academic/primer3: Updated for version 2.6.1.

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

6 files changed, 53 insertions, 52 deletions

diff --git a/academic/primer3/README b/academic/primer3/README
index 51977f2f12..3b57af159d 100644
--- a/academic/primer3/README
+++ b/academic/primer3/README
@@ -1,14 +1,24 @@
 Primer3 is a widely used program for designing PCR primers (PCR =
-"Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool
-in genetics and molecular biology. Primer3 can design hybridization
-probes and sequencing primers.
+"Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool in
+genetics and molecular biology. Primer3 can design hybridization probes
+and sequencing primers.
 
 PCR is used for many different goals. Consequently, primer3 has many
 different input parameters that you control and that tell primer3
 exactly what characteristics make good primers for your goals.
 
-For details and citation:
-Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for
-general users and for biologist programmers. In: Krawetz S, Misener S
-(eds) Bioinformatics Methods and Protocols: Methods in Molecular
-Biology. Humana Press, Totowa, NJ, pp 365-386
+Primer3 picks primers for PCR reactions, considering as criteria:
+* oligonucleotide melting temperature, size, GC content and primer-dimer
+  possibilities,
+* PCR product size
+* positional constraints within the source (template) sequence
+* possibilities for ectopic priming (amplifying the wrong sequence)
+* many other constraints.
+
+All of these criteria are user-specifiable as constraints, and some are
+specifiable as terms in an objective function that characterizes an
+optimal primer pair.
+
+manual online: https://primer3.org/manual.html
+
+For details and citation see "References" in the package's doc folder.
diff --git a/academic/primer3/References b/academic/primer3/References
index 5009a52a1b..f951635a4d 100644
--- a/academic/primer3/References
+++ b/academic/primer3/References
@@ -1,4 +1,21 @@
-Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for general
-users and for biologist programmers. In: Krawetz S, Misener S (eds)
-Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana
-Press, Totowa, NJ, pp 365-386
+We request but do not require that use of this software be cited in publications as
+
+* Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M and Rozen SG.
+Primer3--new capabilities and interfaces.
+Nucleic Acids Res. 2012 Aug 1;40(15):e115.
+The paper is available at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3424584/
+
+and
+
+* Koressaar T and Remm M.
+Enhancements and modifications of primer design program Primer3.
+Bioinformatics 2007;23(10):1289-1291.
+The paper is available at https://www.ncbi.nlm.nih.gov/pubmed/17379693
+
+If you use masker function, please cite:
+* Koressaar T, Lepamets M, Kaplinski L, Raime K, Andreson R and Remm M.
+Primer3_masker: integrating masking of template sequence with primer design software.
+Bioinformatics 2018;34(11):1937-1938.
+The paper is available at https://www.ncbi.nlm.nih.gov/pubmed/29360956
+
+Source code available at https://github.com/primer3-org/primer3.
diff --git a/academic/primer3/gcc-7.patch b/academic/primer3/gcc-7.patch
deleted file mode 100644
index a92d0e77b7..0000000000
--- a/academic/primer3/gcc-7.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-Author:  Andreas Tille <tille@debian.org>
-Last-Update: Sat, 26 Aug 2017 00:32:40 +0200
-Bug-Debian: https://bugs.debian.org/853621
-Description: Fix build with gcc-7
-
---- a/src/thal.c
-+++ b/src/thal.c
-@@ -426,12 +426,12 @@ thal(const unsigned char *oligo_f,
- 	       "Illegal type");
-    o->align_end_1 = -1;
-    o->align_end_2 = -1;
--   if ('\0' == oligo_f) {
-+   if ('\0' == oligo_f[0]) {
-       strcpy(o->msg, "Empty first sequence");
-       o->temp = 0.0;
-       return;
-    }
--   if ('\0' == oligo_r) {
-+   if ('\0' == oligo_r[0]) {
-       strcpy(o->msg, "Empty second sequence");
-       o->temp = 0.0;
-       return;
diff --git a/academic/primer3/primer3.SlackBuild b/academic/primer3/primer3.SlackBuild
index 5281f13889..9a4bd6b511 100644
--- a/academic/primer3/primer3.SlackBuild
+++ b/academic/primer3/primer3.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for primer3
 
-# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com
+# Copyright 2011-2023 Petar Petrov slackalaxy@gmail.com
 # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
@@ -25,7 +25,7 @@
 cd $(dirname $0) ; CWD=$(pwd)
 
 PRGNAM=primer3
-VERSION=${VERSION:-2.4.0}
+VERSION=${VERSION:-2.6.1}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 PKGTYPE=${PKGTYPE:-tgz}
@@ -38,9 +38,6 @@ if [ -z "$ARCH" ]; then
   esac
 fi
 
-# If the variable PRINT_PACKAGE_NAME is set, then this script will report what
-# the name of the created package would be, and then exit. This information
-# could be useful to other scripts.
 if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then
   echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE"
   exit 0
@@ -79,13 +76,10 @@ find -L . \
  \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
  -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
 
-# Thanks to Debian for the patch
-patch -p1 -i $CWD/gcc-7.patch
-
 cd ./src
 
 # Use our CFLAGS
-sed -i -e "s|-O2|$SLKCFLAGS|" -e "s|-g -Wall|-fpermissive|" Makefile
+sed -i -e "s|-O2|$SLKCFLAGS|" Makefile
 
 # Look for configuration files in /usr/share instead of /opt
 sed -i "s:/opt/primer3_config:/usr/share/$PRGNAM/primer3_config:g" thal_main.c primer3_boulder_main.c
@@ -94,7 +88,7 @@ make
 
 # This is recommended, but the tests take a really long time. Be patient
 # if you uncomment the line below.
-# make test
+#make test
 
 install -D -m755 primer3_core $PKG/usr/bin/primer3_core
 install -D -m755 ntdpal $PKG/usr/bin/ntdpal
@@ -108,7 +102,9 @@ ln -s primer3_core primer32_core
 # Copy configuration files and settings to /usr/share
 cd $TMP/$PRGNAM-$VERSION
 mkdir -p $PKG/usr/share/$PRGNAM
-cp -a settings_files src/primer3_config $PKG/usr/share/$PRGNAM
+cp -a \
+  kmer_lists/readme.txt settings_files example src/primer3_config \
+  $PKG/usr/share/$PRGNAM
 
 # Copy the man pages from Debian
 mkdir -p $PKG/usr/man/man1
@@ -122,7 +118,7 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r
 
 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
 cp -a \
-  src/{release_notes.txt,primer3_manual.htm} LICENSE example README.md  \
+  src/{release_notes.txt,primer3_manual.htm} LICENSE README.md  \
   $PKG/usr/doc/$PRGNAM-$VERSION
 cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
 cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
diff --git a/academic/primer3/primer3.info b/academic/primer3/primer3.info
index 861eb56e58..5a9c2ffe17 100644
--- a/academic/primer3/primer3.info
+++ b/academic/primer3/primer3.info
@@ -1,8 +1,8 @@
 PRGNAM="primer3"
-VERSION="2.4.0"
-HOMEPAGE="http://primer3.sourceforge.net/"
-DOWNLOAD="http://sourceforge.net/projects/primer3/files/primer3/2.4.0/primer3-2.4.0.tar.gz"
-MD5SUM="aed6546bdfb60652cd7eba8d51eae8cc"
+VERSION="2.6.1"
+HOMEPAGE="https://primer3.org/"
+DOWNLOAD="https://github.com/primer3-org/primer3/archive/v2.6.1/primer3-2.6.1.tar.gz"
+MD5SUM="d18c095694b586c300c88fab4b116c8c"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES=""
diff --git a/academic/primer3/slack-desc b/academic/primer3/slack-desc
index 9e871a4b8c..4e4ce377e2 100644
--- a/academic/primer3/slack-desc
+++ b/academic/primer3/slack-desc
@@ -13,7 +13,7 @@ primer3: "Polymerase Chain Reaction"). PCR is an essential and
 primer3: ubiquitous tool in genetics and molecular biology. Primer3 can also
 primer3: design hybridization probes and sequencing primers.
 primer3:
-primer3: Home: http://primer3.sourceforge.net/
-primer3: References: /usr/doc/primer3-2.3.7/References
+primer3: https://primer3.org/manual.html
+primer3:
 primer3:
 primer3: