diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/t_coffee/Makefile | 56 | ||||
| -rw-r--r-- | biology/t_coffee/distinfo | 1 | ||||
| -rw-r--r-- | biology/t_coffee/files/patch-lalign-makefile | 37 | ||||
| -rw-r--r-- | biology/t_coffee/files/patch-t_coffee_source-makefile | 10 | ||||
| -rw-r--r-- | biology/t_coffee/pkg-comment | 1 | ||||
| -rw-r--r-- | biology/t_coffee/pkg-descr | 17 | ||||
| -rw-r--r-- | biology/t_coffee/pkg-message | 10 | ||||
| -rw-r--r-- | biology/t_coffee/pkg-plist | 305 |
9 files changed, 438 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index b1798bf04f78..ead96e624098 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -44,6 +44,7 @@ SUBDIR += seaview SUBDIR += seqio SUBDIR += sim4 + SUBDIR += t_coffee SUBDIR += tinker SUBDIR += treeviewx SUBDIR += xdrawchem diff --git a/biology/t_coffee/Makefile b/biology/t_coffee/Makefile new file mode 100644 index 000000000000..f1d3ddb63800 --- /dev/null +++ b/biology/t_coffee/Makefile @@ -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> diff --git a/biology/t_coffee/distinfo b/biology/t_coffee/distinfo new file mode 100644 index 000000000000..62e86cceea4c --- /dev/null +++ b/biology/t_coffee/distinfo @@ -0,0 +1 @@ +MD5 (T-COFFEE_distribution.tar.gz) = a947c75871f56e83ccc1e8444495330a diff --git a/biology/t_coffee/files/patch-lalign-makefile b/biology/t_coffee/files/patch-lalign-makefile new file mode 100644 index 000000000000..4128d3cd6b0f --- /dev/null +++ b/biology/t_coffee/files/patch-lalign-makefile @@ -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 diff --git a/biology/t_coffee/files/patch-t_coffee_source-makefile b/biology/t_coffee/files/patch-t_coffee_source-makefile new file mode 100644 index 000000000000..58e654ff65fd --- /dev/null +++ b/biology/t_coffee/files/patch-t_coffee_source-makefile @@ -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 + diff --git a/biology/t_coffee/pkg-comment b/biology/t_coffee/pkg-comment new file mode 100644 index 000000000000..c0f726dcae6b --- /dev/null +++ b/biology/t_coffee/pkg-comment @@ -0,0 +1 @@ +A multiple DNA or protein sequence alignment package diff --git a/biology/t_coffee/pkg-descr b/biology/t_coffee/pkg-descr new file mode 100644 index 000000000000..304a8fc9eb80 --- /dev/null +++ b/biology/t_coffee/pkg-descr @@ -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> diff --git a/biology/t_coffee/pkg-message b/biology/t_coffee/pkg-message new file mode 100644 index 000000000000..780b03c483ad --- /dev/null +++ b/biology/t_coffee/pkg-message @@ -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. + +-------------------------------------------------------------------------- diff --git a/biology/t_coffee/pkg-plist b/biology/t_coffee/pkg-plist new file mode 100644 index 000000000000..c57ecd5e34fe --- /dev/null +++ b/biology/t_coffee/pkg-plist @@ -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 +%%PORTDOCS%%share/examples/t_coffee/seq/1bgl_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1ckaA_ref4.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1cpt_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1cpt_ref2.pep +%%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 +%%PORTDOCS%%share/examples/t_coffee/seq/1csy_ref2.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1dlc_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1dox_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1eft_ref1.pep +%%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 +%%PORTDOCS%%share/examples/t_coffee/seq/1fjlA_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1fkj_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1fmb_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1gdoA_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1gowA_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1gpb_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1gtr_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1havA_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1havA_ref2.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1hfh_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1hpi_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1idy_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1idy_ref2.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1idy_ref3.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1ivy_ref5.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1krn_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1lcf_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1ldg_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1led_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1lkl_ref4.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1lvl_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1lvl_ref2.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1mfa_ref4.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1mrj_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1pamA_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1pamA_ref2.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1pamA_ref3.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1ped_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1ped_ref2.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1ped_ref3.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1pfc_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1pfc_ref4.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1pgtA_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1pii_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1pkm_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1plc_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1ppn_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1pysA_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1qpg_ref5.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1r69.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1r69_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1r69_ref2.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1r69_ref3.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1rthA_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1sbp_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1sbp_ref2.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1sesA_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1taq_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1tgxA_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1tgxA_ref2.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1thm1_ref5.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1thm2_ref5.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1thm_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1tis_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1ton_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1tvxA_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1tvxA_ref2.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1ubi_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1ubi_ref2.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1ubi_ref3.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1uky_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1uky_ref2.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1uky_ref3.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1vln_ref4.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1wit_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1wit_ref2.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1wit_ref3.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1ycc_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1ycc_ref4.pep +%%PORTDOCS%%share/examples/t_coffee/seq/1zin_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/2ack_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/2cba_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/2cba_ref5.pep +%%PORTDOCS%%share/examples/t_coffee/seq/2fxb_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/2hsdA_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/2hsdA_ref2.pep +%%PORTDOCS%%share/examples/t_coffee/seq/2mhr_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/2myr_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/2myr_ref2.pep +%%PORTDOCS%%share/examples/t_coffee/seq/2myr_ref3.pep +%%PORTDOCS%%share/examples/t_coffee/seq/2pia_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/2pia_ref2.pep +%%PORTDOCS%%share/examples/t_coffee/seq/2pia_ref3.pep +%%PORTDOCS%%share/examples/t_coffee/seq/2trx_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/2trx_ref2.pep +%%PORTDOCS%%share/examples/t_coffee/seq/3cyr_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/3grs_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/3grs_ref2.pep +%%PORTDOCS%%share/examples/t_coffee/seq/3pmg_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/451c_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/4enl_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/4enl_ref2.pep +%%PORTDOCS%%share/examples/t_coffee/seq/4enl_ref3.pep +%%PORTDOCS%%share/examples/t_coffee/seq/5ptp_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/9rnt_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/S51_ref5.pep +%%PORTDOCS%%share/examples/t_coffee/seq/S52_ref5.pep +%%PORTDOCS%%share/examples/t_coffee/seq/actin_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/arp_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/gal4_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/glg_ref1.pep +%%PORTDOCS%%share/examples/t_coffee/seq/kinase1_ref4.pep +%%PORTDOCS%%share/examples/t_coffee/seq/kinase1_ref5.pep +%%PORTDOCS%%share/examples/t_coffee/seq/kinase2_ref4.pep +%%PORTDOCS%%share/examples/t_coffee/seq/kinase2_ref5.pep 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