From 00017f6260e9e0d2951eac42aeea9d8fbb9f1034 Mon Sep 17 00:00:00 2001
From: Petar Petrov <petar.petrov@student.oulu.fi>
Date: Sat, 14 Dec 2013 08:02:52 +0700
Subject: [PATCH] academic/samtools: Added (Sequence Alignment/Map Tools).

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
---
 academic/samtools/README              |  22 ++++
 academic/samtools/References          |   5 +
 academic/samtools/samtools.SlackBuild | 141 ++++++++++++++++++++++++++
 academic/samtools/samtools.info       |  10 ++
 academic/samtools/slack-desc          |  19 ++++
 5 files changed, 197 insertions(+)
 create mode 100644 academic/samtools/README
 create mode 100644 academic/samtools/References
 create mode 100644 academic/samtools/samtools.SlackBuild
 create mode 100644 academic/samtools/samtools.info
 create mode 100644 academic/samtools/slack-desc

diff --git a/academic/samtools/README b/academic/samtools/README
new file mode 100644
index 0000000000..0203586f94
--- /dev/null
+++ b/academic/samtools/README
@@ -0,0 +1,22 @@
+SAM (Sequence Alignment/Map) format is a generic format for storing
+large nucleotide sequence alignments. SAM aims to be a format that:
+
+- Is flexible enough to store all the alignment information generated
+  by various alignment programs
+- Is simple enough to be easily generated by alignment programs or
+  converted from existing alignment formats
+- Is compact in file size
+- Allows most of operations on the alignment to work on a stream
+  without loading the whole alignment into memory
+- Allows the file to be indexed by genomic position to efficiently
+  retrieve all reads aligning to a locus. 
+
+SAM Tools provide various utilities for manipulating alignments in the
+SAM format, including sorting, merging, indexing and generating 
+alignments in a per-position format.
+
+Publication:
+Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N.,
+Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data
+Processing Subgroup (2009) The Sequence alignment/map (SAM) format and
+SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]
diff --git a/academic/samtools/References b/academic/samtools/References
new file mode 100644
index 0000000000..1cc4af9500
--- /dev/null
+++ b/academic/samtools/References
@@ -0,0 +1,5 @@
+Publication:
+Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N.,
+Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data
+Processing Subgroup (2009) The Sequence alignment/map (SAM) format and
+SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]
diff --git a/academic/samtools/samtools.SlackBuild b/academic/samtools/samtools.SlackBuild
new file mode 100644
index 0000000000..a3c0e2d1a7
--- /dev/null
+++ b/academic/samtools/samtools.SlackBuild
@@ -0,0 +1,141 @@
+#!/bin/sh
+
+# Slackware build script for samtools
+
+# Copyright 2013 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.
+
+# With help about the install paths from Arch Linux AUR:
+# https://aur.archlinux.org/packages/sa/samtools/PKGBUILD
+
+PRGNAM=samtools	
+VERSION=${VERSION:-0.1.19}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
+
+if [ -z "$ARCH" ]; then
+  case "$( uname -m )" in
+    i?86) ARCH=i486 ;;
+    arm*) ARCH=arm ;;
+       *) ARCH=$( uname -m ) ;;
+  esac
+fi
+
+CWD=$(pwd)
+TMP=${TMP:-/tmp/SBo}
+PKG=$TMP/package-$PRGNAM
+OUTPUT=${OUTPUT:-/tmp}
+
+if [ "$ARCH" = "i486" ]; then
+  SLKCFLAGS="-O2 -march=i486 -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.bz2
+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 {} \;
+
+# Use our CFLAGS/CXXFLAGS
+sed -i "/^C.*.*FLAGS/s/=/+=/" Makefile
+
+CFLAGS="$SLKCFLAGS" \
+make
+make razip
+
+# Install samtools, razip and bam library
+install -D -m755 samtools $PKG/usr/bin/samtools
+install -D -m755 razip	  $PKG/usr/bin/razip
+install -D -m644 libbam.a $PKG/usr/lib${LIBDIRSUFFIX}/libbam.a
+
+# Install bcftools its library and vsfutils
+cd bcftools
+install -D -m755 bcftools $PKG/usr/bin/bcftools
+install -D -m644 libbcf.a $PKG/usr/lib${LIBDIRSUFFIX}/libbcf.a
+install -D -m755 vcfutils.pl $PKG/usr/bin/vcfutils.pl
+
+# Include additional executables
+cd ../misc
+install -D -m755 ace2sam	$PKG/usr/libexec/$PRGNAM/ace2sam
+install -D -m755 bamcheck	$PKG/usr/libexec/$PRGNAM/bamcheck
+install -D -m755 maq2sam-long	$PKG/usr/libexec/$PRGNAM/maq2sam-long
+install -D -m755 maq2sam-short	$PKG/usr/libexec/$PRGNAM/maq2sam-short
+install -D -m755 md5fa		$PKG/usr/libexec/$PRGNAM/md5fa
+install -D -m755 md5sum-lite	$PKG/usr/libexec/$PRGNAM/md5sum-lite
+install -D -m755 wgsim		$PKG/usr/libexec/$PRGNAM/wgsim
+
+# Include some scripts
+mkdir -p $PKG/usr/share/$PRGNAM
+cp -a \
+  *.pl *.lua *.py plot-bamcheck \
+  $PKG/usr/share/$PRGNAM
+
+# Include bam header files
+cd ..
+mkdir -p  $PKG/usr/include/bam
+ for f in *.h ; do
+   install -m644 $f "$PKG/usr/include/bam"
+ done
+
+# Install manpage
+install -D -m644 $PRGNAM.1 $PKG/usr/man/man1/$PRGNAM.1
+
+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
+
+find $PKG/usr/man -type f -exec gzip -9 {} \;
+for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cp -a \
+  AUTHORS COPYING INSTALL NEWS \
+  $PKG/usr/doc/$PRGNAM-$VERSION
+cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
+cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
+
+# Fix permissions in the package...
+find $PKG/usr/{doc,include,share} \
+-type d -exec chmod 755 {} \; -o \
+-type f -exec chmod 644 {} \;
+
+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/samtools/samtools.info b/academic/samtools/samtools.info
new file mode 100644
index 0000000000..51a89dca1e
--- /dev/null
+++ b/academic/samtools/samtools.info
@@ -0,0 +1,10 @@
+PRGNAM="samtools"
+VERSION="0.1.19"
+HOMEPAGE="http://samtools.sourceforge.net/"
+DOWNLOAD="http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2"
+MD5SUM="ff8b46e6096cfb452003b1ec5091d86a"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+REQUIRES=""
+MAINTAINER="Petar Petrov"
+EMAIL="ppetrov@paju.oulu.fi"
diff --git a/academic/samtools/slack-desc b/academic/samtools/slack-desc
new file mode 100644
index 0000000000..ce768600c2
--- /dev/null
+++ b/academic/samtools/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------------------------------------------------------|
+samtools: samtools (Sequence Alignment/Map Tools)
+samtools:
+samtools: AM (Sequence Alignment/Map) format is a generic format for
+samtools: storing large nucleotide sequence alignments. SAM Tools provide
+samtools: various utilities for manipulating alignments in the SAM format,
+samtools: including sorting, merging, indexing and generating alignments
+samtools: in a per-position format.
+samtools:
+samtools: Home: http://samtools.sourceforge.net/
+samtools: References: /usr/doc/samtools-0.1.19/References
+samtools: