4 files changed, 9 insertions, 442 deletions

diff --git a/biology/primer3/Makefile b/biology/primer3/Makefile
index 3be018d83ebe..2b60d38501c8 100644
--- a/biology/primer3/Makefile
+++ b/biology/primer3/Makefile
@@ -2,16 +2,18 @@
 # $FreeBSD$
 
 PORTNAME=	primer3
-PORTVERSION=	1.1.4
+PORTVERSION=	2.3.5
 CATEGORIES=	biology
 MASTER_SITES=	SF
 
 MAINTAINER=	wen@FreeBSD.org
 COMMENT=	Primer3 helps to choose primers for PCR reactions
 
+LICENSE=	GPLv2
+
 USE_GMAKE=	yes
-WRKSRC=		${WRKDIR}/src
-DOCUMENTS=	README.txt example
+WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}/src
+PLIST_FILES=	bin/primer3
 
 post-patch:
 	@${REINPLACE_CMD} \
@@ -20,24 +22,9 @@ post-patch:
 		-e 's#CC_OPTS = -g#CC_OPTS =#;' \
 		-e 's#LDFLAGS = -g#LDFLAGS +=#;' \
 		-e 's#^WHITEHEAD_SPECIFIC_HACK.*##;' \
-		${WRKDIR}/src/Makefile
+		${WRKSRC}/Makefile
 
 do-install:
-	@${INSTALL_PROGRAM} ${WRKDIR}/src/primer3_core ${PREFIX}/bin/primer3
-	@${MKDIR} ${DATADIR}
-	@${INSTALL_DATA} ${WRKDIR}/COPYING.txt ${DATADIR}
-.if !defined(NOPORTDOCS)
-	@${MKDIR} ${DOCSDIR}
-.for file in ${DOCUMENTS}
-	@${INSTALL_DATA} ${WRKDIR}/${file} ${DOCSDIR}
-.endfor
-	@${RM} -rf ${WRKDIR}/test/primer*_list_tmp
-	@${MKDIR} ${EXAMPLESDIR}
-	@cd ${WRKDIR}/test && ${FIND} * | ${CPIO} --quiet \
-		-pdum -R ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}
-.endif
-
-post-install:
-	@${CAT} ${DATADIR}/COPYING.txt
+	@${INSTALL_PROGRAM} ${WRKSRC}/primer3_core ${PREFIX}/bin/primer3
 
 .include <bsd.port.mk>
diff --git a/biology/primer3/distinfo b/biology/primer3/distinfo
index 448663abf74a..6bc735ac29ec 100644
--- a/biology/primer3/distinfo
+++ b/biology/primer3/distinfo
@@ -1,2 +1,2 @@
-SHA256 (primer3-1.1.4.tar.gz) = 1cb045791afd3c4033956a65687ca0c1b1a6607ac84705bf4ed7d7151691980b
-SIZE (primer3-1.1.4.tar.gz) = 974628
+SHA256 (primer3-2.3.5.tar.gz) = e0c06a36dc384f656835a8d5ecb4b5069493b7dd98775b38a233863ab591c54b
+SIZE (primer3-2.3.5.tar.gz) = 1655871
diff --git a/biology/primer3/pkg-message b/biology/primer3/pkg-message
deleted file mode 100644
index e0265f7c7892..000000000000
--- a/biology/primer3/pkg-message
+++ /dev/null
@@ -1,41 +0,0 @@
- Copyright (c) 1996,1997,1998
-        Whitehead Institute for Biomedical Research. All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-1.      Redistributions must reproduce the above copyright notice, this
-list of conditions and the following disclaimer in the  documentation
-and/or other materials provided with the distribution.  Redistributions of
-source code must also reproduce this information in the source code itself.
-
-2.      If the program is modified, redistributions must include a notice
-(in the same places as above) indicating that the redistributed program is
-not identical to the version distributed by Whitehead Institute.
-
-3.      All advertising materials mentioning features or use of this
-software  must display the following acknowledgment:
-        This product includes software developed by the
-        Whitehead Institute for Biomedical Research.
-
-4.      The name of the Whitehead Institute may not be used to endorse or
-promote products derived from this software without specific prior written
-permission.
-
-We also request that use of this software be cited in publications as 
-
-Steve Rozen, Helen J. Skaletsky (1996,1997,1998)
-   Primer3. Code available at
-   http://www-genome.wi.mit.edu/genome_software/other/primer3.html
-
-THIS SOFTWARE IS PROVIDED BY THE WHITEHEAD INSTITUTE ``AS IS'' AND  ANY
-EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE  IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE  ARE
-DISCLAIMED. IN NO EVENT SHALL THE WHITEHEAD INSTITUTE BE LIABLE  FOR ANY
-DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL  DAMAGES
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS  OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)  HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
-SUCH DAMAGE.
diff --git a/biology/primer3/pkg-plist b/biology/primer3/pkg-plist
deleted file mode 100644
index 8bbd779a715a..000000000000
--- a/biology/primer3/pkg-plist
+++ /dev/null
@@ -1,379 +0,0 @@
-bin/primer3
-%%PORTDOCS%%%%DOCSDIR%%/README.txt
-%%PORTDOCS%%%%DOCSDIR%%/example
-%%PORTDOCS%%%%EXAMPLESDIR%%/Makefile
-%%PORTDOCS%%%%EXAMPLESDIR%%/dpal_input
-%%PORTDOCS%%%%EXAMPLESDIR%%/dpal_long_input
-%%PORTDOCS%%%%EXAMPLESDIR%%/dpal_long_score_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/dpal_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/dpal_score_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/dpal_test.pl
-%%PORTDOCS%%%%EXAMPLESDIR%%/long_seq_input
-%%PORTDOCS%%%%EXAMPLESDIR%%/long_seq_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/long_seq_tm_test.pl
-%%PORTDOCS%%%%EXAMPLESDIR%%/not_for_production.lib
-%%PORTDOCS%%%%EXAMPLESDIR%%/not_for_production_Ns.lib
-%%PORTDOCS%%%%EXAMPLESDIR%%/not_for_production_Xs.lib
-%%PORTDOCS%%%%EXAMPLESDIR%%/oligotm.txt
-%%PORTDOCS%%%%EXAMPLESDIR%%/oligotm_test.pl
-%%PORTDOCS%%%%EXAMPLESDIR%%/p3-tmpl-mispriming_input
-%%PORTDOCS%%%%EXAMPLESDIR%%/p3-tmpl-mispriming_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/p3test.pl
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_input
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/AGAG.for
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/AGAG.rev
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-02.txt.for
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-02.txt.rev
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-03.txt.for
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-03.txt.rev
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-06.txt.for
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-06.txt.rev
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-19.txt.for
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-19.txt.rev
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-21.txt.for
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-21.txt.rev
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP04-07.txt.for
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP04-07.txt.rev
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test.for
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test.rev
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test_w_middle.for
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test_w_middle.int
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test_w_middle.rev
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/long_seq.for
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/long_seq.rev
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/targets_test.for
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/targets_test.rev
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_boundary1_formatted_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_boundary1_input
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_boundary1_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_boundary_formatted_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_boundary_input
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_boundary_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_check_input
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_check_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_end_pathology_input
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_end_pathology_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/MAX_PRIMER_LENGTH.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/MAX_PRIMER_LENGTH.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/MAX_PRIMER_LENGTH.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_1.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_1.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_1.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_2.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_2.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_2.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_3.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_3.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_3.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_4.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_4.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_4.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_dna_conc.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_dna_conc.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_dna_conc.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_1.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_1.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_1.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_2.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_2.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_2.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_3.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_3.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_3.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_4.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_4.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_4.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_1.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_1.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_1.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_2.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_2.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_2.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_3.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_3.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_3.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_1.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_1.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_1.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_2.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_2.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_2.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_3.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_3.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_3.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns_int.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns_int.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns_int.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_1.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_1.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_1.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_2.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_2.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_2.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_3.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_3.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_3.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_4.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_4.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_4.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_salt_conc.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_salt_conc.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_salt_conc.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any_int.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any_int.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any_int.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end_int.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end_int.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end_int.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_1.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_1.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_1.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_product_size.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_product_size.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_product_size.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/gc_clamp_min_size.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/gc_clamp_min_size.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/gc_clamp_min_size.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/incorrect_task.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/incorrect_task.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/incorrect_task.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_gc_content_obj_fn.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_gc_content_obj_fn.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_gc_content_obj_fn.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_obj_fn.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_obj_fn.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_obj_fn.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm_int.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm_int.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm_int.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm_int.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm_int.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm_int.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_limit_int.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_limit_int.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_limit_int.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product_int.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product_int.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product_int.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm_int.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm_int.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm_int.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mishyb_obj_fn.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mishyb_obj_fn.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mishyb_obj_fn.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mispr_obj_fn.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mispr_obj_fn.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mispr_obj_fn.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_equal.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_equal.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_equal.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_terminal_equal.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_terminal_equal.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_terminal_equal.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size_int.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size_int.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size_int.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size_int.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size_int.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size_int.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pair_mispr.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pair_mispr.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pair_mispr.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pr_gc_content_obj_fn.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pr_gc_content_obj_fn.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pr_gc_content_obj_fn.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_size_obj_fn.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_size_obj_fn.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_size_obj_fn.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_tm_obj_fn.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_tm_obj_fn.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_tm_obj_fn.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err1.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err1.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err1.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err2.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err2.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err2.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err3.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err3.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err3.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err4.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err4.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err4.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err5.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err5.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err5.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err6.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err6.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err6.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err1.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err1.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err1.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err2.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err2.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err2.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err3.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err3.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err3.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err4.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err4.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err4.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err5.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err5.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err5.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err6.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err6.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err6.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality1.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality1.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality1.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality2.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality2.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality2.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality3.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality3.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality3.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality4.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality4.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality4.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/too_many_product_sizes.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/too_many_product_sizes.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/too_many_product_sizes.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_min_size.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_min_size.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_min_size.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_num_return.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_num_return.out
-%%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_formatted_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_input
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal_formatted_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal_input
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_lib_amb_codes_input
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_lib_amb_codes_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_formatted_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary1_input
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary1_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary2_formatted_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary2_input
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary2_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_formatted_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_formatted_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_formatted_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_formatted_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_task_input
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_task_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_tm_lc_masking_formatted_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_tm_lc_masking_input
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_tm_lc_masking_output
-%%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%%/vgrep.pl
-%%DATADIR%%/COPYING.txt
-@dirrm %%DATADIR%%
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/primer_list_last
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/primer_global_err
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/primer1_list_last
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%
-%%PORTDOCS%%@dirrm %%DOCSDIR%%