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Fri, 25 Nov 2022 23:55:13 GMT (envelope-from git) Date: Fri, 25 Nov 2022 23:55:13 GMT Message-Id: <202211252355.2APNtDwd004929@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: 8b43ef57fd38 - main - biology/augustus: New port: Genome annotation tool List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 8b43ef57fd38af532b6619eaade5b35b053b4afd Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=8b43ef57fd38af532b6619eaade5b35b053b4afd commit 8b43ef57fd38af532b6619eaade5b35b053b4afd Author: Yuri Victorovich AuthorDate: 2022-11-25 23:50:50 +0000 Commit: Yuri Victorovich 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}/${PORTNAME}/scripts/pasapolyA2hints.pl.orig + +.include diff --git a/biology/augustus/distinfo b/biology/augustus/distinfo new file mode 100644 index 000000000000..108ef5b16514 --- /dev/null +++ b/biology/augustus/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1669409399 +SHA256 (Gaius-Augustus-Augustus-v3.5.0_GH0.tar.gz) = 5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686 +SIZE (Gaius-Augustus-Augustus-v3.5.0_GH0.tar.gz) = 225918930 diff --git a/biology/augustus/files/patch-Makefile b/biology/augustus/files/patch-Makefile new file mode 100644 index 000000000000..bbc8028a8378 --- /dev/null +++ b/biology/augustus/files/patch-Makefile @@ -0,0 +1,30 @@ +- workaround for The 'install' target doesn't work when stage directory is necessary, see https://github.com/Gaius-Augustus/Augustus/issues/366 + +--- Makefile.orig 2022-09-23 17:06:14 UTC ++++ Makefile +@@ -30,16 +30,16 @@ PREFIX = /usr/local + INSTALLDIR = /opt/augustus-$(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 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