primer3.SlackBuild 3.7 KB

123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121
  1. #!/bin/sh
  2. # Slackware build script for primer3
  3. # Copyright 2011-2013 Petar Petrov, petar.petrov@student.oulu.fi
  4. # All rights reserved.
  5. #
  6. # Redistribution and use of this script, with or without modification, is
  7. # permitted provided that the following conditions are met:
  8. #
  9. # 1. Redistributions of this script must retain the above copyright
  10. # notice, this list of conditions and the following disclaimer.
  11. #
  12. # THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
  13. # WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
  14. # MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
  15. # EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
  16. # SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
  17. # PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
  18. # OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
  19. # WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
  20. # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
  21. # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  22. PRGNAM=primer3
  23. VERSION=${VERSION:-2.3.6}
  24. BUILD=${BUILD:-1}
  25. TAG=${TAG:-_SBo}
  26. if [ -z "$ARCH" ]; then
  27. case "$( uname -m )" in
  28. i?86) ARCH=i486 ;;
  29. arm*) ARCH=arm ;;
  30. *) ARCH=$( uname -m ) ;;
  31. esac
  32. fi
  33. CWD=$(pwd)
  34. TMP=${TMP:-/tmp/SBo}
  35. PKG=$TMP/package-$PRGNAM
  36. OUTPUT=${OUTPUT:-/tmp}
  37. if [ "$ARCH" = "i486" ]; then
  38. SLKCFLAGS="-O2 -march=i486 -mtune=i686"
  39. LIBDIRSUFFIX=""
  40. elif [ "$ARCH" = "i686" ]; then
  41. SLKCFLAGS="-O2 -march=i686 -mtune=i686"
  42. LIBDIRSUFFIX=""
  43. elif [ "$ARCH" = "x86_64" ]; then
  44. SLKCFLAGS="-O2 -fPIC"
  45. LIBDIRSUFFIX="64"
  46. else
  47. SLKCFLAGS="-O2"
  48. LIBDIRSUFFIX=""
  49. fi
  50. set -e
  51. rm -rf $PKG
  52. mkdir -p $TMP $PKG $OUTPUT
  53. cd $TMP
  54. rm -rf $PRGNAM-$VERSION
  55. tar xvf $CWD/${PRGNAM}-src-${VERSION}.tar.gz
  56. cd $PRGNAM-$VERSION
  57. chown -R root:root .
  58. find -L . \
  59. \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
  60. -o -perm 511 \) -exec chmod 755 {} \; -o \
  61. \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
  62. -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
  63. cd ./src
  64. # Use our CFLAGS
  65. sed -i "/^CFLAGS/s/=/+=/" Makefile
  66. # Look for configuration files in /usr/share instead of /opt
  67. sed -i "s:/opt/primer3_config:/usr/share/$PRGNAM/primer3_config:g" thal_main.c primer3_boulder_main.c
  68. CFLAGS="$SLKCFLAGS" \
  69. CXXFLAGS="$SLKCFLAGS" \
  70. make
  71. # This is recommended, but the tests take a really long time.
  72. # Be patient if you uncomment the next line.
  73. # make test
  74. install -D -m755 primer3_core $PKG/usr/bin/primer3_core
  75. install -D -m755 ntdpal $PKG/usr/bin/ntdpal
  76. install -D -m755 ntthal $PKG/usr/bin/ntthal
  77. install -D -m755 oligotm $PKG/usr/bin/oligotm
  78. # eprimer32 from EMBOSS, expects the binary to be called primer32_core
  79. cd $PKG/usr/bin
  80. ln -s primer3_core primer32_core
  81. # Copy configuration files and settings to /usr/share
  82. cd $TMP/$PRGNAM-$VERSION
  83. mkdir -p $PKG/usr/share/$PRGNAM
  84. cp -a src/primer3_config \
  85. primer3_v1_1_4_default_settings.txt \
  86. primer3web_v0_4_0_default_settings.txt \
  87. primer3web_v3_0_0_default_settings.txt \
  88. $PKG/usr/share/$PRGNAM
  89. find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
  90. | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
  91. mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
  92. cp -a \
  93. src/release_notes.txt COPYING.txt example primer3_manual.htm \
  94. $PKG/usr/doc/$PRGNAM-$VERSION
  95. cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
  96. cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
  97. mkdir -p $PKG/install
  98. cat $CWD/slack-desc > $PKG/install/slack-desc
  99. cd $PKG
  100. /sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}