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Update to version 36.3.6d

Browse source 
PR:		ports/181883
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
This commit is contained in:
Pawel Pekala 2013-10-29 19:32:15 +00:00
parent f6502a6a6c
commit dfc46ed8d1
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=331982
5 changed files with 115 additions and 94 deletions
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73
biology/fasta3/Makefile
View file

@ -2,7 +2,7 @@
# $FreeBSD$
PORTNAME= fasta3
PORTVERSION= 36.3.6
PORTVERSION= 36.3.6d
CATEGORIES= biology
MASTER_SITES= http://faculty.virginia.edu/wrpearson/fasta/fasta36/
DISTNAME= fasta-${PORTVERSION}
@ -10,59 +10,60 @@ DISTNAME= fasta-${PORTVERSION}
MAINTAINER= ports@FreeBSD.org
COMMENT= Collection of programs for searching DNA and protein databases
OPTIONS_DEFINE= DOCS EXAMPLES
NO_CDROM= May not be sold or incorporated into a commercial product
WRKSRC= ${WRKDIR}/${DISTNAME}
BUILD_WRKSRC= ${WRKSRC}/src
INSTALL_WRKSRC= ${BUILD_WRKSRC}
SUB_FILES= pkg-message
MAKEFILE= Makefile.freebsd
MAKE_ENV= THR_LIBS="-pthread" XDIR="${STAGEDIR}${PREFIX}/bin" \
FASTA_HOST="$$(${UNAME} -n)"
XDIR= ${PREFIX}/bin
FASTA_HOST!= /usr/bin/uname -n
SUB_FILES= pkg-message
MAKE_ENV+= THR_LIBS=${PTHREAD_LIBS} XDIR=${XDIR} \
FASTA_HOST='"${FASTA_HOST}"'
PLIST_SUB= VER="${PORTVERSION:R:R}"
FASTA3_DOCS= README.versions \
MAN1_LINKS= fastf35.1 fasts35.1 fastm35.1 fastx35.1 fasty35.1 \
ggsearch35.1 lalign35.1 ssearch35.1 tfasta35.1 tfastf35.1 \
tfasts35.1 tfastx35.1 tfasty35.1 prfx35.1 prss35.1
MAN1_FILES= fasta36.1 fastf3.1 fasts3.1 prss3.1 map_db.1 ps_lav.1
DOC_FILES= README.versions \
fasta_func.doc readme.* fasta.defaults \
fasta.options fasta_versions.html changes*.html
DATA= data/*.mat
EXAMPLES= seq/*.aa seq/*.lc seq/*.seq seq/*.lib
MAN1= fasta36.1 fastf3.1 fasts3.1 prss3.1 map_db.1 ps_lav.1
MLINKS= fasta36.1 tfasta35.1 fasta36.1 fastx35.1 fasta36.1 tfastx35.1 \
fasta36.1 fasty35.1 fasta36.1 tfasty35.1 fasta36.1 ssearch35.1 \
fasta36.1 fastf35.1 fasta36.1 fasts35.1 fasta36.1 tfasts35.1 \
fasta36.1 fastm35.1 fasta36.1 tfastf35.1 fasta36.1 ggsearch35.1 \
fasta36.1 lalign35.1 fasta36.1 prss35.1 fasta36.1 prfx35.1
PLIST_SUB= VER=${PORTVERSION:R:R}
NO_STAGE= yes
post-patch:
@ ${CP} ${WRKSRC}/make/${MAKEFILE} ${BUILD_WRKSRC}/
@${CP} ${WRKSRC}/make/${MAKEFILE} ${BUILD_WRKSRC}
post-install:
${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${PREFIX}/bin/
${INSTALL_DATA} ${WRKSRC}/conf/fastlibs ${PREFIX}/etc/fastlibs.sample
@ ${MKDIR} ${DATADIR}
(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} * ${STAGEDIR}${PREFIX}/bin)
(cd ${WRKSRC}/conf && ${INSTALL_DATA} fastlibs \
${STAGEDIR}${PREFIX}/etc/fastlibs.sample)
@${MKDIR} ${STAGEDIR}${DATADIR}
.for data in ${DATA}
${INSTALL_DATA} ${WRKSRC}/${data} ${DATADIR}
(cd ${WRKSRC} && ${INSTALL_DATA} ${data} ${STAGEDIR}${DATADIR})
.endfor
@ ${MKDIR} ${EXAMPLESDIR}
.for manpage in ${MAN1_FILES}
(cd ${WRKSRC}/doc && ${INSTALL_MAN} ${manpage} \
${STAGEDIR}${MAN1PREFIX}/man/man1)
.endfor
.for links in ${MAN1_LINKS}
(${LN} -sf fasta36.1 ${STAGEDIR}${MAN1PREFIX}/man/man1/${links})
.endfor
@${MKDIR} ${STAGEDIR}${DOCSDIR}
.for i in COPYRIGHT FASTA_LIST README
(cd ${WRKSRC} && ${INSTALL_DATA} ${i} ${STAGEDIR}${DOCSDIR})
.endfor
.for docfile in ${DOC_FILES}
(cd ${WRKSRC}/doc && ${INSTALL_DATA} ${docfile} ${STAGEDIR}${DOCSDIR})
.endfor
@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
.for ex in ${EXAMPLES}
${INSTALL_DATA} ${WRKSRC}/${ex} ${EXAMPLESDIR}
(cd ${WRKSRC} && ${INSTALL_DATA} ${ex} ${STAGEDIR}${EXAMPLESDIR})
.endfor
.for manpage in ${MAN1}
${INSTALL_MAN} ${WRKSRC}/doc/${manpage} ${MAN1PREFIX}/man/man1/
.endfor
.if !defined(NOPORTDOCS)
@ ${MKDIR} ${DOCSDIR}
${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR}
${INSTALL_DATA} ${WRKSRC}/COPYRIGHT ${DOCSDIR}
${INSTALL_DATA} ${WRKSRC}/FASTA_LIST ${DOCSDIR}
.for docfile in ${FASTA3_DOCS}
@ ${INSTALL_DATA} ${WRKSRC}/doc/${docfile} ${DOCSDIR}
.endfor
.endif
@ ${CAT} ${PKGMESSAGE}
.include <bsd.port.mk>

4
biology/fasta3/distinfo
View file

@ -1,2 +1,2 @@
SHA256 (fasta-36.3.6.tar.gz) = d6c526c307941fe8c98a16406cb01df6bb5712d3c2b7f4a90e126ceba682db6f
SIZE (fasta-36.3.6.tar.gz) = 995298
SHA256 (fasta-36.3.6d.tar.gz) = 6392741abecc8b25daeee53389584f48cee8a8ea7340c7f8cc97e149720a5730
SIZE (fasta-36.3.6d.tar.gz) = 997714

2
biology/fasta3/files/patch-Makefile.freebsd
View file

@ -13,7 +13,7 @@
BIN = ../bin
-XDIR = /usr/local/bin
+XDIR = ${LOCALBASE}/bin
+XDIR?= ${LOCALBASE}/bin
LIB_M+= -lm

1
biology/fasta3/pkg-descr
View file

@ -14,5 +14,4 @@ Molecular Biology 132:185-219.
The FASTA3 suite is distributed freely subject to the condition that it may
not be sold or incorporated into a commercial product.
Author: William R Pearson <wrp@virginia.edu>
WWW: http://fasta.bioch.virginia.edu/

129
biology/fasta3/pkg-plist
View file

@ -17,11 +17,38 @@ bin/tfasts%%VER%%
bin/tfastx%%VER%%
bin/tfasty%%VER%%
etc/fastlibs.sample
%%PORTDOCS%%%%DOCSDIR%%/README
man/man1/fasta36.1.gz
man/man1/fastf3.1.gz
man/man1/fastf35.1.gz
man/man1/fastm35.1.gz
man/man1/fasts3.1.gz
man/man1/fasts35.1.gz
man/man1/fastx35.1.gz
man/man1/fasty35.1.gz
man/man1/ggsearch35.1.gz
man/man1/lalign35.1.gz
man/man1/map_db.1.gz
man/man1/prfx35.1.gz
man/man1/prss3.1.gz
man/man1/prss35.1.gz
man/man1/ps_lav.1.gz
man/man1/ssearch35.1.gz
man/man1/tfasta35.1.gz
man/man1/tfastf35.1.gz
man/man1/tfasts35.1.gz
man/man1/tfastx35.1.gz
man/man1/tfasty35.1.gz
%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
%%PORTDOCS%%%%DOCSDIR%%/FASTA_LIST
%%PORTDOCS%%%%DOCSDIR%%/README
%%PORTDOCS%%%%DOCSDIR%%/README.versions
%%PORTDOCS%%%%DOCSDIR%%/changes_v34.html
%%PORTDOCS%%%%DOCSDIR%%/changes_v35.html
%%PORTDOCS%%%%DOCSDIR%%/changes_v36.html
%%PORTDOCS%%%%DOCSDIR%%/fasta.defaults
%%PORTDOCS%%%%DOCSDIR%%/fasta.options
%%PORTDOCS%%%%DOCSDIR%%/fasta_func.doc
%%PORTDOCS%%%%DOCSDIR%%/fasta_versions.html
%%PORTDOCS%%%%DOCSDIR%%/readme.v30
%%PORTDOCS%%%%DOCSDIR%%/readme.v30t6
%%PORTDOCS%%%%DOCSDIR%%/readme.v30t7
@ -33,57 +60,51 @@ etc/fastlibs.sample
%%PORTDOCS%%%%DOCSDIR%%/readme.v35
%%PORTDOCS%%%%DOCSDIR%%/readme.v36
%%PORTDOCS%%%%DOCSDIR%%/readme.w32
%%PORTDOCS%%%%DOCSDIR%%/fasta.defaults
%%PORTDOCS%%%%DOCSDIR%%/fasta.options
%%PORTDOCS%%%%DOCSDIR%%/fasta_versions.html
%%PORTDOCS%%%%DOCSDIR%%/changes_v34.html
%%PORTDOCS%%%%DOCSDIR%%/changes_v35.html
%%PORTDOCS%%%%DOCSDIR%%/changes_v36.html
%%EXAMPLESDIR%%/dyr_human.aa
%%EXAMPLESDIR%%/egmsmg.aa
%%EXAMPLESDIR%%/gstt1_drome.aa
%%EXAMPLESDIR%%/gtm1_human.aa
%%EXAMPLESDIR%%/gtt1_drome.aa
%%EXAMPLESDIR%%/h10_human.aa
%%EXAMPLESDIR%%/hahu.aa
%%EXAMPLESDIR%%/lcbo.aa
%%EXAMPLESDIR%%/m1r.aa
%%EXAMPLESDIR%%/m2.aa
%%EXAMPLESDIR%%/mchu.aa
%%EXAMPLESDIR%%/mgstm1.aa
%%EXAMPLESDIR%%/ms1.aa
%%EXAMPLESDIR%%/musplfm.aa
%%EXAMPLESDIR%%/mwkw.aa
%%EXAMPLESDIR%%/mwrtc1.aa
%%EXAMPLESDIR%%/myosin_bp.aa
%%EXAMPLESDIR%%/n0.aa
%%EXAMPLESDIR%%/n1.aa
%%EXAMPLESDIR%%/n2.aa
%%EXAMPLESDIR%%/n2s.aa
%%EXAMPLESDIR%%/n2t.aa
%%EXAMPLESDIR%%/ngt.aa
%%EXAMPLESDIR%%/ngts.aa
%%EXAMPLESDIR%%/oohu.aa
%%EXAMPLESDIR%%/prio_atepa.aa
%%EXAMPLESDIR%%/qrhuld.aa
%%EXAMPLESDIR%%/titin_hum.aa
%%EXAMPLESDIR%%/xurt8c.aa
%%EXAMPLESDIR%%/xurtg.aa
%%EXAMPLESDIR%%/mgstm1.lc
%%EXAMPLESDIR%%/xurt8c.lc
%%EXAMPLESDIR%%/bovgh.seq
%%EXAMPLESDIR%%/bovprl.seq
%%EXAMPLESDIR%%/gst.seq
%%EXAMPLESDIR%%/hsgstm1b.seq
%%EXAMPLESDIR%%/humgstd.seq
%%EXAMPLESDIR%%/mgstm1.seq
%%EXAMPLESDIR%%/mgstm1_genclone.seq
%%EXAMPLESDIR%%/mgtt2_x.seq
%%EXAMPLESDIR%%/titin_hum.seq
%%EXAMPLESDIR%%/mu.lib
%%EXAMPLESDIR%%/n2_fs.lib
%%EXAMPLESDIR%%/n_fs.lib
%%EXAMPLESDIR%%/prot_test.lib
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bovgh.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bovprl.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dyr_human.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/egmsmg.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gst.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gstt1_drome.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gtm1_human.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gtt1_drome.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h10_human.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hahu.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hsgstm1b.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/humgstd.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lcbo.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/m1r.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/m2.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mchu.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.lc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1_genclone.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgtt2_x.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ms1.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mu.lib
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/musplfm.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mwkw.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mwrtc1.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myosin_bp.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n0.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n1.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2_fs.lib
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2s.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2t.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n_fs.lib
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ngt.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ngts.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/oohu.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prio_atepa.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prot_test.lib
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/qrhuld.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/titin_hum.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/titin_hum.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurt8c.aa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurt8c.lc
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurtg.aa
%%DATADIR%%/blosum45.mat
%%DATADIR%%/blosum50.mat
%%DATADIR%%/blosum62.mat
@ -97,6 +118,6 @@ etc/fastlibs.sample
%%DATADIR%%/pam250.mat
%%DATADIR%%/rna.mat
%%DATADIR%%/vtml160.mat
%%PORTDOCS%%@dirrm %%DOCSDIR%%
@dirrm %%EXAMPLESDIR%%
@dirrm %%DATADIR%%
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
%%PORTDOCS%%@dirrm %%DOCSDIR%%