academic/STAR: Added (Spliced Transcripts Alignment to a Reference).

Signed-off-by: David Spencer <idlemoor@slackbuilds.org>

5 files changed, 146 insertions, 0 deletions

diff --git a/academic/STAR/README b/academic/STAR/README
new file mode 100644
index 0000000000..3608afef93
--- /dev/null
+++ b/academic/STAR/README
@@ -0,0 +1,7 @@
+STAR aligns short and long RNA-seq reads to a reference genome using
+uncompressed suffix arrays, resulting in fast, accurate mapping.
+STAR is capable of unbiased de novo detection of canonical junctions,
+can discover non-canonical splices and chimeric (fusion) transcripts and
+can map full-length RNA sequences.
+
+Reference: https://www.ncbi.nlm.nih.gov/pubmed/23104886
diff --git a/academic/STAR/STAR.SlackBuild b/academic/STAR/STAR.SlackBuild
new file mode 100644
index 0000000000..aa89b2927f
--- /dev/null
+++ b/academic/STAR/STAR.SlackBuild
@@ -0,0 +1,96 @@
+#!/bin/sh
+
+# Slackware build script for STAR
+
+# Copyright 2018 Rob van Nues
+# 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=STAR
+VERSION=${VERSION:-2.6.0c}
+BUILD=${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" = "x86_64" ]; then
+  SLKCFLAGS="-O2 -fPIC -fsigned-char"
+  LIBDIRSUFFIX="64"
+else
+  echo "Sorry, this program does not run/compile on your architecture ($ARCH)"
+  exit 1
+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 {} \;
+
+# https://sources.debian.org/data/main/r/rna-star/2.6.0b+dfsg-1/debian/patches/reproducible.patch
+# (with minor modification)
+patch -p1 < $CWD/reproducible.patch
+
+cd source
+
+  make ${PRGNAM} CFLAGS="$SLKCFLAGS" CXXFLAGSextra="$SLKCFLAGS"
+
+  mkdir -p $PKG/usr/bin
+  install -Dm755 $PRGNAM "$PKG/usr/bin/${PRGNAM}"
+
+  make clean
+  make ${PRGNAM}long CXXFLAGSextra="$CXXFLAGS"
+  install -Dm755 ${PRGNAM}long "$PKG/usr/bin/${PRGNAM}long"
+
+cd ..
+
+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-$VERSION
+cp -a \
+  source/parametersDefault doc/${PRGNAM}manual.pdf CHANGES.md LICENSE README.md RELEASEnotes.md \
+  $PKG/usr/doc/$PRGNAM-$VERSION
+cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
+
+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/STAR/STAR.info b/academic/STAR/STAR.info
new file mode 100644
index 0000000000..2ba024dafd
--- /dev/null
+++ b/academic/STAR/STAR.info
@@ -0,0 +1,10 @@
+PRGNAM="STAR"
+VERSION="2.6.0c"
+HOMEPAGE="https://github.com/alexdobin/STAR"
+DOWNLOAD="UNSUPPORTED"
+MD5SUM=""
+DOWNLOAD_x86_64="https://github.com/alexdobin/STAR/archive/2.6.0c/STAR-2.6.0c.tar.gz"
+MD5SUM_x86_64="014e44faa78c13e781bb74d9b5cf00d8"
+REQUIRES=""
+MAINTAINER="Rob van Nues"
+EMAIL="rvnues { at } disroot { dot } org"
diff --git a/academic/STAR/reproducible.patch b/academic/STAR/reproducible.patch
new file mode 100644
index 0000000000..f340376023
--- /dev/null
+++ b/academic/STAR/reproducible.patch
@@ -0,0 +1,14 @@
+Description: make build reproducible
+ Stops build hostname and directory from being recorded in the artifact.
+Author: Sascha Steinbiss <sascha@steinbiss.name>
+--- a/source/Makefile
++++ b/source/Makefile
+@@ -18,7 +18,7 @@
+ LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a
+ LDFLAGS_gdb += $(LDFLAGS_shared)
+ 
+-COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(shell echo `date` $(HOSTNAME):`pwd`)"'
++COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="<unrecorded>"'
+ 
+ CXXFLAGS_common := -pipe -std=c++11 -Wall -Wextra -fopenmp $(COMPTIMEPLACE) $(CCFLAGS_common_add)
+ CXXFLAGS_main += -O3 $(CXXFLAGS_common)
diff --git a/academic/STAR/slack-desc b/academic/STAR/slack-desc
new file mode 100644
index 0000000000..433a7dfbb0
--- /dev/null
+++ b/academic/STAR/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------------------------------------------------------|
+STAR: STAR (Spliced Transcripts Alignment to a Reference)
+STAR:
+STAR: STAR aligns short and long RNA-seq reads to a reference genome using
+STAR: uncompressed suffix arrays, resulting in fast, accurate mapping.
+STAR: STAR is capable of unbiased de novo detection of canonical junctions,
+STAR: can discover non-canonical splices and chimeric (fusion) transcripts
+STAR: and can map full-length RNA sequences.
+STAR:
+STAR: https://github.com/alexdobin/STAR
+STAR: Reference: https://www.ncbi.nlm.nih.gov/pubmed/23104886
+STAR: