diff options
5 files changed, 183 insertions, 10 deletions
diff --git a/academic/muscle/README b/academic/muscle/README
index 4db82130b5..2a8b2c538d 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
-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.
+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 input.fasta aligned.fasta > stable.fasta
+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 0000000000..057c81da47
--- /dev/null
+++ b/academic/muscle/muscle.1
@@ -0,0 +1,135 @@
+.\" Title: MUSCLE
+.\" Author: Robert Elgar
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <>
+.\" Date: 02/06/2008
+.\" Manual: Muscle Manual
+.\" Source: muscle 3.7
+.TH "MUSCLE" "1" "02/06/2008" "muscle 3.7" "Muscle Manual"
+.\" disable hyphenation
+.\" disable justification (adjust text to left margin only) l
+muscle - Multiple Protein Sequence Alignment
+.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]
+This manual page documents briefly the
+aligns protein sequences and is considered superior and faster than Clustal\ W\.
+\fB\-in \fR\fB\fIinput file\fR\fR
+.RS 4
+Path to FASTA formatted input file
+\fB\-out \fR\fB\fIoutput file\fR\fR
+.RS 4
+Path to output file, FASTA formatted by default
+.RS 4
+Find diagonals (faster for similar sequences)
+\fB\-maxiters \fR\fB\fIn\fR\fR
+.RS 4
+Maximum number of iterations (integer, default 16)
+\fB\-maxhours \fR\fB\fIn\fR\fR
+.RS 4
+Maximum time to iterate in hours (default no limit)
+\fB\-maxmb \fR\fB\fIm\fR\fR
+.RS 4
+Maximum memory to allocate in Mb (default 80% of RAM)
+.RS 4
+Write output in HTML format (default FASTA)
+.RS 4
+Write output in MSF format (default FASTA)
+.RS 4
+Write output in Clustal\ W format (default FASTA)
+.RS 4
+As \-clw, with \'CLUSTAL W (1\.81)\' header
+\fB\-log[a] \fR\fB\fIlogfile\fR\fR
+.RS 4
+Log to file (append if \-loga, overwrite if \-log)
+.RS 4
+Do not write progress messages to stderr
+.RS 4
+Output sequences in input order (default is \-group)
+.RS 4
+Group sequences by similarity (this is the default)
+.RS 4
+Display version information and exit
+\fBRobert Elgar\fR
+.sp -1n
+.IP "" 4
+Wrote Muscle\.
+\fBSteffen Moeller\fR <\&moeller@debian\.org\&>
+.sp -1n
+.IP "" 4
+Wrote this manpage\.
+\fBCharles Plessy\fR <\&charles\-debian\-nospam@plessy\.org\&>
+.sp -1n
+.IP "" 4
+Updated this manpage\.
+Copyright \(co 2003, 2004 Steffen Moeller (manpage)
+Copyright \(co 2007, 2008 Charles Plessy (manpage)
+Muscle is in the public domain, and therefore not subjected to copyright\.
+This manual page was written by Steffen Moeller moeller@debian\.org for the
+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\.
diff --git a/academic/muscle/muscle.SlackBuild b/academic/muscle/muscle.SlackBuild
index 9e69c5b702..2258892211 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
+# Copyright 2011-2020 Petar Petrov
# All rights reserved.
# Redistribution and use of this script, with or without modification, is
@@ -24,9 +24,11 @@
if [ -z "$ARCH" ]; then
case "$( uname -m )" in
i?86) ARCH=i586 ;;
@@ -63,6 +65,7 @@ rm -rf ${PRGNAM}-${VERSION}
mkdir -p ${PRGNAM}-${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" \
install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM
+install -D -m755 $PKG/usr/bin/$
+# 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/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
mkdir -p $PKG/install
diff --git a/academic/muscle/ b/academic/muscle/
index e7671cd1bc..e747bd6443 100644
--- a/academic/muscle/
+++ b/academic/muscle/
@@ -1,8 +1,12 @@
+ \
+MD5SUM="1b7c9661f275a82d3cf708f923736bf8 \
+ fceeab190ff13576bfd681a601e7859b \
+ 58bb1b7989cf6f2c197dd46552759a40"
diff --git a/academic/muscle/slack-desc b/academic/muscle/slack-desc
index 5e4e7da441..d3d95c0c28 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: Home:
-muscle: References: /usr/doc/muscle-3.8.31/References