academic/stringtie: Added (Assembler of RNA-Seq alignments).

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

4 files changed, 131 insertions, 0 deletions

diff --git a/academic/stringtie/README b/academic/stringtie/README
new file mode 100644
index 0000000000000..0ffb8ddea5edc
--- /dev/null
+++ b/academic/stringtie/README
@@ -0,0 +1,11 @@
+StringTie is a fast and highly efficient assembler of RNA-Seq
+alignments into potential transcripts. It uses a novel network flow
+algorithm as well as an optional de novo assembly step to assemble and
+quantitate full-length transcripts representing multiple splice
+variants for each gene locus. Its input can include not only the
+alignments of raw reads used by other transcript assemblers, but also
+alignments longer sequences that have been assembled from those reads.
+
+In order to identify differentially expressed genes between
+experiments, StringTie's output can be processed by specialized
+software like Ballgown, Cuffdiff or other programs (DESeq2, edgeR).
diff --git a/academic/stringtie/slack-desc b/academic/stringtie/slack-desc
new file mode 100644
index 0000000000000..8f72782c51c9c
--- /dev/null
+++ b/academic/stringtie/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------------------------------------------------------|
+stringtie: stringtie (Assembler of RNA-Seq alignments)
+stringtie:
+stringtie: StringTie is a fast and highly efficient assembler of RNA-Seq
+stringtie: alignments into potential transcripts. It uses a novel network
+stringtie: flow algorithm as well as an optional de novo assembly step to
+stringtie: assemble and quantitate full-length transcripts representing
+stringtie: multiple splice variants for each gene locus.
+stringtie:
+stringtie: Home: http://ccb.jhu.edu/software/stringtie/
+stringtie:
+stringtie:
diff --git a/academic/stringtie/stringtie.SlackBuild b/academic/stringtie/stringtie.SlackBuild
new file mode 100644
index 0000000000000..51f471e71a4e3
--- /dev/null
+++ b/academic/stringtie/stringtie.SlackBuild
@@ -0,0 +1,91 @@
+#!/bin/sh
+
+# Slackware build script for stringtie
+
+# Copyright 2018 Petar Petrov slackalaxy@gmail.com
+# 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=stringtie
+VERSION=${VERSION:-1.3.5}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
+
+if [ -z "$ARCH" ]; then
+  case "$( uname -m )" in
+    i?86) ARCH=i586 ;;
+    arm*) ARCH=arm ;;
+       *) ARCH=$( uname -m ) ;;
+  esac
+fi
+
+CWD=$(pwd)
+TMP=${TMP:-/tmp/SBo}
+PKG=$TMP/package-$PRGNAM
+OUTPUT=${OUTPUT:-/tmp}
+
+if [ "$ARCH" = "i586" ]; then
+  SLKCFLAGS="-O2 -march=i586 -mtune=i686"
+  LIBDIRSUFFIX=""
+elif [ "$ARCH" = "i686" ]; then
+  SLKCFLAGS="-O2 -march=i686 -mtune=i686"
+  LIBDIRSUFFIX=""
+elif [ "$ARCH" = "x86_64" ]; then
+  SLKCFLAGS="-O2 -fPIC"
+  LIBDIRSUFFIX="64"
+else
+  SLKCFLAGS="-O2"
+  LIBDIRSUFFIX=""
+fi
+
+set -e
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+rm -rf $PRGNAM-$VERSION
+tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
+cd $PRGNAM-$VERSION
+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 {} \;
+
+CXXFLAGS="$SLKCFLAGS" \
+make release
+
+install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM
+
+find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
+  | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cp -a \
+  LICENSE README.md \
+  $PKG/usr/doc/$PRGNAM-$VERSION
+cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
+
+# Copy the slack-desc (and a custom doinst.sh if necessary) into ./install
+mkdir -p $PKG/install
+cat $CWD/slack-desc > $PKG/install/slack-desc
+
+cd $PKG
+/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
diff --git a/academic/stringtie/stringtie.info b/academic/stringtie/stringtie.info
new file mode 100644
index 0000000000000..6ab44c841aa6f
--- /dev/null
+++ b/academic/stringtie/stringtie.info
@@ -0,0 +1,10 @@
+PRGNAM="stringtie"
+VERSION="1.3.5"
+HOMEPAGE="http://ccb.jhu.edu/software/stringtie/"
+DOWNLOAD="https://github.com/gpertea/stringtie/archive/v1.3.5/stringtie-1.3.5.tar.gz"
+MD5SUM="64e5a271dd1b4408728c5f16ce1222ff"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+REQUIRES=""
+MAINTAINER="Petar Petrov"
+EMAIL="slackalaxy@gmail.com"