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
-%%PORTDOCS%%share/examples/primer3/primer_global_err/empty_1.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_self_end.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_self_any_int.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_self_end_int.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/empty_product_size.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/gc_clamp_min_size.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/incorrect_task.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/io_gc_content_obj_fn.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/io_obj_fn.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/max_min_tm.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/max_min_tm_int.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/max_opt_tm.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/max_opt_tm_int.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/max_size_limit_int.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/max_size_min_product.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/max_size_min_product_int.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/min_opt_tm.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/min_opt_tm_int.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/mishyb_obj_fn.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/mispr_obj_fn.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/no=.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/no_terminal=.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/opt_max_size.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/opt_max_size_int.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/opt_min_size.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/opt_min_size_int.out
-%%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
-%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_int_err2.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_int_err3.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_int_err4.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_int_err5.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_int_err6.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/seq_quality1.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/seq_quality2.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/seq_quality3.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/seq_quality4.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/too_many_product_sizes.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/zero_min_size.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/zero_num_return.out
-%%PORTDOCS%%share/examples/primer3/primer_global_err/MAX_PRIMER_LENGTH.out2
-%%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
-%%PORTDOCS%%share/examples/primer3/primer_global_err/io_obj_fn.out2
-%%PORTDOCS%%share/examples/primer3/primer_global_err/max_min_tm.out2
-%%PORTDOCS%%share/examples/primer3/primer_global_err/max_min_tm_int.out2
-%%PORTDOCS%%share/examples/primer3/primer_global_err/max_opt_tm.out2
-%%PORTDOCS%%share/examples/primer3/primer_global_err/max_opt_tm_int.out2
-%%PORTDOCS%%share/examples/primer3/primer_global_err/max_size_limit_int.out2
-%%PORTDOCS%%share/examples/primer3/primer_global_err/max_size_min_product.out2
-%%PORTDOCS%%share/examples/primer3/primer_global_err/max_size_min_product_int.out2
-%%PORTDOCS%%share/examples/primer3/primer_global_err/min_opt_tm.out2
-%%PORTDOCS%%share/examples/primer3/primer_global_err/min_opt_tm_int.out2
-%%PORTDOCS%%share/examples/primer3/primer_global_err/mishyb_obj_fn.out2
-%%PORTDOCS%%share/examples/primer3/primer_global_err/mispr_obj_fn.out2
-%%PORTDOCS%%share/examples/primer3/primer_global_err/no=.out2
-%%PORTDOCS%%share/examples/primer3/primer_global_err/no_terminal=.out2
-%%PORTDOCS%%share/examples/primer3/primer_global_err/opt_max_size.out2
-%%PORTDOCS%%share/examples/primer3/primer_global_err/opt_max_size_int.out2
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+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err3.out
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+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err6.out
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+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/MAX_PRIMER_LENGTH.out2
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+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_3.out2
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+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns_int.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_1.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_2.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_3.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_4.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_salt_conc.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any_int.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end_int.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_1.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_product_size.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/gc_clamp_min_size.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/incorrect_task.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_gc_content_obj_fn.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_obj_fn.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm_int.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm_int.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_limit_int.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product_int.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm_int.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mishyb_obj_fn.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mispr_obj_fn.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no=.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_terminal=.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size_int.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size_int.out2
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+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pr_gc_content_obj_fn.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_size_obj_fn.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_tm_obj_fn.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err1.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err2.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err3.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err4.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err5.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err6.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err1.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err2.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err3.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err4.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err5.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err6.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality1.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality2.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality3.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality4.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/too_many_product_sizes.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_min_size.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_num_return.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_human_input
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_human_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_input
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_input
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal_input
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/AGAG.for
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/AGAG.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-02.txt.for
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-02.txt.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-03.txt.for
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-03.txt.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat1.for
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat1.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat1.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat2.for
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat2.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat2.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat3.for
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat3.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat3.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06.txt.for
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06.txt.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-19.txt.for
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-19.txt.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-21.txt.for
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-21.txt.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP04-07.txt.for
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP04-07.txt.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/case_problem_test.for
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/case_problem_test.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test.for
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test_w_middle.for
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test_w_middle.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test_w_middle.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/long_seq.for
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/long_seq.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/targets_test.for
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/targets_test.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary1_input
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary1_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary2_input
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary2_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_input
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_long_lib_input
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_long_lib_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_must_use_input
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_must_use_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_num_best_input
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_num_best_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_obj_fn_input
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_obj_fn_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_position_penalty_input
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_position_penalty_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_quality_boundary_input
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_quality_boundary_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_rat_input
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_rat_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_repeat_boundary1_lib
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_repeat_boundary2_lib
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_repeat_long_lib
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_start_codon_input
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_start_codon_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_syntax_input
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_syntax_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_task_input
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_task_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_test.pl
+%%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib1
+%%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib2
+%%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib3
+%%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib4
+%%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib5
+%%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib6
+%%PORTDOCS%%%%EXAMPLESDIR%%/long_seq_tm_test.pl
+%%PORTDOCS%%%%EXAMPLESDIR%%/not_for_production_Ns.lib
+%%PORTDOCS%%%%EXAMPLESDIR%%/not_for_production_Xs.lib
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_boundary1_formatted_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_boundary_formatted_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_boundary_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_formatted_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal_formatted_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_lib_amb_codes_input
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_lib_amb_codes_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary1_formatted_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary2_formatted_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_formatted_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_must_use_formatted_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_position_penalty_formatted_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_task_formatted_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_template_mispriming_input
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_template_mispriming_output
 bin/primer3
-share/primer3/Copyright
-share/primer3/primer3_www.cgi
-share/primer3/primer3_www_help.html
-share/primer3/primer3_www_results.cgi
-share/primer3/primer3_www_results_help.html
-@dirrm share/primer3
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/
-%%PORTDOCS%%@dirrm share/examples/primer3/primer1_list_last
-%%PORTDOCS%%@dirrm share/examples/primer3/primer_global_err
-%%PORTDOCS%%@dirrm share/examples/primer3/primer_list_last
-%%PORTDOCS%%@dirrm share/examples/primer3/
+%%DATADIR%%/Copyright
+@dirrm %%DATADIR%%
+%%PORTDOCS%%@dirrm %%DOCSDIR%%
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/primer1_list_last
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/primer_global_err
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/primer_list_last
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%