academic/muscle: Update script and added manual page.

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

5 files changed, 183 insertions, 10 deletions

diff --git a/academic/muscle/README b/academic/muscle/README
index 4db82130b553c..2a8b2c538da0a 100644
--- a/academic/muscle/README
+++ b/academic/muscle/README
@@ -3,7 +3,29 @@ nucleotide sequences. A range of options is provided that give you the
 choice of optimizing accuracy, speed, or some compromise between the 
 two.
 
-For details and citation:
-Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high 
-accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797. 
-doi:10.1093/nar/gkh340
+Fast, accurate and easy to use
+MUSCLE is one of the best-performing multiple alignment programs
+according to published benchmark tests, with accuracy and speed that
+are consistently better than CLUSTALW. MUSCLE can align hundreds of
+sequences in seconds. Most users learn everything they need to know
+about MUSCLE in a few minutes—only a handful of command-line options
+are needed to perform common alignment tasks.
+
+NOTE about the "-stable" option no longer being supported:
+The "-stable" option had a bug, which sometimes resulted in incorrect
+alignments to be produced. The author has created a python script to
+be used as a workaround. The SlackBuild includes it and its usage is:
+
+  python muscle-stable.py input.fasta aligned.fasta > stable.fasta
+
+Papers
+There are two papers. The first (NAR) introduced the algorithm, and is
+the primary citation if you use the program. The second (in BMC Bio-
+informatics) gives more technical details, including descriptions of
+non-default options.
+
+Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high
+accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797
+
+Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with
+reduced time and space complexity BMC Bioinformatics, (5) 113
diff --git a/academic/muscle/muscle.1 b/academic/muscle/muscle.1
new file mode 100644
index 0000000000000..057c81da478e3
--- /dev/null
+++ b/academic/muscle/muscle.1
@@ -0,0 +1,135 @@
+.\"     Title: MUSCLE
+.\"    Author: Robert Elgar
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\"      Date: 02/06/2008
+.\"    Manual: Muscle Manual
+.\"    Source: muscle 3.7
+.\"
+.TH "MUSCLE" "1" "02/06/2008" "muscle 3.7" "Muscle Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+muscle - Multiple Protein Sequence Alignment
+.SH "SYNOPSIS"
+.HP 7
+\fBmuscle\fR \fB\-in\ \fR\fB\fIinput\ file\ (fasta)\fR\fR [\fB\-out\ \fR\fB\fIoutput\ file\ (default\ fasta)\fR\fR] [\fB\-diags\fR] [\fB\-log\ \fR\fB\fIlog\ file\fR\fR] [\fB\-maxiters\ \fR\fB\fIn\fR\fR] [\fB\-maxhours\ \fR\fB\fIn\fR\fR] [\fB\-maxmb\ \fR\fB\fIm\fR\fR] [\fB\-html\fR] [\fB\-msf\fR] [\fB\-clw\fR] [\fB\-clwstrict\fR] [\fB\-log[a]\ \fR\fB\fIlogfile\fR\fR] [\fB\-quiet\fR] [\fB\-stable\fR] [\fB\-group\fR] [\fB\-version\fR]
+.SH "DESCRIPTION"
+.PP
+This manual page documents briefly the
+\fBmuscle\fR
+command\.
+.PP
+\fBmuscle\fR
+aligns protein sequences and is considered superior and faster than Clustal\ W\.
+.SH "OPTIONS"
+.PP
+\fB\-in \fR\fB\fIinput file\fR\fR
+.RS 4
+Path to FASTA formatted input file
+.RE
+.PP
+\fB\-out \fR\fB\fIoutput file\fR\fR
+.RS 4
+Path to output file, FASTA formatted by default
+.RE
+.PP
+\fB\-diags\fR
+.RS 4
+Find diagonals (faster for similar sequences)
+.RE
+.PP
+\fB\-maxiters \fR\fB\fIn\fR\fR
+.RS 4
+Maximum number of iterations (integer, default 16)
+.RE
+.PP
+\fB\-maxhours \fR\fB\fIn\fR\fR
+.RS 4
+Maximum time to iterate in hours (default no limit)
+.RE
+.PP
+\fB\-maxmb \fR\fB\fIm\fR\fR
+.RS 4
+Maximum memory to allocate in Mb (default 80% of RAM)
+.RE
+.PP
+\fB\-html\fR
+.RS 4
+Write output in HTML format (default FASTA)
+.RE
+.PP
+\fB\-msf\fR
+.RS 4
+Write output in MSF format (default FASTA)
+.RE
+.PP
+\fB\-clw\fR
+.RS 4
+Write output in Clustal\ W format (default FASTA)
+.RE
+.PP
+\fB\-clwstrict\fR
+.RS 4
+As \-clw, with \'CLUSTAL W (1\.81)\' header
+.RE
+.PP
+\fB\-log[a] \fR\fB\fIlogfile\fR\fR
+.RS 4
+Log to file (append if \-loga, overwrite if \-log)
+.RE
+.PP
+\fB\-quiet\fR
+.RS 4
+Do not write progress messages to stderr
+.RE
+.PP
+\fB\-stable\fR
+.RS 4
+Output sequences in input order (default is \-group)
+.RE
+.PP
+\fB\-group\fR
+.RS 4
+Group sequences by similarity (this is the default)
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+Display version information and exit
+.RE
+.SH "SEE ALSO"
+.PP
+
+\fBclustalw\fR(1),
+\fBseaview\fR(1),
+\fBt_coffee\fR(1)\.
+.SH "AUTHORS"
+.PP
+\fBRobert Elgar\fR
+.sp -1n
+.IP "" 4
+Wrote Muscle\.
+.PP
+\fBSteffen Moeller\fR <\&moeller@debian\.org\&>
+.sp -1n
+.IP "" 4
+Wrote this manpage\.
+.PP
+\fBCharles Plessy\fR <\&charles\-debian\-nospam@plessy\.org\&>
+.sp -1n
+.IP "" 4
+Updated this manpage\.
+.SH "COPYRIGHT"
+Copyright \(co 2003, 2004 Steffen Moeller (manpage)
+.br
+Copyright \(co 2007, 2008 Charles Plessy (manpage)
+.br
+.PP
+Muscle is in the public domain, and therefore not subjected to copyright\.
+.PP
+This manual page was written by Steffen Moeller moeller@debian\.org for the
+Debian(TM)
+system (but may be used by others)\. Permission is granted to copy, distribute and/or modify this document as if it were in public domain\.
+.sp
diff --git a/academic/muscle/muscle.SlackBuild b/academic/muscle/muscle.SlackBuild
index 9e69c5b702685..2258892211d47 100644
--- a/academic/muscle/muscle.SlackBuild
+++ b/academic/muscle/muscle.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for muscle
 
-# Copyright 2011-2019 Petar Petrov slackalaxy@gmail.com
+# Copyright 2011-2020 Petar Petrov slackalaxy@gmail.com
 # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
@@ -24,9 +24,11 @@
 
 PRGNAM=muscle
 VERSION=${VERSION:-3.8.1551}
-BUILD=${BUILD:-1}
+BUILD=${BUILD:-2}
 TAG=${TAG:-_SBo}
 
+MANUAL=muscle_userguide3.8.pdf
+
 if [ -z "$ARCH" ]; then
   case "$( uname -m )" in
     i?86) ARCH=i586 ;;
@@ -63,6 +65,7 @@ rm -rf ${PRGNAM}-${VERSION}
 mkdir -p ${PRGNAM}-${VERSION}
 cd ${PRGNAM}-${VERSION}
 tar xvf $CWD/${PRGNAM}_src_${VERSION}.tar.gz
+tar xvf $CWD/stable.tar.gz
 
 chown -R root:root .
 find -L . \
@@ -78,12 +81,21 @@ CFLAGS="$SLKCFLAGS" \
 make
 
 install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM
+install -D -m755 stable.py $PKG/usr/bin/$PRGNAM-stable.py
+
+# Thanks to Debian for the man page
+mkdir -p $PKG/usr/man/man1
+cp $CWD/$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
 cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
+cat $CWD/$MANUAL > $PKG/usr/doc/$PRGNAM-$VERSION/$MANUAL
 cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
 
 mkdir -p $PKG/install
diff --git a/academic/muscle/muscle.info b/academic/muscle/muscle.info
index e7671cd1bcc28..e747bd644335a 100644
--- a/academic/muscle/muscle.info
+++ b/academic/muscle/muscle.info
@@ -1,8 +1,12 @@
 PRGNAM="muscle"
 VERSION="3.8.1551"
 HOMEPAGE="http://www.drive5.com/muscle/"
-DOWNLOAD="http://www.drive5.com/muscle/muscle_src_3.8.1551.tar.gz"
-MD5SUM="1b7c9661f275a82d3cf708f923736bf8"
+DOWNLOAD="http://www.drive5.com/muscle/muscle_src_3.8.1551.tar.gz \
+	http://www.drive5.com/muscle/stable.tar.gz \
+	http://www.drive5.com/muscle/muscle_userguide3.8.pdf"
+MD5SUM="1b7c9661f275a82d3cf708f923736bf8 \
+	fceeab190ff13576bfd681a601e7859b \
+	58bb1b7989cf6f2c197dd46552759a40"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES=""
diff --git a/academic/muscle/slack-desc b/academic/muscle/slack-desc
index 5e4e7da441ca5..d3d95c0c280f3 100644
--- a/academic/muscle/slack-desc
+++ b/academic/muscle/slack-desc
@@ -13,7 +13,7 @@ muscle: or nucleotide sequences. A range of options is provided that give
 muscle: you the choice of optimizing accuracy, speed, or some compromise
 muscle: between the two.
 muscle:
-muscle: Home: http://www.drive5.com/muscle/
-muscle: References: /usr/doc/muscle-3.8.31/References
+muscle: http://www.drive5.com/muscle/
+muscle: http://www.drive5.com/muscle/stable.html
 muscle:
 muscle: