academic/mumsa: Added (A tool to assess MSA quality)

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

5 files changed, 152 insertions, 0 deletions

diff --git a/academic/mumsa/README b/academic/mumsa/README
new file mode 100644
index 0000000000..3fad0cf560
--- /dev/null
+++ b/academic/mumsa/README
@@ -0,0 +1,17 @@
+Mumsa is a tool for automatic assessment of alignment quality. A number
+of alternate (to be compared) multiple alignments have to be generated
+and submitted. 
+
+Mumsa computes:
+- the average overlap score (AOS), reflecting the difficulty of aligning
+  the sequences
+- multiple overlap score (MOS) indicating the quality of each individual
+  alignment. 
+
+Both scores range between one and zero.
+
+CITING
+Lassmann T, Sonnhammer EL. Kalign, Kalignvu and Mumsa: web servers for
+multiple sequence alignment. Nucleic Acids Res. 2006 Jul 1;34(Web Server
+issue): W596-9. doi: 10.1093/nar/gkl191.
+PMID: 16845078; PMCID: PMC1538774
diff --git a/academic/mumsa/References.txt b/academic/mumsa/References.txt
new file mode 100644
index 0000000000..5dd7f95313
--- /dev/null
+++ b/academic/mumsa/References.txt
@@ -0,0 +1,4 @@
+Lassmann T, Sonnhammer EL. Kalign, Kalignvu and Mumsa: web servers for
+multiple sequence alignment. Nucleic Acids Res. 2006 Jul 1;34(Web Server
+issue): W596-9. doi: 10.1093/nar/gkl191.
+PMID: 16845078; PMCID: PMC1538774
diff --git a/academic/mumsa/mumsa.SlackBuild b/academic/mumsa/mumsa.SlackBuild
new file mode 100644
index 0000000000..6d9d8cf01e
--- /dev/null
+++ b/academic/mumsa/mumsa.SlackBuild
@@ -0,0 +1,102 @@
+#!/bin/bash
+
+# Slackware build script for <mumsa>
+
+# Copyright 2022 Petar Petrov slackalaxy at gmail dot 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.
+
+
+cd $(dirname $0) ; CWD=$(pwd)
+
+PRGNAM=mumsa
+VERSION=${VERSION:-1.0}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
+PKGTYPE=${PKGTYPE:-tgz}
+
+if [ -z "$ARCH" ]; then
+  case "$( uname -m )" in
+    i?86) ARCH=i586 ;;
+    arm*) ARCH=arm ;;
+       *) ARCH=$( uname -m ) ;;
+  esac
+fi
+
+if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then
+  echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE"
+  exit 0
+fi
+
+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.tgz
+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 {} \;
+
+sed -i "/^CFLAGS/s/=/+=/" Makefile
+CFLAGS="$SLKCFLAGS" \
+CXXFLAGS="$SLKCFLAGS" \
+PREFIX=/usr make
+make
+
+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 \
+  COPYING \
+  $PKG/usr/doc/$PRGNAM-$VERSION
+cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
+cat $CWD/References.txt > $PKG/usr/doc/$PRGNAM-$VERSION/References.txt
+
+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
diff --git a/academic/mumsa/mumsa.info b/academic/mumsa/mumsa.info
new file mode 100644
index 0000000000..86eb69b883
--- /dev/null
+++ b/academic/mumsa/mumsa.info
@@ -0,0 +1,10 @@
+PRGNAM="mumsa"
+VERSION="1.0"
+HOMEPAGE="https://msa.sbc.su.se/cgi-bin/msa.cgi"
+DOWNLOAD="https://msa.sbc.su.se/downloads/mumsa-1.0.tgz"
+MD5SUM="80ad4dbd2dc2e5402ad9753c25cc896b"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+REQUIRES=""
+MAINTAINER="Petar Petrov"
+EMAIL="slackalaxy@gmail.com"
diff --git a/academic/mumsa/slack-desc b/academic/mumsa/slack-desc
new file mode 100644
index 0000000000..2f487a6eba
--- /dev/null
+++ b/academic/mumsa/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------------------------------------------------------|
+mumsa: mumsa (A tool to assess MSA quality)
+mumsa:
+mumsa: Mumsa is a tool for automatic assessment of alignment quality.
+mumsa:
+mumsa: https://msa.sbc.su.se/cgi-bin/msa.cgi
+mumsa: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538774/
+mumsa:
+mumsa:
+mumsa:
+mumsa:
+mumsa: