academic/amplicon: Added (Design PCR primers)

Signed-off-by: Niels Horn <niels.horn@slackbuilds.org>

8 files changed, 108 insertions, 0 deletions

diff --git a/academic/amplicon/README b/academic/amplicon/README
new file mode 100644
index 0000000000..395b56f031
--- /dev/null
+++ b/academic/amplicon/README
@@ -0,0 +1,10 @@
+Amplicon is a tool for designing PCR primers where groups of related 
+DNA sequences can be assessed in aligned form. Other useful features 
+that are not common in other PCR primer design software are handling 
+of gapped sequences and degenerate sites in aligned DNA. Amplicon can 
+import aligned DNA sequences produced by Clustal, or aligned 
+sequences in MEGA or Fasta format.
+
+For details and citation:
+Jarman SN (2004) Amplicon: software for designing PCR primers on 
+aligned DNA sequences. Bioinformatics 20: 1644-1645.
diff --git a/academic/amplicon/References b/academic/amplicon/References
new file mode 100644
index 0000000000..cef68629d6
--- /dev/null
+++ b/academic/amplicon/References
@@ -0,0 +1,8 @@
+References
+
+Jarman SN (2004) Amplicon: software for designing PCR primers on aligned
+DNA sequences. Bioinformatics 20: 1644-1645.
+
+Jarman SN, Deagle BE, Gales NJ (2004) Group-specific polymerase chain
+reaction for DNA-based analysis of species diversity and identity in
+dietary samples. Molecular Ecology 13: 1313-1322.
diff --git a/academic/amplicon/amplicon.SlackBuild b/academic/amplicon/amplicon.SlackBuild
new file mode 100644
index 0000000000..715746b531
--- /dev/null
+++ b/academic/amplicon/amplicon.SlackBuild
@@ -0,0 +1,51 @@
+#!/bin/sh
+
+# Slackware build script for amplicon
+# Written by Petar Petrov, <ppetrov@paju.oulu.fi> and 
+# hereby submitted to the public domain
+
+# THIS SLACKBUILD IS DISTRIBUTETD IN THE HOPE OF BEING 
+# USEFUL BUT WITHOUT ANY WARRANTY. THE AUTHOR IS _NOT_ 
+# RESPONSIBLE FOR ANY DAMAGE OR DATA LOSS CAUSED BY IT.
+
+PRGNAM=amplicon			
+VERSION=${VERSION:-b09.1}
+ARCH=noarch	
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}		
+
+CWD=$(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
+gunzip -c $CWD/Amplicon-Linux-$VERSION.py.gz > amplicon.py
+
+# Fix the window size
+sed "s:root.maxsize(965,570):root.maxsize(1400,800):" -i amplicon.py
+
+install -D -m755 amplicon.py $PKG/usr/bin/amplicon.py
+
+# Manu item and icon
+mkdir -p $PKG/usr/share/{applications,pixmaps}
+cp $CWD/amplicon.desktop $PKG/usr/share/applications/
+cp $CWD/amplicon.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/amplicon/amplicon.desktop b/academic/amplicon/amplicon.desktop
new file mode 100644
index 0000000000..7444f0c78a
--- /dev/null
+++ b/academic/amplicon/amplicon.desktop
@@ -0,0 +1,7 @@
+[Desktop Entry]
+Categories=Education;
+Exec=python /usr/bin/amplicon.py
+Icon=amplicon.png
+Name=Amplicon
+StartupNotify=false
+Type=Application
diff --git a/academic/amplicon/amplicon.info b/academic/amplicon/amplicon.info
new file mode 100644
index 0000000000..baf1232189
--- /dev/null
+++ b/academic/amplicon/amplicon.info
@@ -0,0 +1,10 @@
+PRGNAM="amplicon"
+VERSION="b09.1"
+HOMEPAGE="http://amplicon.sourceforge.net/"
+DOWNLOAD="http://downloads.sourceforge.net/amplicon/Amplicon-Linux-b09.1.py.gz"
+MD5SUM="43e6bedbe16b7f423a88286910f8749a"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+MAINTAINER="Petar Petrov"
+EMAIL="ppetrov@paju.oulu.fi"
+APPROVED="Niels Horn"
diff --git a/academic/amplicon/amplicon.png b/academic/amplicon/amplicon.png
new file mode 100644
index 0000000000..d1fbd59445
--- /dev/null
+++ b/academic/amplicon/amplicon.png
diff --git a/academic/amplicon/doinst.sh b/academic/amplicon/doinst.sh
new file mode 100644
index 0000000000..01ca62b341
--- /dev/null
+++ b/academic/amplicon/doinst.sh
@@ -0,0 +1,3 @@
+if [ -x /usr/bin/update-desktop-database ]; then
+  /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1
+fi
\ No newline at end of file
diff --git a/academic/amplicon/slack-desc b/academic/amplicon/slack-desc
new file mode 100644
index 0000000000..e3c789afa1
--- /dev/null
+++ b/academic/amplicon/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 ':'.
+
+        |-----handy-ruler------------------------------------------------------|
+amplicon: amplicon (Design PCR primers on aligned sequences)
+amplicon:
+amplicon: Amplicon is a tool for designing PCR primers where groups of related
+amplicon: DNA sequences can be assessed in aligned form. This is especially
+amplicon: useful for designing 'group-specific' PCR primer sets that produce
+amplicon: amplicons from a targer group of species, but not from other groups
+amplicon: of species.
+amplicon:
+amplicon:
+amplicon: References: /usr/doc/amplicon-$VERSION/References
+amplicon: Home: http://amplicon.sourceforge.net/