pkgsrc-WIP-changes archive
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index][Old Index]
maker: Import maker-3.01.03 as wip/maker.
Module Name: pkgsrc-wip
Committed By: Brook Milligan <brook%nmsu.edu@localhost>
Pushed By: brook
Date: Mon Sep 13 13:55:37 2021 -0600
Changeset: 869a821297ad0ec7963ccf27d695307ac91e202c
Modified Files:
Makefile
Added Files:
maker/DESCR
maker/Makefile
maker/PLIST
maker/distinfo
maker/patches/patch-src_Build.PL
Log Message:
maker: Import maker-3.01.03 as wip/maker.
MAKER is a portable and easily configurable genome annotation
pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic
genome projects to independently annotate their genomes and to create
genome databases. MAKER identifies repeats, aligns ESTs and proteins
to a genome, produces ab-initio gene predictions and automatically
synthesizes these data into gene annotations having evidence-based
quality values. MAKER is also easily trainable: outputs of preliminary
runs can be used to automatically retrain its gene prediction
algorithm, producing higher quality gene-models on seusequent
runs. MAKER's inputs are minimal and its ouputs can be directly loaded
into a GMOD database. They can also be viewed in the Apollo genome
browser; this feature of MAKER provides an easy means to annotate,
view and edit individual contigs and BACs without the overhead of a
database. MAKER should prove especially useful for emerging model
organism projects with minimal bioinformatics expertise and computer
resources.
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=869a821297ad0ec7963ccf27d695307ac91e202c
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
Makefile | 1 +
maker/DESCR | 16 +++
maker/Makefile | 67 ++++++++++++
maker/PLIST | 230 +++++++++++++++++++++++++++++++++++++++
maker/distinfo | 7 ++
maker/patches/patch-src_Build.PL | 17 +++
6 files changed, 338 insertions(+)
diffs:
diff --git a/Makefile b/Makefile
index b3e1c4b1b1..8bfce28d0e 100644
--- a/Makefile
+++ b/Makefile
@@ -2294,6 +2294,7 @@ SUBDIR+= majordomo-devel
SUBDIR+= makedict
SUBDIR+= makejvf
SUBDIR+= makepp
+SUBDIR+= maker
SUBDIR+= malaga
SUBDIR+= maloc
SUBDIR+= man
diff --git a/maker/DESCR b/maker/DESCR
new file mode 100644
index 0000000000..b5fdc76013
--- /dev/null
+++ b/maker/DESCR
@@ -0,0 +1,16 @@
+MAKER is a portable and easily configurable genome annotation
+pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic
+genome projects to independently annotate their genomes and to create
+genome databases. MAKER identifies repeats, aligns ESTs and proteins
+to a genome, produces ab-initio gene predictions and automatically
+synthesizes these data into gene annotations having evidence-based
+quality values. MAKER is also easily trainable: outputs of preliminary
+runs can be used to automatically retrain its gene prediction
+algorithm, producing higher quality gene-models on seusequent
+runs. MAKER's inputs are minimal and its ouputs can be directly loaded
+into a GMOD database. They can also be viewed in the Apollo genome
+browser; this feature of MAKER provides an easy means to annotate,
+view and edit individual contigs and BACs without the overhead of a
+database. MAKER should prove especially useful for emerging model
+organism projects with minimal bioinformatics expertise and computer
+resources.
diff --git a/maker/Makefile b/maker/Makefile
new file mode 100644
index 0000000000..4ac8cdf3c8
--- /dev/null
+++ b/maker/Makefile
@@ -0,0 +1,67 @@
+# $NetBSD$
+
+DISTNAME= maker-3.01.03
+CATEGORIES= biology
+MASTER_SITES= http://weatherby.genetics.utah.edu/maker_downloads/E446/83FE/1E2C/EFF4EA9B639AD79928609B719046/ # XXX - private link
+EXTRACT_SUFX= .tgz
+
+MAINTAINER= pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE= https://www.yandell-lab.org/software/maker.html
+COMMENT= Genome annotation pipeline
+LICENSE= artistic OR gnu-gpl-v3
+
+WRKSRC= ${WRKDIR}/maker
+USE_TOOLS+= pax perl
+USE_LANGUAGES= # none
+
+DEPENDS+= bioperl>=1.7.7:../../biology/bioperl
+DEPENDS+= p5-DBD-SQLite>=1.66:../../databases/p5-DBD-SQLite
+DEPENDS+= p5-DBD-postgresql>=3.14.2:../../databases/p5-DBD-postgresql # option?
+DEPENDS+= p5-Bit-Vector>=7.4:../../devel/p5-Bit-Vector
+DEPENDS+= p5-IO-All>=0.87:../../devel/p5-IO-All
+DEPENDS+= p5-Inline-C>=0.81:../../devel/p5-Inline-C
+DEPENDS+= p5-Want>=0.29:../../devel/p5-Want
+DEPENDS+= p5-forks>=0.36:../../devel/p5-forks
+
+DEPENDS+= p5-Perl-Unsafe-Signals>=0.03:../../wip/p5-Perl-Unsafe-Signals # devel
+DEPENDS+= exonerate>=2.2.0:../../wip/exonerate
+DEPENDS+= repeatmasker>=4.1.2.1:../../wip/repeatmasker
+DEPENDS+= SNAP>=0.0.0.20190603:../../wip/SNAP
+
+REPLACE_PERL+= lib/Datastore/bin/ds_dir
+REPLACE_PERL+= lib/Datastore/bin/ds_do
+REPLACE_PERL+= lib/File/maintain.pl
+REPLACE_PERL+= lib/Gene_obj.pm
+REPLACE_PERL+= lib/Longest_orf.pm
+REPLACE_PERL+= lib/Nuc_translator.pm
+REPLACE_PERL+= lib/Widget/fgenesh/fgenesh_wrap
+REPLACE_PERL+= lib/Widget/genemark/gmhmm_wrap
+
+INSTALLATION_DIRS+= maker share/doc/maker
+
+post-extract:
+ ${CHMOD} a-x ${WRKSRC}/lib/CGL/Annotation/GFF3/DictyBase.pm
+ ${CHMOD} a-x ${WRKSRC}/lib/CGL/Annotation/GFF3/FlyBase.pm
+ ${CHMOD} a-x ${WRKSRC}/lib/CGL/Annotation/GFF3/Maker.pm
+ ${CHMOD} a-x ${WRKSRC}/lib/CGL/Annotation/GFF3/WormBase.pm
+ ${CHMOD} a-x ${WRKSRC}/lib/CGL/Annotation/GFF3/nGASP.pm
+ ${CHMOD} a-x ${WRKSRC}/lib/CGL/Annotation/GFF3/nGASP2.pm
+ ${CHMOD} a-x ${WRKSRC}/lib/Dumper/XML/Game_Xml.pm
+ ${CHMOD} a-x ${WRKSRC}/lib/evaluator/gff3_to_phatHit/FlyBase.pm
+ ${CHMOD} a-x ${WRKSRC}/lib/evaluator/gff3_to_phatHit/Maker.pm
+ ${CHMOD} a-x ${WRKSRC}/lib/evaluator/gff3_to_phatHit/WormBase.pm
+ ${CHMOD} a-x ${WRKSRC}/lib/polisher/exonerate/altest.pm
+ ${CHMOD} a-x ${WRKSRC}/lib/polisher/exonerate/est.pm
+ ${CHMOD} a-x ${WRKSRC}/lib/polisher/exonerate/protein.pm
+
+do-configure:
+ cd ${WRKSRC}/src && ${PERL5} Build.PL
+
+do-build:
+ cd ${WRKSRC}/src && ${PERL5} Build install
+
+do-install:
+ cd ${WRKSRC} && ${PAX} -rw bin lib data ${DESTDIR}${PREFIX}/maker
+ ${INSTALL_DATA} ${WRKSRC}/README ${DESTDIR}${PREFIX}/share/doc/maker
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/maker/PLIST b/maker/PLIST
new file mode 100644
index 0000000000..6b3a3e8067
--- /dev/null
+++ b/maker/PLIST
@@ -0,0 +1,230 @@
+@comment $NetBSD$
+maker/bin/AED_cdf_generator.pl
+maker/bin/cegma2zff
+maker/bin/chado2gff3
+maker/bin/compare_gff3_to_chado
+maker/bin/cufflinks2gff3
+maker/bin/evaluator
+maker/bin/fasta_merge
+maker/bin/fasta_tool
+maker/bin/genemark_gtf2gff3
+maker/bin/gff3_merge
+maker/bin/ipr_update_gff
+maker/bin/iprscan2gff3
+maker/bin/maker
+maker/bin/maker2chado
+maker/bin/maker2eval_gtf
+maker/bin/maker2jbrowse
+maker/bin/maker2wap
+maker/bin/maker2zff
+maker/bin/maker_functional_fasta
+maker/bin/maker_functional_gff
+maker/bin/maker_map_ids
+maker/bin/map2assembly
+maker/bin/map_data_ids
+maker/bin/map_fasta_ids
+maker/bin/map_gff_ids
+maker/bin/match2gene.pl
+maker/bin/quality_filter.pl
+maker/bin/split_gff3
+maker/bin/tophat2gff3
+maker/bin/train_augustus.pl
+maker/bin/zff2genbank.pl
+maker/data/dpp_contig.fasta
+maker/data/dpp_est.fasta
+maker/data/dpp_protein.fasta
+maker/data/evm_weights.txt
+maker/data/hsap_contig.fasta
+maker/data/hsap_est.fasta
+maker/data/hsap_protein.fasta
+maker/data/te_proteins.fasta
+maker/lib/Bio/Search/HSP/PhatHSP.pod
+maker/lib/Bio/Search/HSP/PhatHSP/Base.pm
+maker/lib/Bio/Search/HSP/PhatHSP/augustus.pm
+maker/lib/Bio/Search/HSP/PhatHSP/blastn.pm
+maker/lib/Bio/Search/HSP/PhatHSP/blastx.pm
+maker/lib/Bio/Search/HSP/PhatHSP/cdna2genome.pm
+maker/lib/Bio/Search/HSP/PhatHSP/est2genome.pm
+maker/lib/Bio/Search/HSP/PhatHSP/evm.pm
+maker/lib/Bio/Search/HSP/PhatHSP/fgenesh.pm
+maker/lib/Bio/Search/HSP/PhatHSP/genemark.pm
+maker/lib/Bio/Search/HSP/PhatHSP/gff3.pm
+maker/lib/Bio/Search/HSP/PhatHSP/protein2genome.pm
+maker/lib/Bio/Search/HSP/PhatHSP/qrna.pm
+maker/lib/Bio/Search/HSP/PhatHSP/rapsearch.pm
+maker/lib/Bio/Search/HSP/PhatHSP/repeatmasker.pm
+maker/lib/Bio/Search/HSP/PhatHSP/snap.pm
+maker/lib/Bio/Search/HSP/PhatHSP/snoscan.pm
+maker/lib/Bio/Search/HSP/PhatHSP/tblastx.pm
+maker/lib/Bio/Search/HSP/PhatHSP/trnascan.pm
+maker/lib/Bio/Search/Hit/PhatHit.pod
+maker/lib/Bio/Search/Hit/PhatHit/Base.pm
+maker/lib/Bio/Search/Hit/PhatHit/augustus.pm
+maker/lib/Bio/Search/Hit/PhatHit/blastn.pm
+maker/lib/Bio/Search/Hit/PhatHit/blastx.pm
+maker/lib/Bio/Search/Hit/PhatHit/cdna2genome.pm
+maker/lib/Bio/Search/Hit/PhatHit/est2genome.pm
+maker/lib/Bio/Search/Hit/PhatHit/evm.pm
+maker/lib/Bio/Search/Hit/PhatHit/fgenesh.pm
+maker/lib/Bio/Search/Hit/PhatHit/genemark.pm
+maker/lib/Bio/Search/Hit/PhatHit/gff3.pm
+maker/lib/Bio/Search/Hit/PhatHit/protein2genome.pm
+maker/lib/Bio/Search/Hit/PhatHit/qrna.pm
+maker/lib/Bio/Search/Hit/PhatHit/rapsearch.pm
+maker/lib/Bio/Search/Hit/PhatHit/repeatmasker.pm
+maker/lib/Bio/Search/Hit/PhatHit/snap.pm
+maker/lib/Bio/Search/Hit/PhatHit/snoscan.pm
+maker/lib/Bio/Search/Hit/PhatHit/tblastx.pm
+maker/lib/Bio/Search/Hit/PhatHit/trnascan.pm
+maker/lib/Bio/SearchIO/wublasttable.pm
+maker/lib/CGL/Annotation.pm
+maker/lib/CGL/Annotation/Feature.pm
+maker/lib/CGL/Annotation/Feature/Contig.pm
+maker/lib/CGL/Annotation/Feature/Exon.pm
+maker/lib/CGL/Annotation/Feature/Gene.pm
+maker/lib/CGL/Annotation/Feature/Intron.pm
+maker/lib/CGL/Annotation/Feature/Protein.pm
+maker/lib/CGL/Annotation/Feature/Sequence_variant.pm
+maker/lib/CGL/Annotation/Feature/Transcript.pm
+maker/lib/CGL/Annotation/FeatureLocation.pm
+maker/lib/CGL/Annotation/FeatureRelationship.pm
+maker/lib/CGL/Annotation/GFF3/DictyBase.pm
+maker/lib/CGL/Annotation/GFF3/FlyBase.pm
+maker/lib/CGL/Annotation/GFF3/Maker.pm
+maker/lib/CGL/Annotation/GFF3/Maker_snap.pm
+maker/lib/CGL/Annotation/GFF3/WormBase.pm
+maker/lib/CGL/Annotation/GFF3/nGASP.pm
+maker/lib/CGL/Annotation/GFF3/nGASP2.pm
+maker/lib/CGL/Annotation/Iterator.pm
+maker/lib/CGL/Annotation/Trace.pm
+maker/lib/CGL/Clone.pm
+maker/lib/CGL/Ontology/GO.pm
+maker/lib/CGL/Ontology/Node.pm
+maker/lib/CGL/Ontology/NodeRelationship.pm
+maker/lib/CGL/Ontology/Ontology.pm
+maker/lib/CGL/Ontology/Parser/OBO.pm
+maker/lib/CGL/Ontology/SO.pm
+maker/lib/CGL/Ontology/Trace.pm
+maker/lib/CGL/Revcomp.pm
+maker/lib/CGL/TranslationMachine.pm
+maker/lib/CGL/Version.pm
+maker/lib/CGL/gene_ontology.obo
+maker/lib/CGL/so.new.obo
+maker/lib/CGL/so.obo
+maker/lib/CGL/sofa.obo
+maker/lib/Datastore/Base.pm
+maker/lib/Datastore/CG.pm
+maker/lib/Datastore/MD5.pm
+maker/lib/Datastore/bin/ds_dir
+maker/lib/Datastore/bin/ds_do
+maker/lib/Dumper/GFF/GFFV3.pm
+maker/lib/Dumper/XML/Game.pm
+maker/lib/Dumper/XML/Game_Xml.pm
+maker/lib/Error.pm
+maker/lib/Error/Simple.pm
+maker/lib/Fasta.pm
+maker/lib/FastaChunk.pm
+maker/lib/FastaChunker.pm
+maker/lib/FastaDB.pm
+maker/lib/FastaFile.pm
+maker/lib/FastaSeq.pm
+maker/lib/File/NFSLock.pm
+maker/lib/File/Which.pm
+maker/lib/File/maintain.pl
+maker/lib/GFFDB.pm
+maker/lib/GI.pm
+maker/lib/Gene_obj.pm
+maker/lib/IO/Prompt.pm
+maker/lib/Iterator.pm
+maker/lib/Iterator/Any.pm
+maker/lib/Iterator/Fasta.pm
+maker/lib/Iterator/GFF3.pm
+maker/lib/Longest_orf.pm
+maker/lib/MWAS_util.pm
+maker/lib/Nuc_translator.pm
+maker/lib/Parallel/Application.pm
+maker/lib/PhatHit_utils.pm
+maker/lib/PostData.pm
+maker/lib/Proc/ProcessTable_simple.pm
+maker/lib/Proc/Signal.pm
+maker/lib/Process/IPRchunk.pm
+maker/lib/Process/MpiChunk.pm
+maker/lib/Process/MpiTiers.pm
+maker/lib/Process/mapChunk.pm
+maker/lib/Shadower.pm
+maker/lib/SimpleCluster.pm
+maker/lib/SpaceBase.pm
+maker/lib/Widget.pm
+maker/lib/Widget/PolyBayes.pm
+maker/lib/Widget/RepeatMasker.pm
+maker/lib/Widget/augustus.pm
+maker/lib/Widget/blastn.pm
+maker/lib/Widget/blastx.pm
+maker/lib/Widget/evm.pm
+maker/lib/Widget/exonerate.pm
+maker/lib/Widget/exonerate/cdna2genome.pm
+maker/lib/Widget/exonerate/est2genome.pm
+maker/lib/Widget/exonerate/protein2genome.pm
+maker/lib/Widget/fgenesh.pm
+maker/lib/Widget/fgenesh/fgenesh_wrap
+maker/lib/Widget/formatdb.pm
+maker/lib/Widget/formater.pm
+maker/lib/Widget/genemark.pm
+maker/lib/Widget/genemark/gmhmm_wrap
+maker/lib/Widget/iprscan.pm
+maker/lib/Widget/pressdb.pm
+maker/lib/Widget/primer3.pm
+maker/lib/Widget/qrna.pm
+maker/lib/Widget/rapsearch.pm
+maker/lib/Widget/setdb.pm
+maker/lib/Widget/snap.pm
+maker/lib/Widget/snoscan.pm
+maker/lib/Widget/tblastx.pm
+maker/lib/Widget/trnascan.pm
+maker/lib/Widget/xdformat.pm
+maker/lib/auto/Datastore/.packlist
+maker/lib/auto/Datastore/Base/autosplit.ix
+maker/lib/auto/Datastore/CG/autosplit.ix
+maker/lib/auto/Datastore/MD5/autosplit.ix
+maker/lib/auto/Error/.packlist
+maker/lib/basiclog.pm
+maker/lib/clean.pm
+maker/lib/cluster.pm
+maker/lib/compare.pm
+maker/lib/ds_utility.pm
+maker/lib/evaluator/AED.pm
+maker/lib/evaluator/Widget/blast.pm
+maker/lib/evaluator/evaluate.pm
+maker/lib/evaluator/fathom_utils.pm
+maker/lib/evaluator/funs.pm
+maker/lib/evaluator/gff3_to_phatHit/FlyBase.pm
+maker/lib/evaluator/gff3_to_phatHit/Maker.pm
+maker/lib/evaluator/gff3_to_phatHit/WormBase.pm
+maker/lib/evaluator/gff3_to_phatHit/gff3_classifier.pm
+maker/lib/evaluator/hey_gff3_to_phatHit.pm
+maker/lib/evaluator/maker_gff.pm
+maker/lib/evaluator/master_codes
+maker/lib/evaluator/pseudo_hit.pm
+maker/lib/evaluator/quality_index.pm
+maker/lib/evaluator/quality_seq.pm
+maker/lib/evaluator/scoring.pm
+maker/lib/evaluator/so_classifier.pm
+maker/lib/exonerate/splice_info.pm
+maker/lib/external_gff/PhatHit.pm
+maker/lib/external_gff/PhatHsp.pm
+maker/lib/iprscan/runlog.pm
+maker/lib/maker/auto_annotator.pm
+maker/lib/maker/join.pm
+maker/lib/maker/quality_index.pm
+maker/lib/maker/sens_spec.pm
+maker/lib/polisher.pm
+maker/lib/polisher/exonerate.pm
+maker/lib/polisher/exonerate/altest.pm
+maker/lib/polisher/exonerate/est.pm
+maker/lib/polisher/exonerate/protein.pm
+maker/lib/repeat_mask_seq.pm
+maker/lib/runlog.pm
+maker/lib/shadow_AED.pm
+share/doc/maker/README
+@pkgdir maker/lib/verifier
+@pkgdir maker/lib/Parallel/Application
diff --git a/maker/distinfo b/maker/distinfo
new file mode 100644
index 0000000000..ddf21a2d36
--- /dev/null
+++ b/maker/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+SHA1 (maker-3.01.03.tgz) = a90bd2d6501b986df38f4422cd3a5ee0a25d2096
+RMD160 (maker-3.01.03.tgz) = dd7de7af1b863a915961cb23167a2a67deaab013
+SHA512 (maker-3.01.03.tgz) = a1cc47768589686912ed5f3450ff8befce5c8e8a44f6dfb1506f555ba98501053b9c0f0ef76ff56636b4f44e33fe5cc51d5fbe44362c3a640f6998ba7bc39bd4
+Size (maker-3.01.03.tgz) = 13647120 bytes
+SHA1 (patch-src_Build.PL) = d16b62ed93b97eaa9efbba3d9c78d2285f1b6db4
diff --git a/maker/patches/patch-src_Build.PL b/maker/patches/patch-src_Build.PL
new file mode 100644
index 0000000000..339eca7820
--- /dev/null
+++ b/maker/patches/patch-src_Build.PL
@@ -0,0 +1,17 @@
+$NetBSD$
+
+Do not install MPI support.
+
+--- src/Build.PL.orig 2017-10-17 19:27:18.000000000 +0000
++++ src/Build.PL
+@@ -128,9 +128,7 @@ if(my $any = $build->args('AnyDBM_ISA'))
+ }
+
+ #ask for MPI
+-my $go = $build->y_n("\nMAKER supports distributed parallelization via MPI.\n".
+- "Would you like to configure MAKER for MPI (This\n".
+- "requires that you have an MPI client installed)?", 'N');
++my $go = 0;
+ $build->feature(mpi_support => $go);
+ $build->config_mpi() if($go);
+
Home |
Main Index |
Thread Index |
Old Index