diff options
Diffstat (limited to 'biology/primer3')
| -rw-r--r-- | biology/primer3/Makefile | 16 | ||||
| -rw-r--r-- | biology/primer3/distinfo | 4 | ||||
| -rw-r--r-- | biology/primer3/pkg-plist | 713 |
3 files changed, 365 insertions, 368 deletions
diff --git a/biology/primer3/Makefile b/biology/primer3/Makefile index 6de7e6a91bab..21852c614346 100644 --- a/biology/primer3/Makefile +++ b/biology/primer3/Makefile @@ -6,20 +6,17 @@ # PORTNAME= primer3 -PORTVERSION= 0.9 +PORTVERSION= 1.0.0 CATEGORIES= biology MASTER_SITES= http://frodo.wi.mit.edu/primer3/ -DISTNAME= ${PORTNAME}_${PORTVERSION:S/./_/}_test +DISTNAME= ${PORTNAME}_${PORTVERSION} MAINTAINER= tonym@biolateral.com.au COMMENT= Primer3 helps to choose primers for PCR reactions USE_REINPLACE= yes WRKSRC= ${WRKDIR}/${DISTNAME}/src -CPIO= cpio --quiet -pdum -R DOCUMENTS= README example -CGI_EXAMPLES= primer3_www.cgi primer3_www_help.html \ - primer3_www_results.cgi primer3_www_results_help.html post-patch: @${REINPLACE_CMD} \ @@ -33,18 +30,15 @@ do-install: @${INSTALL_PROGRAM} ${WRKSRC}/primer3_core ${PREFIX}/bin/primer3 @${MKDIR} ${DATADIR} @${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/Copyright ${DATADIR} -.for file in ${CGI_EXAMPLES} - @${INSTALL_DATA} ${WRKSRC}/${file} ${DATADIR} -.endfor .if !defined(NOPORTDOCS) @${MKDIR} ${DOCSDIR} .for file in ${DOCUMENTS} @${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/${file} ${DOCSDIR} .endfor - @${RMDIR} ${WRKDIR}/${DISTNAME}/test/primer*_list_tmp + @${RM} -rf ${WRKDIR}/${DISTNAME}/test/primer*_list_tmp @${MKDIR} ${EXAMPLESDIR} - @cd ${WRKDIR}/${DISTNAME}/test && ${FIND} * | \ - ${CPIO} ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR} + @cd ${WRKDIR}/${DISTNAME}/test && ${FIND} * | ${CPIO} --quiet \ + -pdum -R ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR} .endif post-install: diff --git a/biology/primer3/distinfo b/biology/primer3/distinfo index 2797a6effc63..36903a617a25 100644 --- a/biology/primer3/distinfo +++ b/biology/primer3/distinfo @@ -1,2 +1,2 @@ -MD5 (primer3_0_9_test.tar.gz) = 1ae09013c982eb67953cc4dd5b837088 -SIZE (primer3_0_9_test.tar.gz) = 948375 +MD5 (primer3_1.0.0.tar.gz) = 58605ee607f6218a2a775345b10d15fa +SIZE (primer3_1.0.0.tar.gz) = 936696 diff --git a/biology/primer3/pkg-plist b/biology/primer3/pkg-plist index a6e27b47b1d4..9641035d99d8 100644 --- a/biology/primer3/pkg-plist +++ b/biology/primer3/pkg-plist @@ -1,358 +1,361 @@ %%PORTDOCS%%%%DOCSDIR%%/README %%PORTDOCS%%%%DOCSDIR%%/example -%%PORTDOCS%%share/examples/primer3/dpal_gen.pl -%%PORTDOCS%%share/examples/primer3/dpal_input -%%PORTDOCS%%share/examples/primer3/dpal_long_input -%%PORTDOCS%%share/examples/primer3/dpal_long_score_output -%%PORTDOCS%%share/examples/primer3/dpal_output -%%PORTDOCS%%share/examples/primer3/dpal_score_output -%%PORTDOCS%%share/examples/primer3/dpal_test.pl -%%PORTDOCS%%share/examples/primer3/long_seq_input -%%PORTDOCS%%share/examples/primer3/long_seq_output -%%PORTDOCS%%share/examples/primer3/not_for_production.lib -%%PORTDOCS%%share/examples/primer3/primer1_input -%%PORTDOCS%%share/examples/primer3/primer1_list_last/AGAG.for -%%PORTDOCS%%share/examples/primer3/primer1_list_last/AGAG.rev -%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP01-02.txt.for -%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP01-02.txt.rev -%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP01-03.txt.for -%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP01-03.txt.rev -%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP01-06.txt.for -%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP01-06.txt.rev -%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP01-19.txt.for -%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP01-19.txt.rev -%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP01-21.txt.for -%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP01-21.txt.rev -%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP04-07.txt.for -%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP04-07.txt.rev -%%PORTDOCS%%share/examples/primer3/primer1_list_last/included_test.for -%%PORTDOCS%%share/examples/primer3/primer1_list_last/included_test.rev -%%PORTDOCS%%share/examples/primer3/primer1_list_last/included_test_w_middle.for -%%PORTDOCS%%share/examples/primer3/primer1_list_last/included_test_w_middle.int -%%PORTDOCS%%share/examples/primer3/primer1_list_last/long_seq.for -%%PORTDOCS%%share/examples/primer3/primer1_list_last/included_test_w_middle.rev -%%PORTDOCS%%share/examples/primer3/primer1_list_last/long_seq.rev -%%PORTDOCS%%share/examples/primer3/primer1_list_last/targets_test.for -%%PORTDOCS%%share/examples/primer3/primer1_list_last/targets_test.rev -%%PORTDOCS%%share/examples/primer3/primer1_output -%%PORTDOCS%%share/examples/primer3/primer_boundary1_formated_output -%%PORTDOCS%%share/examples/primer3/primer_boundary1_input -%%PORTDOCS%%share/examples/primer3/primer_boundary1_output -%%PORTDOCS%%share/examples/primer3/primer_boundary_formated_output -%%PORTDOCS%%share/examples/primer3/primer_boundary_input -%%PORTDOCS%%share/examples/primer3/primer_boundary_output -%%PORTDOCS%%share/examples/primer3/primer_check_input -%%PORTDOCS%%share/examples/primer3/primer_check_output -%%PORTDOCS%%share/examples/primer3/primer_end_pathology_input -%%PORTDOCS%%share/examples/primer3/primer_end_pathology_output -%%PORTDOCS%%share/examples/primer3/primer_global_err/MAX_PRIMER_LENGTH.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_dna_conc.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_float_1.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_float_2.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_float_3.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_float_4.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_gc_1.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_gc_2.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_gc_3.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_gc_int_1.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_gc_int_2.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_gc_int_3.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_num_ns.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_num_ns_int.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_product_sizes_1.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_product_sizes_2.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_product_sizes_3.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_product_sizes_4.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_self_any.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_salt_conc.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_self_any_int.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_self_end.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_self_end_int.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/empty_1.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/empty_product_size.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/gc_clamp_min_size.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/incorrect_task.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/io_gc_content_obj_fn.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/io_obj_fn.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/max_min_tm.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/max_min_tm_int.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/max_opt_tm.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/max_opt_tm_int.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/max_size_limit_int.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/max_size_min_product.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/max_size_min_product_int.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/min_opt_tm.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/min_opt_tm_int.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/mishyb_obj_fn.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/mispr_obj_fn.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/no=.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/no_terminal=.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/opt_max_size.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/opt_max_size_int.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/opt_min_size.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/opt_min_size_int.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/pair_mispr.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/pr_gc_content_obj_fn.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/product_size_obj_fn.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/product_tm_obj_fn.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_err.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_err1.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_err2.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_err3.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_err4.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_err5.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_err6.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_int_err.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_int_err1.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_int_err2.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_int_err3.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_int_err4.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_int_err5.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_int_err6.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/seq_quality1.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/seq_quality2.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/seq_quality3.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/seq_quality4.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/too_many_product_sizes.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/zero_min_size.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/zero_num_return.in -%%PORTDOCS%%share/examples/primer3/primer_global_err/MAX_PRIMER_LENGTH.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_dna_conc.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_float_1.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_float_2.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_float_3.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_float_4.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_gc_1.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_gc_2.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_gc_3.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_gc_int_1.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_gc_int_2.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_gc_int_3.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_num_ns.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_num_ns_int.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_product_sizes_1.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_product_sizes_2.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_product_sizes_3.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_product_sizes_4.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_salt_conc.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_self_any.out 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-%%PORTDOCS%%share/examples/primer3/primer_global_err/pair_mispr.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/pr_gc_content_obj_fn.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/product_size_obj_fn.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/product_tm_obj_fn.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_err.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_err1.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_err2.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_err3.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_err4.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_err5.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_err6.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_int_err.out -%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_int_err1.out 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-%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_gc_1.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_dna_conc.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_float_1.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_float_2.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_float_3.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_float_4.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_gc_2.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_gc_3.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_gc_int_1.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_gc_int_2.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_gc_int_3.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_num_ns.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_num_ns_int.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_product_sizes_1.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_product_sizes_2.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_product_sizes_3.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_product_sizes_4.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_salt_conc.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_self_any.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_self_any_int.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_self_end.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_self_end_int.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/empty_1.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/empty_product_size.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/gc_clamp_min_size.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/incorrect_task.out2 -%%PORTDOCS%%share/examples/primer3/primer_global_err/io_gc_content_obj_fn.out2 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