academic/HMMER: Added (biosequence analysis).

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

4 files changed, 156 insertions, 0 deletions

diff --git a/academic/HMMER/HMMER.SlackBuild b/academic/HMMER/HMMER.SlackBuild
new file mode 100644
index 0000000000000..ed7b38faeb32d
--- /dev/null
+++ b/academic/HMMER/HMMER.SlackBuild
@@ -0,0 +1,108 @@
+#!/bin/sh
+
+# Slackware build script for HMMER
+
+# Copyright 2016 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=HMMER
+SRCNAM=hmmer
+VERSION=${VERSION:-3.1b2}
+BUILD=${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 $SRCNAM-$VERSION
+tar xvf $CWD/$SRCNAM-$VERSION.tar.gz
+cd $SRCNAM-$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 {} \;
+
+CFLAGS="$SLKCFLAGS" \
+CXXFLAGS="$SLKCFLAGS" \
+./configure \
+  --prefix=/usr \
+  --libdir=/usr/lib${LIBDIRSUFFIX} \
+  --sysconfdir=/etc \
+  --localstatedir=/var \
+  --mandir=/usr/man \
+  --docdir=/usr/doc/$PRGNAM-$VERSION \
+  --build=$ARCH-slackware-linux
+
+make
+make check
+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
+
+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
+
+# Include some tutorial examples
+mkdir -p $PKG/usr/share/$PRGNAM
+cp -a tutorial/* $PKG/usr/share/$PRGNAM
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cp -a \
+  INSTALL LICENSE README release-notes Userguide.pdf \
+  $PKG/usr/doc/$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/HMMER/HMMER.info b/academic/HMMER/HMMER.info
new file mode 100644
index 0000000000000..e05cab2782a27
--- /dev/null
+++ b/academic/HMMER/HMMER.info
@@ -0,0 +1,10 @@
+PRGNAM="HMMER"
+VERSION="3.1b2"
+HOMEPAGE="http://hmmer.org/"
+DOWNLOAD="http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz"
+MD5SUM="c8c141018bc0ccd7fc37b33f2b945d5f"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+REQUIRES=""
+MAINTAINER="Petar Petrov"
+EMAIL="slackalaxy@gmail.com"
diff --git a/academic/HMMER/README b/academic/HMMER/README
new file mode 100644
index 0000000000000..7129424d65512
--- /dev/null
+++ b/academic/HMMER/README
@@ -0,0 +1,19 @@
+HMMER: biosequence analysis using profile hidden Markov models
+
+HMMER is used for searching sequence databases for sequence homologs,
+and for making sequence alignments. It implements methods using
+probabilistic models called profile hidden Markov models (profile HMMs).
+
+HMMER is often used together with a profile database, such as Pfam or
+many of the databases that participate in Interpro. But HMMER can also
+work with query sequences, not just profiles, just like BLAST. For
+example, you can search a protein query sequence against a database with
+phmmer, or do an iterative search with jackhmmer.
+
+HMMER is designed to detect remote homologs as sensitively as possible,
+relying on the strength of its underlying probability models. In the
+past, this strength came at significant computational expense, but as
+of the new HMMER3 project, HMMER is now essentially as fast as BLAST.
+
+Publications:
+http://hmmer.org/publications.html
diff --git a/academic/HMMER/slack-desc b/academic/HMMER/slack-desc
new file mode 100644
index 0000000000000..a14f68d22cc57
--- /dev/null
+++ b/academic/HMMER/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------------------------------------------------------|
+HMMER: HMMER (Biosequence analysis using profile hidden Markov models)
+HMMER:
+HMMER: HMMER is used for searching sequence databases for sequence
+HMMER: homologs, and for making sequence alignments. It implements
+HMMER: methods using probabilistic models called profile hidden Markov
+HMMER: models (profile HMMs).
+HMMER:
+HMMER: Home: http://hmmer.org/
+HMMER: Publications: http://hmmer.org/publications.html
+HMMER:
+HMMER: