academic/samtools: Updated for version 1.9 + new maintainer.

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

5 files changed, 69 insertions, 97 deletions

diff --git a/academic/samtools/README b/academic/samtools/README
index 0203586f94..ea600cbe26 100644
--- a/academic/samtools/README
+++ b/academic/samtools/README
@@ -1,22 +1,11 @@
-SAM (Sequence Alignment/Map) format is a generic format for storing
-large nucleotide sequence alignments. SAM aims to be a format that:
+Prior to the introduction of HTSlib, SAMtools and BCFtools were distributed
+in a single samtools-0.1.x package.
+This old version remains available from SBo as samtools-legacy
 
-- 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. 
+Samtools is now distributed as an individual package.
+Installation is set up so that the code uses an external HTSlib (also at SBo).
+Although deprecated upstream, in the case that people need parts of samtools-legacy
+(e.g header files or libbam) these can be installed from this package by modifying
+the samtools.Slackbuild.
 
-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]
+Note that the sam.h of htslib differs from sam.h coming with samtools.
diff --git a/academic/samtools/References b/academic/samtools/References
deleted file mode 100644
index 1cc4af9500..0000000000
--- a/academic/samtools/References
+++ /dev/null
@@ -1,5 +0,0 @@
-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
index 02dff9fbbe..daa7e87daf 100644
--- a/academic/samtools/samtools.SlackBuild
+++ b/academic/samtools/samtools.SlackBuild
@@ -3,7 +3,7 @@
 # Slackware build script for samtools
 
 # Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com
-# All rights reserved.
+# Copyright 2017-2018 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:
@@ -22,17 +22,26 @@
 #  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=${VERSION:-0.1.19}
+PRGNAM=samtools
+VERSION=${VERSION:-1.9}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
+# Some applications still rely on the legacy samtools API instead of using htslib
+# exclusively, in that case, install the headers in /usr/include/bam and the static
+# libbam library as well by declaring (uncommenting):
+#SAMLIB="yes"
+# and commenting out:
+SAMLIB="no"
+
+# WARNING: this package and htslib both provide a "sam.h" that aren't actually
+# compatible with each other. Be extra careful about which file you're actually
+# #including when using either of these packages for development work.
+
+
 if [ -z "$ARCH" ]; then
   case "$( uname -m )" in
-    i?86) ARCH=i486 ;;
+    i?86) ARCH=i586 ;;
     arm*) ARCH=arm ;;
        *) ARCH=$( uname -m ) ;;
   esac
@@ -43,8 +52,8 @@ TMP=${TMP:-/tmp/SBo}
 PKG=$TMP/package-$PRGNAM
 OUTPUT=${OUTPUT:-/tmp}
 
-if [ "$ARCH" = "i486" ]; then
-  SLKCFLAGS="-O2 -march=i486 -mtune=i686"
+if [ "$ARCH" = "i586" ]; then
+  SLKCFLAGS="-O2 -march=i586 -mtune=i686"
   LIBDIRSUFFIX=""
 elif [ "$ARCH" = "i686" ]; then
   SLKCFLAGS="-O2 -march=i686 -mtune=i686"
@@ -58,7 +67,6 @@ else
 fi
 
 set -e
-
 rm -rf $PKG
 mkdir -p $TMP $PKG $OUTPUT
 cd $TMP
@@ -70,51 +78,23 @@ 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 {} \;
+  -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
 
-# Use our CFLAGS/CXXFLAGS
-sed -i "/^C.*.*FLAGS/s/=/+=/" Makefile
+# force linking to installed htslib
+rm -r htslib-$VERSION
 
 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
+CXXFLAGS="$SLKCFLAGS" \
+./configure \
+  --prefix=/usr \
+  --libdir=/usr/lib${LIBDIRSUFFIX} \
+  --with-htslib=system \
+  --mandir=/usr/man \
+  --docdir=/usr/doc/$PRGNAM-$VERSION \
+  --build=$ARCH-slackware-linux
 
-# 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
+make
+make install DESTDIR=$PKG
 
 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
@@ -124,18 +104,26 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r
 
 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
 cp -a \
-  AUTHORS COPYING INSTALL NEWS \
+  AUTHORS LICENSE README INSTALL NEWS examples \
   $PKG/usr/doc/$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 $PKG/usr/share/$PRGNAM-$VERSION
+
+cp -a \
+  misc/*.lua \
+  $PKG/usr/share/$PRGNAM-$VERSION
 
 mkdir -p $PKG/install
 cat $CWD/slack-desc > $PKG/install/slack-desc
 
+# include samtools-API if set above
+if [ "$SAMLIB" = "yes" ] ; then
+  mkdir -p $PKG/usr/include/bam
+  mkdir -p $PKG/usr/lib${LIBDIRSUFFIX}
+  install -m644 libbam.a "$PKG/usr/lib${LIBDIRSUFFIX}"
+  install -m644 *.h "$PKG/usr/include/bam"
+fi
+
 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
index 79136533ae..1d724a44e4 100644
--- a/academic/samtools/samtools.info
+++ b/academic/samtools/samtools.info
@@ -1,10 +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"
+VERSION="1.9"
+HOMEPAGE="http://www.htslib.org"
+DOWNLOAD="https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2"
+MD5SUM="cca9a40d9b91b007af2ff905cb8b5924"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
-REQUIRES=""
-MAINTAINER="Petar Petrov"
-EMAIL="slackalaxy@gmail.com"
+REQUIRES="htslib"
+MAINTAINER="Rob van Nues"
+EMAIL="sborg63@disroot.org"
diff --git a/academic/samtools/slack-desc b/academic/samtools/slack-desc
index ce768600c2..8f1c434e47 100644
--- a/academic/samtools/slack-desc
+++ b/academic/samtools/slack-desc
@@ -8,12 +8,12 @@
         |-----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: SAM (Sequence Alignment/Map) format is a generic format for
+samtools: storing large nucleotide sequence alignments. The original samtools 
+samtools: package has been split into three separate but tightly coordinated 
+samtools: projects: htslib (C-library for handling high-throughput sequencing 
+samtools: data); samtools (for handling SAM, BAM, CRAM) and bcftools (for 
+samtools: handling VCF, BCF). Both samtools and bcftools are set up to use
+samtools: system-wide installed hstlib sources.
+samtools: Home: http://www.htslib.org
 samtools: