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biology/p5-transdecoder: Upgrade to 5.4.0

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Minor clean up to silence portlint
Approved by:    jrm (mentor, implicit)
This commit is contained in:
Jason W. Bacon 2018-10-23 12:51:20 +00:00
parent d73ac6dfb6
commit d201617835
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=482836
4 changed files with 44 additions and 30 deletions
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25
biology/p5-transdecoder/Makefile
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@ -1,9 +1,8 @@
# $FreeBSD$
PORTNAME= transdecoder
PORTVERSION= 2.1.0
PORTREVISION= 1
DISTVERSIONPREFIX=v
DISTVERSIONPREFIX= TransDecoder-v
DISTVERSION= 5.4.0
CATEGORIES= biology perl5
PKGNAMEPREFIX= p5-
@ -15,31 +14,35 @@ LICENSE= BSD3CLAUSE
RUN_DEPENDS= cd-hit>=4.6.1:biology/cd-hit \
p5-URI>0:net/p5-URI
NO_BUILD= yes
NO_ARCH= yes
USES= perl5 shebangfix
USE_GITHUB= yes
GH_PROJECT= TransDecoder
SHEBANG_FILES= sample_data/cufflinks_example/runMe.sh \
sample_data/pasa_example/runMe.sh \
sample_data/simple_transcriptome_target/runMe.sh \
util/pfam_mpi.pbs
USE_GITHUB= yes
GH_PROJECT= TransDecoder
NO_BUILD= yes
NO_ARCH= yes
PERL_MOD_DIR= ${PREFIX}/${SITE_PERL_REL}/${PORTNAME}
PERL_UTIL_DIR= ${PREFIX}/libexec/${PORTNAME}
SCRIPTS= ${WRKSRC}/TransDecoder.LongOrfs \
${WRKSRC}/TransDecoder.Predict
post-patch:
${REINPLACE_CMD} \
@${REINPLACE_CMD} \
-e 's|$$FindBin::RealBin/PerlLib|${PERL_MOD_DIR}|g' \
-e 's|$$FindBin::Bin/../PerlLib|${PERL_MOD_DIR}|g' \
-e 's|$$FindBin::RealBin/util|${PERL_UTIL_DIR}|g' \
${WRKSRC}/TransDecoder* ${WRKSRC}/util/*.pl
${SCRIPTS} \
${WRKSRC}/util/*.pl
do-install:
${MKDIR} ${STAGEDIR}${PERL_MOD_DIR} ${STAGEDIR}${PERL_UTIL_DIR}
@${MKDIR} ${STAGEDIR}${PERL_MOD_DIR} ${STAGEDIR}${PERL_UTIL_DIR}
${INSTALL_SCRIPT} ${WRKSRC}/PerlLib/* ${STAGEDIR}${PERL_MOD_DIR}
${INSTALL_SCRIPT} ${WRKSRC}/TransDecoder* ${STAGEDIR}${PREFIX}/bin
${INSTALL_SCRIPT} ${SCRIPTS} ${STAGEDIR}${PREFIX}/bin
${INSTALL_SCRIPT} ${WRKSRC}/util/*.pl ${STAGEDIR}${PERL_UTIL_DIR}
.include <bsd.port.mk>

5
biology/p5-transdecoder/distinfo
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@ -1,2 +1,3 @@
SHA256 (transdecoder-TransDecoder-v2.1.0_GH0.tar.gz) = 681a8dd72e482cb322d74d8431ddcda61f25c53ad5453d0e22c02c92b2157b24
SIZE (transdecoder-TransDecoder-v2.1.0_GH0.tar.gz) = 11500688
TIMESTAMP = 1540225907
SHA256 (transdecoder-TransDecoder-TransDecoder-v5.4.0_GH0.tar.gz) = a6fa776c6eac30922632df1a5362b7564bfcb05728daeb53d0c2c3a9dc899df5
SIZE (transdecoder-TransDecoder-TransDecoder-v5.4.0_GH0.tar.gz) = 15748557

8
biology/p5-transdecoder/pkg-descr
View File

@ -1,6 +1,6 @@
TransDecoder identifies candidate coding regions within transcript
sequences, such as those generated by de novo RNA-Seq transcript
assembly using Trinity, or constructed based on RNA-Seq alignments
to the genome using Tophat and Cufflinks.
TransDecoder identifies candidate coding regions within transcript sequences,
such as those generated by de novo RNA-Seq transcript assembly using Trinity,
or constructed based on RNA-Seq alignments to the genome using Tophat and
Cufflinks.
WWW: http://transdecoder.github.io/

36
biology/p5-transdecoder/pkg-plist
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@ -1,22 +1,23 @@
bin/TransDecoder.LongOrfs
bin/TransDecoder.LongOrfs.bak
bin/TransDecoder.Predict
bin/TransDecoder.Predict.bak
%%SITE_PERL%%/transdecoder/DelimParser.pm
%%SITE_PERL%%/transdecoder/Fasta_reader.pm
%%SITE_PERL%%/transdecoder/Fasta_retriever.pm
%%SITE_PERL%%/transdecoder/GFF3_utils.pm
%%SITE_PERL%%/transdecoder/GFF3_utils2.pm
%%SITE_PERL%%/transdecoder/GTF.pm
%%SITE_PERL%%/transdecoder/GTF_utils2.pm
%%SITE_PERL%%/transdecoder/Gene_obj.pm
%%SITE_PERL%%/transdecoder/Gene_obj_indexer.pm
%%SITE_PERL%%/transdecoder/Longest_orf.pm
%%SITE_PERL%%/transdecoder/Nuc_translator.pm
%%SITE_PERL%%/transdecoder/TiedHash.pm
%%SITE_PERL%%/transdecoder/Overlap_piler.pm
%%SITE_PERL%%/transdecoder/PWM.pm
%%SITE_PERL%%/transdecoder/Pipeliner.pm
%%SITE_PERL%%/transdecoder/Process_cmd.pm
%%SITE_PERL%%/transdecoder/overlapping_nucs.ph
libexec/transdecoder/cdna_alignment_orf_to_genome_orf.pl
libexec/transdecoder/compute_base_probs.pl
libexec/transdecoder/create_start_PSSM.pl
libexec/transdecoder/cufflinks_gtf_genome_to_cdna_fasta.pl
libexec/transdecoder/cufflinks_gtf_to_alignment_gff3.pl
libexec/transdecoder/cufflinks_gtf_to_bed.pl
libexec/transdecoder/extract_FL_subset.pl
libexec/transdecoder/exclude_similar_proteins.pl
libexec/transdecoder/fasta_prot_checker.pl
libexec/transdecoder/ffindex_resume.pl
libexec/transdecoder/gene_list_to_gff.pl
libexec/transdecoder/get_FL_accs.pl
@ -24,9 +25,18 @@ libexec/transdecoder/get_longest_ORF_per_transcript.pl
libexec/transdecoder/get_top_longest_fasta_entries.pl
libexec/transdecoder/gff3_file_to_bed.pl
libexec/transdecoder/gff3_file_to_proteins.pl
libexec/transdecoder/index_gff3_files_by_isoform.pl
libexec/transdecoder/gff3_gene_to_gtf_format.pl
libexec/transdecoder/gtf_genome_to_cdna_fasta.pl
libexec/transdecoder/gtf_to_alignment_gff3.pl
libexec/transdecoder/gtf_to_bed.pl
libexec/transdecoder/nr_ORFs_gff3.pl
libexec/transdecoder/pfam_runner.pl
libexec/transdecoder/refine_gff3_group_iso_strip_utrs.pl
libexec/transdecoder/refine_hexamer_scores.pl
libexec/transdecoder/remove_eclipsed_ORFs.pl
libexec/transdecoder/score_CDS_liklihood_all_6_frames.pl
libexec/transdecoder/seq_n_baseprobs_to_logliklihood_vals.pl
libexec/transdecoder/score_CDS_likelihood_all_6_frames.pl
libexec/transdecoder/select_best_ORFs_per_transcript.pl
libexec/transdecoder/seq_n_baseprobs_to_loglikelihood_vals.pl
libexec/transdecoder/start_codon_refinement.pl
libexec/transdecoder/train_start_PWM.pl
libexec/transdecoder/uri_unescape.pl