diff options
| -rw-r--r-- | biology/t_coffee/Makefile | 38 | ||||
| -rw-r--r-- | biology/t_coffee/distinfo | 4 | ||||
| -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-descr | 4 | ||||
| -rw-r--r-- | biology/t_coffee/pkg-message | 10 | ||||
| -rw-r--r-- | biology/t_coffee/pkg-plist | 456 |
7 files changed, 175 insertions, 384 deletions
diff --git a/biology/t_coffee/Makefile b/biology/t_coffee/Makefile index ce6bd55fd374..86b1078ecbbc 100644 --- a/biology/t_coffee/Makefile +++ b/biology/t_coffee/Makefile @@ -6,41 +6,33 @@ # 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_${PORTVERSION} -MAINTAINER= ports@FreeBSD.org +MAINTAINER= fernan@iib.unsam.edu.ar COMMENT= A multiple DNA or protein sequence alignment package BUILD_DEPENDS= clustalw:${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 -MAKEFILE= makefile -PKGMESSAGE= ${WRKDIR}/pkg-message - -post-build: - @ cd ${WRKSRC}/lalign && ${SETENV} ${MAKE_ENV} ${MAKE} \ - ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET} +MAKE_ENV= MV=${MV} USER_BIN=${PREFIX}/bin \ + CLUSTALW_4_TCOFFEE=${LOCALBASE}/bin/clustalw -.include <bsd.port.pre.mk> +MAKEFILE= makefile +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 +40,6 @@ post-install: @ ${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 --git a/biology/t_coffee/distinfo b/biology/t_coffee/distinfo index 0da98a2be8e8..5589c4f91de5 100644 --- a/biology/t_coffee/distinfo +++ b/biology/t_coffee/distinfo @@ -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 --git a/biology/t_coffee/files/patch-lalign-makefile b/biology/t_coffee/files/patch-lalign-makefile deleted file mode 100644 index 4128d3cd6b0f..000000000000 --- a/biology/t_coffee/files/patch-lalign-makefile +++ /dev/null @@ -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 --git a/biology/t_coffee/files/patch-t_coffee_source-makefile b/biology/t_coffee/files/patch-t_coffee_source-makefile deleted file mode 100644 index 58e654ff65fd..000000000000 --- a/biology/t_coffee/files/patch-t_coffee_source-makefile +++ /dev/null @@ -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 --git a/biology/t_coffee/pkg-descr b/biology/t_coffee/pkg-descr index 304a8fc9eb80..ff1051aeb958 100644 --- a/biology/t_coffee/pkg-descr +++ b/biology/t_coffee/pkg-descr @@ -4,6 +4,10 @@ From the website: (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 --git a/biology/t_coffee/pkg-message b/biology/t_coffee/pkg-message deleted file mode 100644 index 780b03c483ad..000000000000 --- a/biology/t_coffee/pkg-message +++ /dev/null @@ -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 --git a/biology/t_coffee/pkg-plist b/biology/t_coffee/pkg-plist index 1100b4a356bb..d719ed2fdec2 100644 --- a/biology/t_coffee/pkg-plist +++ b/biology/t_coffee/pkg-plist @@ -1,305 +1,161 @@ +bin/t_coffee +bin/msf_aln2fasta_aln.pl +bin/blast_aln2fasta_aln.pl +bin/fasta_aln2fasta_aln_unique_name.pl +bin/extract_from_pdb +bin/fugue_client +bin/t_coffee_dpa +bin/t_coffee_dpa2 +bin/mocca %%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 -%%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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+%%EXAMPLESDIR%%/test/reference_test.aln +%%EXAMPLESDIR%%/test/test.pep %%PORTDOCS%%@dirrm %%DOCSDIR%% +@dirrm %%EXAMPLESDIR%%/seq +@dirrm %%EXAMPLESDIR%%/test +@dirrm %%EXAMPLESDIR%% |