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Add t_coffee 1.37, a multiple DNA or protein sequence alignment package.

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This commit is contained in:
Johann Visagie 2002-01-25 14:58:16 +00:00
parent 7c6bb30099
commit a3a6a2eb07
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=53719
9 changed files with 438 additions and 0 deletions
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1
biology/Makefile
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@ -44,6 +44,7 @@
SUBDIR += seaview
SUBDIR += seqio
SUBDIR += sim4
SUBDIR += t_coffee
SUBDIR += tinker
SUBDIR += treeviewx
SUBDIR += xdrawchem

56
biology/t_coffee/Makefile Normal file
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@ -0,0 +1,56 @@
# New ports collection makefile for: t_coffee
# Date created: 27 June 2001
# Whom: Johann Visagie <wjv@FreeBSD.org>
#
# $FreeBSD$
#
PORTNAME= t_coffee
PORTVERSION= 1.37
CATEGORIES= biology
MASTER_SITES= http://igs-server.cnrs-mrs.fr/~cnotred/Packages/
DISTNAME= T-COFFEE_distribution
MAINTAINER= wjv@FreeBSD.org
BUILD_DEPENDS= clustalw:${PORTSDIR}/biology/clustalw
RUN_DEPENDS= ${BUILD_DEPENDS}
WRKSRC= ${WRKDIR}/${DISTNAME}_Version_${PORTVERSION}
BUILD_WRKSRC= ${WRKSRC}/t_coffee_source
MAKE_ENV= MV=${MV} USER_BIN=${LOCALBASE}/bin \
CLUSTALW_4_TCOFFEE=${LOCALBASE}/bin/clustalw
MAKEFILE= makefile
PKGMESSAGE= ${WRKDIR}/pkg-message
post-build:
@ cd ${WRKSRC}/lalign && ${SETENV} ${MAKE_ENV} ${MAKE} \
${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET}
.include <bsd.port.pre.mk>
do-install:
.for binfile in t_coffee_source/t_coffee lalign/lalign2list
@ ${INSTALL_PROGRAM} ${WRKSRC}/${binfile} ${PREFIX}/bin
.endfor
.for scriptfile in extract_from_pdb mocca
@ ${INSTALL_SCRIPT} ${WRKSRC}/bin/${scriptfile} ${PREFIX}/bin
.endfor
post-install:
@ ${MKDIR} ${DATADIR}
@ ${INSTALL_DATA} ${WRKSRC}/html/* ${DATADIR}
.if !defined(NOPORTDOCS)
@ ${MKDIR} ${DOCSDIR}
@ ${INSTALL_DATA} ${WRKSRC}/doc/* ${DOCSDIR}
@ ${MKDIR} ${EXAMPLESDIR}
@ ${RMDIR} ${WRKSRC}/example/aln 2>/dev/null || ${TRUE}
@ cd ${WRKSRC}/example && find * \
| cpio --quiet -pdum -R ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}
@ ${SED} -e 's#%%DATADIR%%#${DATADIR}#' ${.CURDIR}/pkg-message \
> ${PKGMESSAGE}
.if !defined(BATCH)
@ ${CAT} ${PKGMESSAGE}
.endif
.endif
.include <bsd.port.post.mk>

1
biology/t_coffee/distinfo Normal file
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@ -0,0 +1 @@
MD5 (T-COFFEE_distribution.tar.gz) = a947c75871f56e83ccc1e8444495330a

37
biology/t_coffee/files/patch-lalign-makefile Normal file
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@ -0,0 +1,37 @@
--- lalign/makefile.orig Wed Jun 13 03:05:02 2001
+++ lalign/makefile Wed Jun 27 17:29:56 2001
@@ -4,14 +4,14 @@
# use the compiler option that invokes signed char's.
#
#sun (bsd)
-CC= cc
+#CC= cc
# for MIPS: CFLAGS= -O -DUNIX -DBIGMEM -DSFCHAR="':'" -signed
-CFLAGS= -O -DUNIX -DBIGMEM -DSFCHAR="':'"
+#CFLAGS= -O -DUNIX -DBIGMEM -DSFCHAR="':'"
LFLAGS= -o
#NRAND= nrand
#IBM RS/6000
-NRAND= nrand48
-RANFLG= -DRAND32
+#NRAND= nrand48
+#RANFLG= -DRAND32
#HZ=60 for sun, mips, 100 for rs/6000, SGI
HZ=60
@@ -25,14 +25,13 @@
lalign2list : lalign.o pam.o lsim.o lgetaa.o ndispn.o time.o
$(CC) lalign.o pam.o lsim.o lgetaa.o ndispn.o time.o $(LFLAGS) lalign2list
- mv lalign2list $(USER_BIN)/lalign2list
lalign.o : lalign.c upam.gbl
pam.o : uascii.gbl upam.gbl
lsim.o : lsim.c zzgmata.gbl upam.gbl
$(CC) $(CFLAGS) -c lsim.c
lgetaa.o : nxgetaa.c upam.gbl uascii.gbl altlib.h
$(CC) $(CFLAGS) -DNOLIB -c nxgetaa.c
- mv nxgetaa.o lgetaa.o
+ $(MV) nxgetaa.o lgetaa.o
ndispn.o : upam.gbl
time.o : time.c
$(CC) $(CFLAGS) -DHZ=$(HZ) -c time.c

10
biology/t_coffee/files/patch-t_coffee_source-makefile Normal file
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@ -0,0 +1,10 @@
--- t_coffee_source/makefile.orig Wed Jul 11 23:40:30 2001
+++ t_coffee_source/makefile Fri Jan 25 15:58:01 2002
@@ -1,7 +1,6 @@
CC=cc
t_coffee: util_constraints_list.o util_domain_constraints_list.o util_analyse_constraints_list.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o t_coffee.o
$(CC) -O -o t_coffee util_constraints_list.o util_domain_constraints_list.o util_analyse_constraints_list.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o t_coffee.o -lm
- mv t_coffee ../bin
all: t_coffee

1
biology/t_coffee/pkg-comment Normal file
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@ -0,0 +1 @@
A multiple DNA or protein sequence alignment package

17
biology/t_coffee/pkg-descr Normal file
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@ -0,0 +1,17 @@
From the website:
T-Coffee is a multiple sequence alignment package. Given a set of sequences
(Proteins or DNA), T-Coffee generates a multiple sequence alignment.
Related publications:
- T-Coffee: A novel method for multiple sequence alignments. C.Notredame,
D. Higgins, J. Heringa, Journal of Molecular Biology,Vol 302,
pp205-217,2000
- COFFEE: A New Objective Function For Multiple Sequence Alignmnent.
C. Notredame, L. Holme and D.G. Higgins,Bioinformatics,Vol 14 (5)
407-422,1998
Author: Cedric Notredame <cedric.notredame@europe.com>
WWW: http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
-- Johann Visagie <wjv@FreeBSD.org>

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biology/t_coffee/pkg-message Normal file
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@ -0,0 +1,10 @@
--------------------------------------------------------------------------
The files required for the T-Coffee web front-end have been installed to:
%%DATADIR%%
In order to use the web front-end, you will need to copy these files to
your web server's cgi-bin directory, or a subdirectory thereof.
--------------------------------------------------------------------------

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biology/t_coffee/pkg-plist Normal file
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@ -0,0 +1,305 @@
%%PORTDOCS%%share/doc/t_coffee/README4T-COFFEE
%%PORTDOCS%%share/doc/t_coffee/t_coffee.pdf
%%PORTDOCS%%share/doc/t_coffee/t_coffee_doc.doc
%%PORTDOCS%%share/doc/t_coffee/t_coffee_doc.html
%%PORTDOCS%%share/doc/t_coffee/t_coffee_doc.pdf
%%PORTDOCS%%share/doc/t_coffee/t_coffee_doc.ps
%%PORTDOCS%%share/examples/t_coffee/seq/1aab_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1aboA_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1aboA_ref2.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ac5_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ad2_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ad3_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1adj_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ag8_ref4.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1aho_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1aisB_ref4.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ajsA_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ajsA_ref2.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ajsA_ref3.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1amk_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ar1_ref4.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ar5A_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1au7A_ref4.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1aym3_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1bbt3_ref1.pep
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%%PORTDOCS%%share/examples/t_coffee/seq/1ckaA_ref4.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1cpt_ref1.pep
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%%PORTDOCS%%share/examples/t_coffee/seq/1csp_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1csp_ref4.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1csy_ref1.pep
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%%PORTDOCS%%share/examples/t_coffee/seq/1eft_ref5.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1ezm_ref1.pep
%%PORTDOCS%%share/examples/t_coffee/seq/1fieA_ref1.pep
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%%PORTDOCS%%share/examples/t_coffee/seq/1hpi_ref1.pep
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%%PORTDOCS%%share/examples/t_coffee/seq/1lcf_ref1.pep
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%%PORTDOCS%%share/examples/t_coffee/seq/2pia_ref1.pep
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%%PORTDOCS%%share/examples/t_coffee/tc_aln/1aab_ref1.t_coffee_aln10
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%%PORTDOCS%%share/examples/t_coffee/tc_aln/1ag8_ref4.t_coffee_aln10
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