ports/74332: update biology/t_coffee and take maintainership
Fernan Aguero
fernan at iib.unsam.edu.ar
Wed Nov 24 20:00:46 UTC 2004
>Number: 74332
>Category: ports
>Synopsis: update biology/t_coffee and take maintainership
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: update
>Submitter-Id: current-users
>Arrival-Date: Wed Nov 24 20:00:45 GMT 2004
>Closed-Date:
>Last-Modified:
>Originator: Fernan Aguero
>Release: FreeBSD 4.10-RELEASE i386
>Organization:
IIB-UNSAM
>Environment:
FreeBSD pi.iib.unsam.edu.ar 4.10-RELEASE FreeBSD 4.10-RELEASE #0: Wed May 26 12:56:43 ART 2004 fernan at pi.iib.unsam.edu.ar:/usr/obj/usr/src/sys/PI i386
>Description:
Update t_coffee to the latest available version.
This version does not include the lalign stuff, so now the port
Makefile is simpler (also because of this, patches are
obsolete).
>How-To-Repeat:
>Fix:
--- t_coffee.diff begins here ---
diff -ruN /usr/ports/biology/t_coffee/Makefile t_coffee/Makefile
--- /usr/ports/biology/t_coffee/Makefile Mon Nov 22 06:09:09 2004
+++ t_coffee/Makefile Wed Nov 24 15:27:50 2004
@@ -6,41 +6,34 @@
#
PORTNAME= t_coffee
-PORTVERSION= 1.37
+PORTVERSION= 2.03
CATEGORIES= biology
MASTER_SITES= http://igs-server.cnrs-mrs.fr/~cnotred/Packages/
-DISTNAME= T-COFFEE_distribution
+DISTNAME= T-COFFEE_distribution_Version_${PORTVERSION}
-MAINTAINER= ports at FreeBSD.org
+MAINTAINER= fernan at iib.unsam.edu.ar
COMMENT= A multiple DNA or protein sequence alignment package
BUILD_DEPENDS= clustalw:${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
+MAKE_ENV= MV=${MV} USER_BIN=${PREFIX}/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>
+SCRIPTS= msf_aln2fasta_aln.pl blast_aln2fasta_aln.pl \
+ fasta_aln2fasta_aln_unique_name.pl extract_from_pdb \
+ fugue_client t_coffee_dpa t_coffee_dpa2 mocca
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_PROGRAM} ${WRKSRC}/bin/t_coffee ${PREFIX}/bin
+.for scriptfile in ${SCRIPTS}
@ ${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}
@@ -48,10 +41,6 @@
@ ${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>
+
+.include <bsd.port.mk>
diff -ruN /usr/ports/biology/t_coffee/distinfo t_coffee/distinfo
--- /usr/ports/biology/t_coffee/distinfo Sat Apr 3 01:03:36 2004
+++ t_coffee/distinfo Wed Nov 24 14:11:36 2004
@@ -1,2 +1,2 @@
-MD5 (T-COFFEE_distribution.tar.gz) = a947c75871f56e83ccc1e8444495330a
-SIZE (T-COFFEE_distribution.tar.gz) = 1368921
+MD5 (T-COFFEE_distribution_Version_2.03.tar.gz) = a86e2d83c17058b03be0170566d634f0
+SIZE (T-COFFEE_distribution_Version_2.03.tar.gz) = 864853
diff -ruN /usr/ports/biology/t_coffee/files/patch-lalign-makefile t_coffee/files/patch-lalign-makefile
--- /usr/ports/biology/t_coffee/files/patch-lalign-makefile Fri Jan 25 11:58:16 2002
+++ t_coffee/files/patch-lalign-makefile Wed Dec 31 21:00:00 1969
@@ -1,37 +0,0 @@
---- 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
diff -ruN /usr/ports/biology/t_coffee/files/patch-t_coffee_source-makefile t_coffee/files/patch-t_coffee_source-makefile
--- /usr/ports/biology/t_coffee/files/patch-t_coffee_source-makefile Fri Jan 25 11:58:16 2002
+++ t_coffee/files/patch-t_coffee_source-makefile Wed Dec 31 21:00:00 1969
@@ -1,10 +0,0 @@
---- 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
-
diff -ruN /usr/ports/biology/t_coffee/pkg-descr t_coffee/pkg-descr
--- /usr/ports/biology/t_coffee/pkg-descr Fri Jan 25 11:58:14 2002
+++ t_coffee/pkg-descr Wed Nov 24 14:54:48 2004
@@ -4,6 +4,10 @@
(Proteins or DNA), T-Coffee generates a multiple sequence alignment.
Related publications:
+ - 3DCoffee: Combining Protein Sequences and Structures within Multiple
+ Sequence Alignments.
+ O. O'Sullivan, K Suhre, C. Abergel, D.G. Higgins, C. Notredame.
+ Journal of Molecular Biology, Vol 340, pp385-395, 2004
- T-Coffee: A novel method for multiple sequence alignments. C.Notredame,
D. Higgins, J. Heringa, Journal of Molecular Biology,Vol 302,
pp205-217,2000
diff -ruN /usr/ports/biology/t_coffee/pkg-message t_coffee/pkg-message
--- /usr/ports/biology/t_coffee/pkg-message Fri Jan 25 11:58:14 2002
+++ t_coffee/pkg-message Wed Dec 31 21:00:00 1969
@@ -1,10 +0,0 @@
---------------------------------------------------------------------------
-
-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.
-
---------------------------------------------------------------------------
diff -ruN /usr/ports/biology/t_coffee/pkg-plist t_coffee/pkg-plist
--- /usr/ports/biology/t_coffee/pkg-plist Sat Oct 25 01:18:25 2003
+++ t_coffee/pkg-plist Wed Nov 24 15:25:47 2004
@@ -1,305 +1,161 @@
-%%PORTDOCS%%%%DOCSDIR%%/README4T-COFFEE
-%%PORTDOCS%%%%DOCSDIR%%/t_coffee.pdf
-%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.doc
-%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.html
-%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.pdf
-%%PORTDOCS%%%%DOCSDIR%%/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
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-%%PORTDOCS%%share/examples/t_coffee/seq/1ar5A_ref1.pep
-%%PORTDOCS%%share/examples/t_coffee/seq/1au7A_ref4.pep
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-%%PORTDOCS%%share/examples/t_coffee/seq/1dox_ref1.pep
-%%PORTDOCS%%share/examples/t_coffee/seq/1eft_ref1.pep
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-%%PORTDOCS%%share/examples/t_coffee/seq/1led_ref1.pep
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-%%PORTDOCS%%share/examples/t_coffee/seq/1lvl_ref1.pep
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+bin/fasta_aln2fasta_aln_unique_name.pl
bin/extract_from_pdb
-bin/lalign2list
+bin/fugue_client
+bin/t_coffee_dpa
+bin/t_coffee_dpa2
bin/mocca
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-%%PORTDOCS%%@dirrm share/examples/t_coffee/seq
-%%PORTDOCS%%@dirrm share/examples/t_coffee
+%%PORTDOCS%%DOCSDIR%%/README4T-COFFEE
+%%PORTDOCS%%DOCSDIR%%/t_coffee.pdf
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+%%EXAMPLESDIR%%/seq/arp_ref1.pep
+%%EXAMPLESDIR%%/seq/gal4_ref1.pep
+%%EXAMPLESDIR%%/seq/glg_ref1.pep
+%%EXAMPLESDIR%%/seq/kinase1_ref4.pep
+%%EXAMPLESDIR%%/seq/kinase1_ref5.pep
+%%EXAMPLESDIR%%/seq/kinase2_ref4.pep
+%%EXAMPLESDIR%%/seq/kinase2_ref5.pep
+%%EXAMPLESDIR%%/seq/kinase3_ref5.pep
+%%EXAMPLESDIR%%/seq/kinase_ref1.pep
+%%EXAMPLESDIR%%/seq/kinase_ref2.pep
+%%EXAMPLESDIR%%/seq/kinase_ref3.pep
+%%EXAMPLESDIR%%/test/reference_test.aln
+%%EXAMPLESDIR%%/test/test.pep
%%PORTDOCS%%@dirrm %%DOCSDIR%%
+ at dirrm %%EXAMPLESDIR%%/seq
+ at dirrm %%EXAMPLESDIR%%/test
+ at dirrm %%EXAMPLESDIR%%
--- t_coffee.diff ends here ---
>Release-Note:
>Audit-Trail:
>Unformatted:
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