/augustus: New port: Genome annotation tool

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From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Fri, 25 Nov 2022 23:55:13 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=8b43ef57fd38af532b6619eaade5b35b053b4afd

commit 8b43ef57fd38af532b6619eaade5b35b053b4afd
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2022-11-25 23:50:50 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2022-11-25 23:55:09 +0000

    biology/augustus: New port: Genome annotation tool
---
 biology/Makefile                                   |    1 +
 biology/augustus/Makefile                          |   46 +
 biology/augustus/distinfo                          |    3 +
 biology/augustus/files/patch-Makefile              |   30 +
 .../files/patch-scripts_pasapolyA2hints.pl         |    8 +
 biology/augustus/pkg-descr                         |    8 +
 biology/augustus/pkg-plist                         | 1523 ++++++++++++++++++++
 7 files changed, 1619 insertions(+)

diff --git a/biology/Makefile b/biology/Makefile
index a4b704020908..fc30f158d16a 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -3,6 +3,7 @@
     SUBDIR += abyss
     SUBDIR += ad2vcf
     SUBDIR += artemis
+    SUBDIR += augustus
     SUBDIR += avida
     SUBDIR += babel
     SUBDIR += bamtools
diff --git a/biology/augustus/Makefile b/biology/augustus/Makefile
new file mode 100644
index 000000000000..fd393183dc52
--- /dev/null
+++ b/biology/augustus/Makefile
@@ -0,0 +1,46 @@
+PORTNAME=	augustus
+DISTVERSIONPREFIX=	v
+DISTVERSION=	3.5.0
+CATEGORIES=	biology science
+PKGNAMESUFFIX=	-gene-prediction
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	Genome annotation tool
+WWW=		http://bioinf.uni-greifswald.de/webaugustus/
+
+LICENSE=	GPLv3
+
+LIB_DEPENDS=	libbamtools.so:biology/bamtools \
+		libboost_iostreams.so:devel/boost-libs \
+		libcolamd.so:math/suitesparse-colamd \
+		libgsl.so:math/gsl \
+		libhts.so:biology/htslib \
+		liblpsolve55.so:math/lp_solve \
+		libmysqlpp.so:databases/mysql++
+RUN_DEPENDS=	samtools:biology/samtools
+
+USES=		gmake localbase:ldflags mysql perl5 python sqlite shebangfix
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	Gaius-Augustus
+GH_PROJECT=	Augustus
+
+SHEBANG_GLOB=	*.pl *.py
+SHEBANG_FILES=	scripts/checkUTR
+
+CXXFLAGS+=	-I${LOCALBASE}/include/bamtools \
+		-I${LOCALBASE}/include/lpsolve \
+		-I${LOCALBASE}/include/mysql
+LDFLAGS+=	-L${LOCALBASE}/lib/mysql
+
+MAKE_ARGS=	INSTALLDIR=${LOCALBASE}/${PORTNAME} RLN="${RLN}"
+
+BINARY_ALIAS=	make=${GMAKE} python3=${PYTHON_CMD}
+
+TEST_TARGET=	test
+
+post-install:
+	@${STRIP_CMD} ${STAGEDIR}${PREFIX}/${PORTNAME}/bin/*
+	@${RM} ${STAGEDIR}${PREFIX}/${PORTNAME}/scripts/pasapolyA2hints.pl.orig
+
+.include <bsd.port.mk>
diff --git a/biology/augustus/distinfo b/biology/augustus/distinfo
new file mode 100644
index 000000000000..108ef5b16514
--- /dev/null
+++ b/biology/augustus/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1669409399
+SHA256 (Gaius-Augustus-Augustus-v3.5.0_GH0.tar.gz) = 5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686
+SIZE (Gaius-Augustus-Augustus-v3.5.0_GH0.tar.gz) = 225918930
diff --git a/biology/augustus/files/patch-Makefile b/biology/augustus/files/patch-Makefile
new file mode 100644
index 000000000000..bbc8028a8378
--- /dev/null
+++ b/biology/augustus/files/patch-Makefile
@@ -0,0 +1,30 @@
+- workaround for The 'install' target doesn't work when stage directory is necessary, see https://github.com/Gaius-Augustus/Augustus/issues/366
+
+--- Makefile.orig	2022-09-23 17:06:14 UTC
++++ Makefile
+@@ -30,16 +30,16 @@ PREFIX = /usr/local
+ INSTALLDIR = /opt/augustus-$(AUGVERSION)
+ 
+ install:
+-	if [ ! $(PWD) -ef $(INSTALLDIR) ] ; then \
+-		install -d $(INSTALLDIR) && \
+-		cp -a config bin scripts $(INSTALLDIR) ; \
++	if [ ! $(PWD) -ef $(DESTDIR)$(INSTALLDIR) ] ; then \
++		install -d $(DESTDIR)$(INSTALLDIR) && \
++		cp -a config bin scripts $(DESTDIR)$(INSTALLDIR) ; \
+ 	fi
+-	ln -sf $(INSTALLDIR)/bin/augustus $(PREFIX)/bin/augustus
+-	ln -sf $(INSTALLDIR)/bin/etraining $(PREFIX)/bin/etraining
+-	ln -sf $(INSTALLDIR)/bin/prepareAlign $(PREFIX)/bin/prepareAlign
+-	ln -sf $(INSTALLDIR)/bin/fastBlockSearch $(PREFIX)/bin/fastBlockSearch
+-	if [ -f $(INSTALLDIR)/bin/load2db ] ; then ln -sf $(INSTALLDIR)/bin/load2db $(PREFIX)/bin/load2db ; fi
+-	if [ -f $(INSTALLDIR)/bin/getSeq ] ; then ln -sf $(INSTALLDIR)/bin/getSeq $(PREFIX)/bin/getSeq ; fi
++	$(RLN) $(DESTDIR)$(INSTALLDIR)/bin/augustus $(DESTDIR)$(PREFIX)/bin/augustus
++	$(RLN) $(DESTDIR)$(INSTALLDIR)/bin/etraining $(DESTDIR)$(PREFIX)/bin/etraining
++	$(RLN) $(DESTDIR)$(INSTALLDIR)/bin/prepareAlign $(DESTDIR)$(PREFIX)/bin/prepareAlign
++	$(RLN) $(DESTDIR)$(INSTALLDIR)/bin/fastBlockSearch $(DESTDIR)$(PREFIX)/bin/fastBlockSearch
++	if [ -f $(DESTDIR)$(INSTALLDIR)/bin/load2db ] ; then $(RLN) $(DESTDIR)$(INSTALLDIR)/bin/load2db $(DESTDIR)$(PREFIX)/bin/load2db ; fi
++	if [ -f $(DESTDIR)$(INSTALLDIR)/bin/getSeq ] ; then $(RLN) $(DESTDIR)$(INSTALLDIR)/bin/getSeq $(DESTDIR)$(PREFIX)/bin/getSeq ; fi
+ 
+ # for internal purposes:
+ release:
diff --git a/biology/augustus/files/patch-scripts_pasapolyA2hints.pl b/biology/augustus/files/patch-scripts_pasapolyA2hints.pl
new file mode 100644
index 000000000000..eaeaac89b9f6
--- /dev/null
+++ b/biology/augustus/files/patch-scripts_pasapolyA2hints.pl
@@ -0,0 +1,8 @@
+--- scripts/pasapolyA2hints.pl.orig	2022-11-25 23:03:59 UTC
++++ scripts/pasapolyA2hints.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/bin env
++#!/usr/bin/env perl
+ use strict;
+ use warnings;
+ use Getopt::Long;
diff --git a/biology/augustus/pkg-descr b/biology/augustus/pkg-descr
new file mode 100644
index 000000000000..886272f727a9
--- /dev/null
+++ b/biology/augustus/pkg-descr
@@ -0,0 +1,8 @@
+AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
+
+AUGUSTUS usually belongs to the most accurate programs for the species it is
+trained for. Often it is the most accurate ab initio program. For example, at
+the independent gene finder assessment (EGASP) on the human ENCODE regions
+AUGUSTUS was the most accurate gene finder among the tested ab initio programs.
+At the more recent nGASP (worm), it was among the best in the ab initio and
+transcript-based categories. See accuracy statistics for further details.
diff --git a/biology/augustus/pkg-plist b/biology/augustus/pkg-plist
new file mode 100644
index 000000000000..38eb9f1ea43d
--- /dev/null
+++ b/biology/augustus/pkg-plist
@@ -0,0 +1,1523 @@
+augustus/bin/aln2wig
+augustus/bin/augustus
+augustus/bin/bam2hints
+augustus/bin/bam2wig
+augustus/bin/compileSpliceCands
+augustus/bin/etraining
+augustus/bin/fastBlockSearch
+augustus/bin/filterBam
+augustus/bin/getSeq
+augustus/bin/homGeneMapping
+augustus/bin/joingenes
+augustus/bin/load2db
+augustus/bin/load2sqlitedb
+augustus/bin/pp_simScore
+augustus/bin/prepareAlign
+augustus/config/cgp/cgp_param_21features_accuracy_largerGrid.convDivCorrect.cfg
+augustus/config/cgp/log_reg_parameters_arabidopsis.cfg
+augustus/config/cgp/log_reg_parameters_default.cfg
+augustus/config/cgp/log_reg_parameters_fly.cfg
+augustus/config/cgp/log_reg_parameters_human.cfg
+augustus/config/cgp/log_reg_parameters_primates.cfg
+augustus/config/cgp/log_reg_parameters_s_aureus.cfg
+augustus/config/extrinsic/extrinsic-cgp.cfg
+augustus/config/extrinsic/extrinsic.E.XNT.cfg
+augustus/config/extrinsic/extrinsic.E.cfg
+augustus/config/extrinsic/extrinsic.M.RM.E.W.P.cfg
+augustus/config/extrinsic/extrinsic.M.RM.E.W.cfg
+augustus/config/extrinsic/extrinsic.M.RM.PB.cfg
+augustus/config/extrinsic/extrinsic.ME.cfg
+augustus/config/extrinsic/extrinsic.MEMS.cfg
+augustus/config/extrinsic/extrinsic.MP.cfg
+augustus/config/extrinsic/extrinsic.MPE.cfg
+augustus/config/extrinsic/extrinsic.MT.cfg
+augustus/config/extrinsic/extrinsic.cfg
+augustus/config/model/constraints_shadow_partial.txt
+augustus/config/model/constraints_shadow_partial_utr.txt
+augustus/config/model/ovlp_len.pbl
+augustus/config/model/ovlp_len_archaea.pbl
+augustus/config/model/states_shadow.cfg
+augustus/config/model/states_shadow_2igenic.cfg
+augustus/config/model/states_shadow_bacterium.cfg
+augustus/config/model/states_shadow_intronless.cfg
+augustus/config/model/states_shadow_utr.cfg
+augustus/config/model/states_shadow_utr_nc.cfg
+augustus/config/model/states_singlestrand.cfg
+augustus/config/model/states_singlestrand_2igenic.cfg
+augustus/config/model/trans_shadow_atleastone.pbl
+augustus/config/model/trans_shadow_bacterium.pbl
+augustus/config/model/trans_shadow_complete.pbl
+augustus/config/model/trans_shadow_complete_utr.pbl
+augustus/config/model/trans_shadow_exactlyone.pbl
+augustus/config/model/trans_shadow_intronless.pbl
+augustus/config/model/trans_shadow_partial.pbl
+augustus/config/model/trans_shadow_partial_utr.pbl
+augustus/config/model/trans_shadow_partial_utr_nc.pbl
+augustus/config/model/trans_singlestrand_atleastone.pbl
+augustus/config/model/trans_singlestrand_complete.pbl
+augustus/config/model/trans_singlestrand_exactlyone.pbl
+augustus/config/model/trans_singlestrand_partial.pbl
+augustus/config/parameters/AUG_CMDLN_PARAMETERS.md
+augustus/config/parameters/aug_cmdln_parameters.json
+augustus/config/profile/blosum55.qij
+augustus/config/profile/blosum62.qij
+augustus/config/profile/default.qij
+augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_exon_probs.pbl
+augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_igenic_probs.pbl
+augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_intron_probs.pbl
+augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.cfg
+augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.cgp.cfg
+augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.utr.cfg
+augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_parameters.cfg
+augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_weightmatrix.txt
+augustus/config/species/Anopheles_gambiae/README.txt
+augustus/config/species/Argopecten_irradians/Argopecten_irradians_exon_probs.pbl
+augustus/config/species/Argopecten_irradians/Argopecten_irradians_igenic_probs.pbl
+augustus/config/species/Argopecten_irradians/Argopecten_irradians_intron_probs.pbl
+augustus/config/species/Argopecten_irradians/Argopecten_irradians_metapars.cfg
+augustus/config/species/Argopecten_irradians/Argopecten_irradians_metapars.cgp.cfg
+augustus/config/species/Argopecten_irradians/Argopecten_irradians_metapars.utr.cfg
+augustus/config/species/Argopecten_irradians/Argopecten_irradians_parameters.cfg
+augustus/config/species/Argopecten_irradians/Argopecten_irradians_weightmatrix.txt
+augustus/config/species/Argopecten_irradians/README.txt
+augustus/config/species/Aurelia_aurita/Aurelia_aurita_exon_probs.pbl
+augustus/config/species/Aurelia_aurita/Aurelia_aurita_igenic_probs.pbl
+augustus/config/species/Aurelia_aurita/Aurelia_aurita_intron_probs.pbl
+augustus/config/species/Aurelia_aurita/Aurelia_aurita_metapars.cfg
+augustus/config/species/Aurelia_aurita/Aurelia_aurita_metapars.cgp.cfg
+augustus/config/species/Aurelia_aurita/Aurelia_aurita_metapars.utr.cfg
+augustus/config/species/Aurelia_aurita/Aurelia_aurita_parameters.cfg
+augustus/config/species/Aurelia_aurita/Aurelia_aurita_weightmatrix.txt
+augustus/config/species/Aurelia_aurita/README.txt
+augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_exon_probs.pbl
+augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_igenic_probs.pbl
+augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_intron_probs.pbl
+augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.cfg
+augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.cgp.cfg
+augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.utr.cfg
+augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_parameters.cfg
+augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_weightmatrix.txt
+augustus/config/species/Bathycoccus_prasinos/README.txt
+augustus/config/species/Berviolum_minutum/Berviolum_minutum_exon_probs.pbl
+augustus/config/species/Berviolum_minutum/Berviolum_minutum_igenic_probs.pbl
+augustus/config/species/Berviolum_minutum/Berviolum_minutum_intron_probs.pbl
+augustus/config/species/Berviolum_minutum/Berviolum_minutum_metapars.cfg
+augustus/config/species/Berviolum_minutum/Berviolum_minutum_metapars.cgp.cfg
+augustus/config/species/Berviolum_minutum/Berviolum_minutum_metapars.utr.cfg
+augustus/config/species/Berviolum_minutum/Berviolum_minutum_parameters.cfg
+augustus/config/species/Berviolum_minutum/Berviolum_minutum_weightmatrix.txt
+augustus/config/species/Berviolum_minutum/README.txt
+augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_exon_probs.pbl
+augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_igenic_probs.pbl
+augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_intron_probs.pbl
+augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.cfg
+augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.cgp.cfg
+augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.utr.cfg
+augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_parameters.cfg
+augustus/config/species/Branchiostoma_floridae/Branchiostoma_floridae_weightmatrix.txt
+augustus/config/species/Branchiostoma_floridae/README.txt
+augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_exon_probs.pbl
+augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_igenic_probs.pbl
+augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_intron_probs.pbl
+augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.cfg
+augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.cgp.cfg
+augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.utr.cfg
+augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_parameters.cfg
+augustus/config/species/Cassiopea_xamachana/Cassiopea_xamachana_weightmatrix.txt
+augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_exon_probs.pbl
+augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_igenic_probs.pbl
+augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_intron_probs.pbl
+augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.cfg
+augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.cgp.cfg
+augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.utr.cfg
+augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_parameters.cfg
+augustus/config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_weightmatrix.txt
+augustus/config/species/Chlamydomonas_eustigma/README.txt
+augustus/config/species/Chloropicon_primus/Chloropicon_primus_exon_probs.pbl
+augustus/config/species/Chloropicon_primus/Chloropicon_primus_igenic_probs.pbl
+augustus/config/species/Chloropicon_primus/Chloropicon_primus_intron_probs.pbl
+augustus/config/species/Chloropicon_primus/Chloropicon_primus_metapars.cfg
+augustus/config/species/Chloropicon_primus/Chloropicon_primus_metapars.cgp.cfg
+augustus/config/species/Chloropicon_primus/Chloropicon_primus_metapars.utr.cfg
+augustus/config/species/Chloropicon_primus/Chloropicon_primus_parameters.cfg
+augustus/config/species/Chloropicon_primus/Chloropicon_primus_weightmatrix.txt
+augustus/config/species/Chloropicon_primus/README.txt
+augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_exon_probs.pbl
+augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_igenic_probs.pbl
+augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_intron_probs.pbl
+augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.cfg
+augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.cgp.cfg
+augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.utr.cfg
+augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_parameters.cfg
+augustus/config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_weightmatrix.txt
+augustus/config/species/Chrysaora_chesapeakei/README.txt
+augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_exon_probs.pbl
+augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_igenic_probs.pbl
+augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_intron_probs.pbl
+augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_metapars.cfg
+augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_metapars.utr.cfg
+augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_parameters.cfg
+augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_utr_probs.pbl
+augustus/config/species/Conidiobolus_coronatus/Conidiobolus_coronatus_weightmatrix.txt
+augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_exon_probs.pbl
+augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_igenic_probs.pbl
+augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_intron_probs.pbl
+augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.cfg
+augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.cgp.cfg
+augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.utr.cfg
+augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_parameters.cfg
+augustus/config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_weightmatrix.txt
+augustus/config/species/Cryptosporidium_hominis/README.txt
+augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_exon_probs.pbl
+augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_igenic_probs.pbl
+augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_intron_probs.pbl
+augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.cfg
+augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.cgp.cfg
+augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.utr.cfg
+augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_parameters.cfg
+augustus/config/species/Cyclotella_cryptica/Cyclotella_cryptica_weightmatrix.txt
+augustus/config/species/Cyclotella_cryptica/README.txt
+augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_exon_probs.pbl
+augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_igenic_probs.pbl
+augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_intron_probs.pbl
+augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.cfg
+augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.cgp.cfg
+augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.utr.cfg
+augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_parameters.cfg
+augustus/config/species/Dermasterias_imbricata/Dermasterias_imbricata_weightmatrix.txt
+augustus/config/species/Dermasterias_imbricata/README.txt
+augustus/config/species/Dunaliella_salina/Dunaliella_salina_exon_probs.pbl
+augustus/config/species/Dunaliella_salina/Dunaliella_salina_igenic_probs.pbl
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