academic/perlprimer: Added (Design primers for PCR and sequencing)

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

8 files changed, 120 insertions, 0 deletions

diff --git a/academic/perlprimer/README b/academic/perlprimer/README
new file mode 100644
index 0000000000..12917e35e9
--- /dev/null
+++ b/academic/perlprimer/README
@@ -0,0 +1,26 @@
+PerlPrimer is a free, open-source GUI application written in Perl 
+that designs primers for standard PCR, bisulphite PCR, real-time PCR 
+(QPCR) and sequencing. It aims to automate and simplify the process 
+of primer design. 
+
+PerlPrimer's current features include the following:
+
+- Calculation of possible primer-dimers
+- Retrieval of genomic or cDNA sequences from Ensembl (including both 
+  sequences automatically for QPCR)
+- Ability to BLAST search primers using the NCBI server or a local 
+  server
+- Results can be saved or optionally exported in a tab-delimited 
+  format that is compatible with most spreadsheet applications.
+- ORF and CpG island detection algorithms
+- Ability to add cloning sequences to primers, automatically adjusted 
+  to be in-frame
+- QPCR primer design without manual intron-exon boundary entry 
+
+For details and citation:
+Marshall OJ. PerlPrimer: cross-platform, graphical primer design for 
+standard, bisulphite and real-time PCR. Bioinformatics 2004 
+20(15):2471-2472
+
+This requires perl-tk and libwww-perl.
+For Real Time PCR, spidey is required. 
diff --git a/academic/perlprimer/References b/academic/perlprimer/References
new file mode 100644
index 0000000000..730eab0e32
--- /dev/null
+++ b/academic/perlprimer/References
@@ -0,0 +1,5 @@
+References
+
+Marshall OJ. PerlPrimer: cross-platform, graphical primer design
+for standard, bisulphite and real-time PCR. Bioinformatics 2004
+20(15):2471-2472
diff --git a/academic/perlprimer/doinst.sh b/academic/perlprimer/doinst.sh
new file mode 100644
index 0000000000..5fb28930db
--- /dev/null
+++ b/academic/perlprimer/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
diff --git a/academic/perlprimer/perlprimer.SlackBuild b/academic/perlprimer/perlprimer.SlackBuild
new file mode 100644
index 0000000000..87be393b78
--- /dev/null
+++ b/academic/perlprimer/perlprimer.SlackBuild
@@ -0,0 +1,50 @@
+#!/bin/sh
+
+# Slackware build script for perlprimer
+# 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=perlprimer		
+VERSION=${VERSION:-1.1.20}
+ARCH=noarch	
+BUILD=${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
+tar -jxvf $CWD/$PRGNAM-$VERSION.tar.bz2
+cd $PRGNAM-$VERSION
+
+install -D -m755 perlprimer.pl $PKG/usr/bin/perlprimer.pl
+
+# Menu item and icon
+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
+cp -a \
+  Changelog ReadMe.txt todo tutorial.html tutorial_files \
+  $PKG/usr/doc/$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/perlprimer/perlprimer.desktop b/academic/perlprimer/perlprimer.desktop
new file mode 100644
index 0000000000..f60fb9a287
--- /dev/null
+++ b/academic/perlprimer/perlprimer.desktop
@@ -0,0 +1,7 @@
+[Desktop Entry]
+Categories=Education;
+Exec=perlprimer.pl
+Icon=perlprimer.png
+Name=Perlprimer
+StartupNotify=false
+Type=Application
diff --git a/academic/perlprimer/perlprimer.info b/academic/perlprimer/perlprimer.info
new file mode 100644
index 0000000000..ad7c5f7d12
--- /dev/null
+++ b/academic/perlprimer/perlprimer.info
@@ -0,0 +1,10 @@
+PRGNAM="perlprimer"
+VERSION="1.1.20"
+HOMEPAGE="http://perlprimer.sourceforge.net/"
+DOWNLOAD="http://downloads.sourceforge.net/perlprimer/perlprimer-1.1.20.tar.bz2"
+MD5SUM="e3ce015cd5301aeb6120b75692008431"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+MAINTAINER="Petar Petrov"
+EMAIL="ppetrov@paju.oulu.fi"
+APPROVED="Niels Horn"
diff --git a/academic/perlprimer/perlprimer.png b/academic/perlprimer/perlprimer.png
new file mode 100644
index 0000000000..f476bbd775
--- /dev/null
+++ b/academic/perlprimer/perlprimer.png
diff --git a/academic/perlprimer/slack-desc b/academic/perlprimer/slack-desc
new file mode 100644
index 0000000000..8e0df5af07
--- /dev/null
+++ b/academic/perlprimer/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------------------------------------------------------|
+perlprimer: perlprimer (Design primers for PCR and sequencing)
+perlprimer:
+perlprimer: PerlPrimer is a free, open-source GUI application written in Perl
+perlprimer: that designs primers for standard PCR, bisulphite PCR, real-time PCR
+perlprimer: (QPCR) and sequencing. It aims to automate and simplify the process
+perlprimer: of primer design.
+perlprimer:
+perlprimer:
+perlprimer:
+perlprimer: References: /usr/doc/perlprimer-$VERSION/References
+perlprimer: Home: http://perlprimer.sourceforge.net/