p5-transdecoder: Upgrade to 5.3.0

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri Sep 14 15:30:14 2018 -0500
Changeset:	a096bce2a9d20c26e439c0e37342db71cdc62ec9

Modified Files:
	p5-transdecoder/Makefile
	p5-transdecoder/PLIST
	p5-transdecoder/distinfo

Log Message:
p5-transdecoder: Upgrade to 5.3.0

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=a096bce2a9d20c26e439c0e37342db71cdc62ec9

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 p5-transdecoder/Makefile | 12 ++++++------
 p5-transdecoder/PLIST    | 35 ++++++++++++++++++++++++++---------
 p5-transdecoder/distinfo |  8 ++++----
 3 files changed, 36 insertions(+), 19 deletions(-)

diffs:
diff --git a/p5-transdecoder/Makefile b/p5-transdecoder/Makefile
index ddc57e4d7a..8442174ec5 100644
--- a/p5-transdecoder/Makefile
+++ b/p5-transdecoder/Makefile
@@ -8,11 +8,11 @@
 # p5-URI-ESC?
 # FIXME: Check use statements in all perl scripts for more deps
 
-DISTNAME=	p5-transdecoder-${PORTVERSION}
+DISTNAME=	p5-transdecoder-${PV}
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=TransDecoder/}
 GITHUB_PROJECT=	TransDecoder
-GITHUB_TAG=	${PORTVERSION}
+GITHUB_TAG=	TransDecoder-v${PV}
 
 MAINTAINER=	bacon%NetBSD.org@localhost
 HOMEPAGE=	http://transdecoder.github.io/
@@ -27,23 +27,23 @@ SUBST_SED.path+=	-e 's|$$FindBin::RealBin/util|${PREFIX}/libexec/TransDecoder/ut
 SUBST_FILES.path+=	${WRKSRC}/TransDecoder*
 SUBST_FILES.path+=	${WRKSRC}/util/*.pl
 
-DEPENDS=	cdhit>=4.6.1:../../biology/cdhit \
+DEPENDS=	cdhit>=4.6.8:../../wip/cdhit \
 		p5-URI>=0:../../www/p5-URI
 
 USE_TOOLS=	perl
 REPLACE_BASH=	sample_data/runMe.sh util/pfam_mpi.pbs
-REPLACE_PERL=	util/*.pl sample_data/*.pl PerlLib/*.pm \
+REPLACE_PERL=	util/*.pl sample_data/*.pl PerlLib/*.pm PerlLib/*.ph \
 		TransDecoder.LongOrfs TransDecoder.Predict
 NO_BUILD=	yes
 
-PORTVERSION=	2.0.1
+PV=		5.3.0
 
 INSTALLATION_DIRS=	bin lib/TransDecoder/PerlLib libexec/TransDecoder/util
 
 do-install:
 	${INSTALL_SCRIPT} ${WRKSRC}/PerlLib/* \
 		${DESTDIR}${PREFIX}/lib/TransDecoder/PerlLib
-	${INSTALL_SCRIPT} ${WRKSRC}/TransDecoder* ${DESTDIR}${PREFIX}/bin
+	${INSTALL_SCRIPT} ${WRKSRC}/TransDecoder.LongOrfs ${WRKSRC}/TransDecoder.Predict ${DESTDIR}${PREFIX}/bin
 	${INSTALL_SCRIPT} ${WRKSRC}/util/*.pl \
 		${DESTDIR}${PREFIX}/libexec/TransDecoder/util
 
diff --git a/p5-transdecoder/PLIST b/p5-transdecoder/PLIST
index 42a42353cc..7bb1b422fe 100644
--- a/p5-transdecoder/PLIST
+++ b/p5-transdecoder/PLIST
@@ -1,26 +1,43 @@
 @comment $NetBSD$
 bin/TransDecoder.LongOrfs
 bin/TransDecoder.Predict
+lib/TransDecoder/PerlLib/DelimParser.pm
 lib/TransDecoder/PerlLib/Fasta_reader.pm
-lib/TransDecoder/PerlLib/GFF3_utils.pm
+lib/TransDecoder/PerlLib/Fasta_retriever.pm
+lib/TransDecoder/PerlLib/GFF3_utils2.pm
+lib/TransDecoder/PerlLib/GTF.pm
+lib/TransDecoder/PerlLib/GTF_utils2.pm
 lib/TransDecoder/PerlLib/Gene_obj.pm
-lib/TransDecoder/PerlLib/Gene_obj_indexer.pm
 lib/TransDecoder/PerlLib/Longest_orf.pm
 lib/TransDecoder/PerlLib/Nuc_translator.pm
-lib/TransDecoder/PerlLib/TiedHash.pm
+lib/TransDecoder/PerlLib/Overlap_piler.pm
+lib/TransDecoder/PerlLib/PWM.pm
+lib/TransDecoder/PerlLib/Pipeliner.pm
+lib/TransDecoder/PerlLib/Process_cmd.pm
+lib/TransDecoder/PerlLib/overlapping_nucs.ph
 libexec/TransDecoder/util/cdna_alignment_orf_to_genome_orf.pl
 libexec/TransDecoder/util/compute_base_probs.pl
-libexec/TransDecoder/util/cufflinks_gtf_genome_to_cdna_fasta.pl
-libexec/TransDecoder/util/cufflinks_gtf_to_alignment_gff3.pl
-libexec/TransDecoder/util/cufflinks_gtf_to_bed.pl
+libexec/TransDecoder/util/exclude_similar_proteins.pl
+libexec/TransDecoder/util/fasta_prot_checker.pl
 libexec/TransDecoder/util/ffindex_resume.pl
 libexec/TransDecoder/util/gene_list_to_gff.pl
+libexec/TransDecoder/util/get_FL_accs.pl
+libexec/TransDecoder/util/get_longest_ORF_per_transcript.pl
 libexec/TransDecoder/util/get_top_longest_fasta_entries.pl
 libexec/TransDecoder/util/gff3_file_to_bed.pl
 libexec/TransDecoder/util/gff3_file_to_proteins.pl
-libexec/TransDecoder/util/index_gff3_files_by_isoform.pl
+libexec/TransDecoder/util/gff3_gene_to_gtf_format.pl
+libexec/TransDecoder/util/gtf_genome_to_cdna_fasta.pl
+libexec/TransDecoder/util/gtf_to_alignment_gff3.pl
+libexec/TransDecoder/util/gtf_to_bed.pl
 libexec/TransDecoder/util/nr_ORFs_gff3.pl
 libexec/TransDecoder/util/pfam_runner.pl
+libexec/TransDecoder/util/refine_gff3_group_iso_strip_utrs.pl
+libexec/TransDecoder/util/refine_hexamer_scores.pl
 libexec/TransDecoder/util/remove_eclipsed_ORFs.pl
-libexec/TransDecoder/util/score_CDS_liklihood_all_6_frames.pl
-libexec/TransDecoder/util/seq_n_baseprobs_to_logliklihood_vals.pl
+libexec/TransDecoder/util/score_CDS_likelihood_all_6_frames.pl
+libexec/TransDecoder/util/select_best_ORFs_per_transcript.pl
+libexec/TransDecoder/util/seq_n_baseprobs_to_loglikelihood_vals.pl
+libexec/TransDecoder/util/start_codon_refinement.pl
+libexec/TransDecoder/util/train_start_PWM.pl
+libexec/TransDecoder/util/uri_unescape.pl
diff --git a/p5-transdecoder/distinfo b/p5-transdecoder/distinfo
index 513e6be78d..e9a0bc4a97 100644
--- a/p5-transdecoder/distinfo
+++ b/p5-transdecoder/distinfo
@@ -1,6 +1,6 @@
 $NetBSD$
 
-SHA1 (p5-transdecoder-2.0.1.tar.gz) = 1a36aa7ecb3af9e984eb9bee818871093fa1ab74
-RMD160 (p5-transdecoder-2.0.1.tar.gz) = d59644fc9f44f428ae5f001543e33ca3b7539aec
-SHA512 (p5-transdecoder-2.0.1.tar.gz) = fd12aeda089a12036e288e58eb0a3c3b9bb1f104f6821102d84ba6ddaec1a9dd32ec7937cd87129ff9814c7c8e26b6b98d27c6af8edd7ed6b5335c4878f649de
-Size (p5-transdecoder-2.0.1.tar.gz) = 9925281 bytes
+SHA1 (p5-transdecoder-5.3.0.tar.gz) = a615b4004aa81ebcc59472feeefafde09755b093
+RMD160 (p5-transdecoder-5.3.0.tar.gz) = bbf692ecba4a2eb2b45733badfc22dc636cd07c4
+SHA512 (p5-transdecoder-5.3.0.tar.gz) = c8f6458ca09831d91a583c0abdb09398493fa1dbc4d63c5f859db12a8005b1b7861c3b6836f59a4947a9b17b660adcc496e7c3805457a21a2572ecbd05de0449
+Size (p5-transdecoder-5.3.0.tar.gz) = 15699957 bytes