Date: Wed, 27 Dec 2006 17:20:34 GMT From: Fernan Aguero<fernan@iib.unsam.edu.ar> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/107246: update primer3 to latest version, take maintainership Message-ID: <200612271720.kBRHKY5C091053@www.freebsd.org> Resent-Message-ID: <200612271730.kBRHUGX1064201@freefall.freebsd.org>
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>Number: 107246 >Category: ports >Synopsis: update primer3 to latest version, take maintainership >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Wed Dec 27 17:30:15 GMT 2006 >Closed-Date: >Last-Modified: >Originator: Fernan Aguero >Release: FreeBSD-6.1 >Organization: IIB-UNSAM >Environment: >Description: Primer3 is now at sourceforge, and the latest version is 1.0.1 (minor changes and bugfixes with respect to the current port version). Attached is an update of the port to 1.0.1 Now, the port maintainer (Tony Maher) was just reset. I know Tony has changed employers so maybe this is the reason why emails sent to his old address have not been replied. I accept to take maintainership of the port if Tony is no longer interested in maintaining. But, please, whoever takes this PR, send an email to Tony at <anthony.maher@uts.edu.au> to ask him about this first (I'm sending this PR using the web form at http://www.freebsd.org/send-pr.html, so I cannot CC this to other parties). Thanks, Fernan >How-To-Repeat: >Fix: Patch attached with submission follows: diff -ruN /usr/ports/biology/primer3/Makefile primer3/Makefile --- /usr/ports/biology/primer3/Makefile Wed Dec 27 13:32:41 2006 +++ primer3/Makefile Wed Dec 27 11:43:11 2006 @@ -2,20 +2,21 @@ # Date created: 25 February 2002 # Whom: Tony Maher <tonym@biolateral.com.au> # -# $FreeBSD: ports/biology/primer3/Makefile,v 1.9 2006/12/26 12:46:33 linimon Exp $ +# $FreeBSD: ports/biology/primer3/Makefile,v 1.8 2006/05/03 23:26:34 edwin Exp $ # PORTNAME= primer3 -PORTVERSION= 1.0.0 +PORTVERSION= 1.0.1 CATEGORIES= biology -MASTER_SITES= http://frodo.wi.mit.edu/primer3/ +MASTER_SITES= ${MASTER_SITE_SOURCEFORGE} +MASTER_SITE_SUBDIR= ${PORTNAME} DISTNAME= ${PORTNAME}_${PORTVERSION} -MAINTAINER= ports@FreeBSD.org +MAINTAINER= fernan@iib.unsam.edu.ar COMMENT= Primer3 helps to choose primers for PCR reactions WRKSRC= ${WRKDIR}/${DISTNAME}/src -DOCUMENTS= README example +DOCUMENTS= README.${PORTNAME}_${PORTVERSION}.txt example post-patch: @${REINPLACE_CMD} \ @@ -28,7 +29,7 @@ do-install: @${INSTALL_PROGRAM} ${WRKSRC}/primer3_core ${PREFIX}/bin/primer3 @${MKDIR} ${DATADIR} - @${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/Copyright ${DATADIR} + @${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/Copyright.txt ${DATADIR} .if !defined(NOPORTDOCS) @${MKDIR} ${DOCSDIR} .for file in ${DOCUMENTS} @@ -41,6 +42,6 @@ .endif post-install: - @${CAT} ${DATADIR}/Copyright + @${CAT} ${DATADIR}/Copyright.txt .include <bsd.port.mk> diff -ruN /usr/ports/biology/primer3/distinfo primer3/distinfo --- /usr/ports/biology/primer3/distinfo Wed Jan 25 11:31:48 2006 +++ primer3/distinfo Wed Dec 27 11:38:31 2006 @@ -1,3 +1,3 @@ -MD5 (primer3_1.0.0.tar.gz) = 58605ee607f6218a2a775345b10d15fa -SHA256 (primer3_1.0.0.tar.gz) = fcbcf2e540e0062f3fa0d723b443b04a1c31e3e03e3aa5d97e3b2f910499f34b -SIZE (primer3_1.0.0.tar.gz) = 936696 +MD5 (primer3_1.0.1.tar.gz) = 4fa33b8667cec1b88f1516d175eb1bed +SHA256 (primer3_1.0.1.tar.gz) = 2f7641d66d75b4830a01d31dbc96c61ffad2b1f047287009906902558a9e165e +SIZE (primer3_1.0.1.tar.gz) = 902576 diff -ruN /usr/ports/biology/primer3/pkg-plist primer3/pkg-plist --- /usr/ports/biology/primer3/pkg-plist Wed Jun 29 14:45:28 2005 +++ primer3/pkg-plist Wed Dec 27 13:29:55 2006 @@ -1,4 +1,5 @@ -%%PORTDOCS%%%%DOCSDIR%%/README +bin/primer3 +%%PORTDOCS%%%%DOCSDIR%%/README.primer3_1.0.1.txt %%PORTDOCS%%%%DOCSDIR%%/example %%PORTDOCS%%%%EXAMPLESDIR%%/dpal_gen.pl %%PORTDOCS%%%%EXAMPLESDIR%%/dpal_input @@ -9,10 +10,24 @@ %%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%%/p3-tmpl-mispriming_input +%%PORTDOCS%%%%EXAMPLESDIR%%/p3-tmpl-mispriming_output +%%PORTDOCS%%%%EXAMPLESDIR%%/p3test.pl %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_input +%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_output %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/AGAG.for %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/AGAG.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/SP01-02.txt.for %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-02.txt.rev %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-03.txt.for @@ -25,24 +40,18 @@ %%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/long_seq.for -%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test_w_middle.rev -%%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/bad_dna_conc.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_1.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_2.in @@ -60,8 +69,8 @@ %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_2.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_3.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_4.in -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_salt_conc.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any_int.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end_int.in @@ -75,15 +84,16 @@ %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm_int.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm_int.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/MAX_PRIMER_LENGTH.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_limit_int.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product.in -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product_int.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product_int.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm_int.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mishyb_obj_fn.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mispr_obj_fn.in -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no=.in -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_terminal=.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_equal.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_terminal_equal.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size_int.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size.in @@ -92,91 +102,91 @@ %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pr_gc_content_obj_fn.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_size_obj_fn.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_tm_obj_fn.in -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err1.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err2.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err3.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err4.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err5.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err6.in -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err1.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err2.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err3.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err4.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err5.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err6.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality1.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality2.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality3.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality4.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/too_many_product_sizes.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_1.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_min_size.in %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_num_return.in -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/MAX_PRIMER_LENGTH.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_1.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_dna_conc.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_1.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_2.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_3.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_4.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_1.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_2.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_3.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_1.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_2.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_3.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns_int.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_1.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_2.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_3.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_4.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_salt_conc.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_1.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any_int.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end_int.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_product_size.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/gc_clamp_min_size.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/incorrect_task.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_gc_content_obj_fn.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_obj_fn.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm_int.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm_int.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/MAX_PRIMER_LENGTH.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_limit_int.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product_int.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm_int.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mishyb_obj_fn.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mispr_obj_fn.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no=.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_terminal=.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_equal.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_terminal_equal.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size_int.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size_int.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pair_mispr.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pr_gc_content_obj_fn.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_size_obj_fn.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_tm_obj_fn.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err1.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err2.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err3.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err4.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err5.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err6.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err1.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err2.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err3.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err4.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err5.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err6.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality1.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality2.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality3.out @@ -184,70 +194,70 @@ %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/too_many_product_sizes.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_min_size.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_num_return.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/MAX_PRIMER_LENGTH.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_1.out2 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_dna_conc.out2 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_1.out2 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_2.out2 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_3.out2 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_4.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_1.out2 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_2.out2 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_3.out2 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_1.out2 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_2.out2 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_3.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns.out2 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns_int.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns.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_any.out2 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end_int.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end.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_min_tm.out2 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm_int.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/MAX_PRIMER_LENGTH.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/max_size_min_product.out2 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm_int.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm.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/no_equal.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_terminal_equal.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_max_size.out2 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size_int.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size.out2 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pair_mispr.out2 %%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_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/repeat_lib_int_err.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 @@ -259,14 +269,31 @@ %%PORTDOCS%%%%EXAMPLESDIR%%/primer_human_output %%PORTDOCS%%%%EXAMPLESDIR%%/primer_input %%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_input +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_formatted_output +%%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/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/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.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/SP01-06-with-repeat1.for %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat1.int %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat1.rev @@ -276,40 +303,34 @@ %%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_obj_fn_input %%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%%/repeat_lib1 %%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 @@ -323,39 +344,18 @@ %%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_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 -%%DATADIR%%/Copyright -@dirrm %%DATADIR%% +%%DATADIR%%/Copyright.txt %%PORTDOCS%%@dirrm %%DOCSDIR%% -%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/primer1_list_last -%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/primer_global_err -%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/primer_list_last -%%PORTDOCS%%@dirrm %%EXAMPLESDIR%% +@dirrm %%EXAMPLESDIR%%/primer1_list_last +@dirrm %%EXAMPLESDIR%%/primer_global_err +@dirrm %%EXAMPLESDIR%%/primer_list_last +@dirrm %%EXAMPLESDIR%% +@dirrm %%DATADIR%% >Release-Note: >Audit-Trail: >Unformatted:
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