academic/amplifx: Added (Manage, test and design your primers).

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

9 files changed, 157 insertions, 0 deletions

diff --git a/academic/amplifx/README b/academic/amplifx/README
new file mode 100644
index 0000000000..c5394bb809
--- /dev/null
+++ b/academic/amplifx/README
@@ -0,0 +1,37 @@
+AmplifX: Manage, test and design your primers for PCR.
+
+The main purpose of AmplifX is to seek in a collection of primers,
+such as any molecular biologist get in his refrigerators, those which
+can be use to amplify a fragment into a target sequence, for example,
+and particularly, to design strategies to screen recombinant clones by
+PCR. Main features:
+
+Manage your primers
+- Import or easily create primer lists
+- Name,comment, sort primers
+- Share simply primer lists (automatic lockout in read only mode of
+  files yet opened by an other user)
+- Automatic calculation of quality score (TM [Santa-Lucia method],
+  length, GC%, autodimer, complexity, etc.)
+- Works with degenerate sequences
+
+Test your primers
+- Localise your primers on target sequences (main file formats
+  supported and "intelligent" copy-paste)
+- Prediction of amplified sequences
+- Interactive graphic map
+- Pertinent informations on matches and amplicons (TM, size, predicted
+  dimers, etc.)
+
+Design your primers
+- Simple and intuitive interface to design new primers for amplifying
+  a fragment choosing the amplicon size and/or the position
+- Many of design options
+
+NOTE:
+This is just repackaging of the ready binary for x86 and will not run
+on x86_64. It will probably work fine on a Slackware multilib box.
+
+How to cite AmplifX:
+AmplifX X.X.X [version number] by Nicolas Jullien; CNRS, Aix-Marseille
+Université - http://crn2m.univ-mrs.fr/pub/amplifx-dist
diff --git a/academic/amplifx/References b/academic/amplifx/References
new file mode 100644
index 0000000000..141ef9025b
--- /dev/null
+++ b/academic/amplifx/References
@@ -0,0 +1,2 @@
+AmplifX X.X.X [version number] by Nicolas Jullien; CNRS, Aix-Marseille
+Université - http://crn2m.univ-mrs.fr/pub/amplifx-dist
diff --git a/academic/amplifx/amplifx b/academic/amplifx/amplifx
new file mode 100644
index 0000000000..0feceb046b
--- /dev/null
+++ b/academic/amplifx/amplifx
@@ -0,0 +1,3 @@
+#!/bin/sh
+cd /opt/amplifx
+./AmplifX &
diff --git a/academic/amplifx/amplifx.SlackBuild b/academic/amplifx/amplifx.SlackBuild
new file mode 100644
index 0000000000..b1b82d6e69
--- /dev/null
+++ b/academic/amplifx/amplifx.SlackBuild
@@ -0,0 +1,75 @@
+#!/bin/sh
+
+# Slackware build script for amplifx
+
+# Copyright 2014 Petar Petrov, petar.petrov@student.oulu.fi
+# All rights reserved.
+#
+# Redistribution and use of this script, with or without modification, is
+# permitted provided that the following conditions are met:
+#
+# 1. Redistributions of this script must retain the above copyright
+#    notice, this list of conditions and the following disclaimer.
+#
+#  THIS SOFTWARE IS PROVIDED BY THE AUTHOR "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 AUTHOR 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.
+
+PRGNAM=amplifx
+SRCNAM=AmplifX_Lin_Latest
+VERSION=${VERSION:-1.7.0}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
+
+ARCH=i386
+
+CWD=$(pwd)
+TMP=${TMP:-/tmp/SBo}
+PKG=$TMP/package-$PRGNAM
+OUTPUT=${OUTPUT:-/tmp}
+
+set -e
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+rm -rf $PRGNAM-$VERSION
+mkdir $PRGNAM-$VERSION
+cd $PRGNAM-$VERSION
+unzip $CWD/$SRCNAM.zip
+chown -R root:root .
+find -L . \
+ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
+  -o -perm 511 \) -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
+ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
+
+# Put things in /opt, as the binary expects the libraries folder to be
+# in its current location.
+mkdir -p $PKG/opt/$PRGNAM
+cp -a ./AmplifX/* $PKG/opt/$PRGNAM
+
+# This is a simple wrapper to go in /usr/bin
+install -D -m755 $CWD/$PRGNAM $PKG/usr/bin/$PRGNAM
+
+mkdir -p $PKG/usr/share/{applications,pixmaps}
+cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications
+cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
+cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
+
+mkdir -p $PKG/install
+cat $CWD/slack-desc > $PKG/install/slack-desc
+cat $CWD/doinst.sh > $PKG/install/doinst.sh
+
+cd $PKG
+/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
diff --git a/academic/amplifx/amplifx.desktop b/academic/amplifx/amplifx.desktop
new file mode 100644
index 0000000000..dfc4d33550
--- /dev/null
+++ b/academic/amplifx/amplifx.desktop
@@ -0,0 +1,7 @@
+[Desktop Entry]
+Categories=Education;
+Exec=amplifx
+Icon=amplifx
+Name=AmplifX
+StartupNotify=false
+Type=Application
diff --git a/academic/amplifx/amplifx.info b/academic/amplifx/amplifx.info
new file mode 100644
index 0000000000..72fe05f382
--- /dev/null
+++ b/academic/amplifx/amplifx.info
@@ -0,0 +1,10 @@
+PRGNAM="amplifx"
+VERSION="1.7.0"
+HOMEPAGE="http://crn2m.univ-mrs.fr/AmplifX"
+DOWNLOAD="http://crn2m.univ-mrs.fr/IMG/zip/AmplifX_Lin_Latest.zip"
+MD5SUM="ff84d1c4a800dcb651beaa877ff7b1ca"
+DOWNLOAD_x86_64="UNSUPPORTED"
+MD5SUM_x86_64=""
+REQUIRES=""
+MAINTAINER="Petar Petrov"
+EMAIL="petar.petrov@student.oulu.fi"
diff --git a/academic/amplifx/amplifx.png b/academic/amplifx/amplifx.png
new file mode 100644
index 0000000000..f764b6458a
--- /dev/null
+++ b/academic/amplifx/amplifx.png
diff --git a/academic/amplifx/doinst.sh b/academic/amplifx/doinst.sh
new file mode 100644
index 0000000000..4e8ba7071d
--- /dev/null
+++ b/academic/amplifx/doinst.sh
@@ -0,0 +1,4 @@
+if [ -x /usr/bin/update-desktop-database ]; then
+  /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1
+fi
+
diff --git a/academic/amplifx/slack-desc b/academic/amplifx/slack-desc
new file mode 100644
index 0000000000..60d74ca6e9
--- /dev/null
+++ b/academic/amplifx/slack-desc
@@ -0,0 +1,19 @@
+# HOW TO EDIT THIS FILE:
+# The "handy ruler" below makes it easier to edit a package description.
+# Line up the first '|' above the ':' following the base package name, and
+# the '|' on the right side marks the last column you can put a character in.
+# You must make exactly 11 lines for the formatting to be correct.  It's also
+# customary to leave one space after the ':' except on otherwise blank lines.
+
+       |-----handy-ruler------------------------------------------------------|
+amplifx: amplifx: (Manage, test and design your primers for PCR)
+amplifx:
+amplifx: The main purpose of AmplifX is to seek in a collection of primers,
+amplifx: such as any molecular biologist get in his refrigerators, those
+amplifx: which can be use to amplify a fragment into a target sequence,
+amplifx: for example, and particularly, to design strategies to screen
+amplifx: recombinant clones by PCR.
+amplifx:
+amplifx: Home: http://crn2m.univ-mrs.fr/AmplifX
+amplifx: References: /usr/doc/amplifx-1.7.0/References
+amplifx: