Attachment 168259 Details for Bug 207993 – Shar archive

Shar archive

p5-transdecoder-shar.txt (text/plain), 3.87 KB, created by Jason W. Bacon on 2016-03-15 21:16:10 UTC

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Creator: Jason W. Bacon

Created: 2016-03-15 21:16:10 UTC

Size: 3.87 KB

patch

obsolete

># This is a shell archive.  Save it in a file, remove anything before
># this line, and then unpack it by entering "sh file".  Note, it may
># create directories; files and directories will be owned by you and
># have default permissions.
>#
># This archive contains:
>#
>#	p5-transdecoder
>#	p5-transdecoder/Makefile
>#	p5-transdecoder/distinfo
>#	p5-transdecoder/pkg-descr
>#	p5-transdecoder/pkg-plist
>#
>echo c - p5-transdecoder
>mkdir -p p5-transdecoder > /dev/null 2>&1
>echo x - p5-transdecoder/Makefile
>sed 's/^X//' >p5-transdecoder/Makefile << '97824733b185d69b0364d9069a10c044'
>X# Created by: Jason Bacon <bacon4000@gmail.com>
>X# $FreeBSD$
>X
>XPORTNAME=	transdecoder
>XPORTVERSION=	2.0.1
>XCATEGORIES=	biology perl5
>XPKGNAMEPREFIX=	p5-
>X
>XMAINTAINER=	bacon4000@gmail.com
>XCOMMENT=	Identify candidate coding regions within transcript sequences
>X
>XLICENSE=	BSD3CLAUSE
>X
>XRUN_DEPENDS=	cd-hit>=4.6.1:${PORTSDIR}/biology/cd-hit \
>X		p5-URI>0:${PORTSDIR}/net/p5-URI
>X
>XNO_BUILD=	yes
>XNO_ARCH=	yes
>XUSES=		perl5 shebangfix
>XSHEBANG_FILES=	sample_data/runMe.sh util/pfam_mpi.pbs
>X
>XUSE_GITHUB=	yes
>XGH_PROJECT=	TransDecoder
>X
>XWRKSRC=		${WRKDIR}/${GH_PROJECT}-${PORTVERSION}
>X
>XPERL_MOD_DIR=	${PREFIX}/${SITE_PERL_REL}/${PORTNAME}
>XPERL_UTIL_DIR=	${PREFIX}/libexec/${PORTNAME}
>X
>Xpost-patch:
>X	${REINPLACE_CMD} \
>X		-e 's|$$FindBin::RealBin/PerlLib|${PERL_MOD_DIR}|g' \
>X		-e 's|$$FindBin::Bin/../PerlLib|${PERL_MOD_DIR}|g' \
>X		-e 's|$$FindBin::RealBin/util|${PERL_UTIL_DIR}|g' \
>X		${WRKSRC}/TransDecoder* ${WRKSRC}/util/*.pl
>X
>Xdo-install:
>X	${MKDIR} ${STAGEDIR}${PERL_MOD_DIR} ${STAGEDIR}${PERL_UTIL_DIR}
>X	${INSTALL_SCRIPT} ${WRKSRC}/PerlLib/* ${STAGEDIR}${PERL_MOD_DIR}
>X	${INSTALL_SCRIPT} ${WRKSRC}/TransDecoder* ${STAGEDIR}${PREFIX}/bin
>X	${INSTALL_SCRIPT} ${WRKSRC}/util/*.pl ${STAGEDIR}${PERL_UTIL_DIR}
>X
>X.include <bsd.port.mk>
>97824733b185d69b0364d9069a10c044
>echo x - p5-transdecoder/distinfo
>sed 's/^X//' >p5-transdecoder/distinfo << '653056f8226d02d9e24626b0578868ae'
>XSHA256 (transdecoder-TransDecoder-2.0.1_GH0.tar.gz) = ce069da72c8a04e739f8c057af4f97187bf587d3f0d3db40465dfc2c89393e22
>XSIZE (transdecoder-TransDecoder-2.0.1_GH0.tar.gz) = 9925281
>653056f8226d02d9e24626b0578868ae
>echo x - p5-transdecoder/pkg-descr
>sed 's/^X//' >p5-transdecoder/pkg-descr << '80111cc2aef71125cc7992da683105d7'
>XTransDecoder identifies candidate coding regions within transcript sequences,
>Xsuch as those generated by de novo RNA-Seq transcript assembly using Trinity,
>Xor constructed based on RNA-Seq alignments to the genome using Tophat and
>XCufflinks.
>X
>XWWW: http://transdecoder.github.io/
>80111cc2aef71125cc7992da683105d7
>echo x - p5-transdecoder/pkg-plist
>sed 's/^X//' >p5-transdecoder/pkg-plist << '30c49b0a369ae87c06ff586fbe4c06f6'
>Xbin/TransDecoder.LongOrfs
>Xbin/TransDecoder.LongOrfs.bak
>Xbin/TransDecoder.Predict
>Xbin/TransDecoder.Predict.bak
>X%%SITE_PERL%%/transdecoder/Fasta_reader.pm
>X%%SITE_PERL%%/transdecoder/GFF3_utils.pm
>X%%SITE_PERL%%/transdecoder/Gene_obj.pm
>X%%SITE_PERL%%/transdecoder/Gene_obj_indexer.pm
>X%%SITE_PERL%%/transdecoder/Longest_orf.pm
>X%%SITE_PERL%%/transdecoder/Nuc_translator.pm
>X%%SITE_PERL%%/transdecoder/TiedHash.pm
>Xlibexec/transdecoder/cdna_alignment_orf_to_genome_orf.pl
>Xlibexec/transdecoder/compute_base_probs.pl
>Xlibexec/transdecoder/cufflinks_gtf_genome_to_cdna_fasta.pl
>Xlibexec/transdecoder/cufflinks_gtf_to_alignment_gff3.pl
>Xlibexec/transdecoder/cufflinks_gtf_to_bed.pl
>Xlibexec/transdecoder/ffindex_resume.pl
>Xlibexec/transdecoder/gene_list_to_gff.pl
>Xlibexec/transdecoder/get_top_longest_fasta_entries.pl
>Xlibexec/transdecoder/gff3_file_to_bed.pl
>Xlibexec/transdecoder/gff3_file_to_proteins.pl
>Xlibexec/transdecoder/index_gff3_files_by_isoform.pl
>Xlibexec/transdecoder/nr_ORFs_gff3.pl
>Xlibexec/transdecoder/pfam_runner.pl
>Xlibexec/transdecoder/remove_eclipsed_ORFs.pl
>Xlibexec/transdecoder/score_CDS_liklihood_all_6_frames.pl
>Xlibexec/transdecoder/seq_n_baseprobs_to_logliklihood_vals.pl
>30c49b0a369ae87c06ff586fbe4c06f6
>exit
>

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Attachments on bug 207993: 168259