academic/meme-suite: Updated for version 5.1.0.

Signed-off-by: Robby Workman <rworkman@slackbuilds.org>

6 files changed, 120 insertions, 96 deletions

diff --git a/academic/meme-suite/README b/academic/meme-suite/README
index f516c7e37141..b48cdaf9f765 100644
--- a/academic/meme-suite/README
+++ b/academic/meme-suite/README
@@ -1,35 +1,31 @@
 The MEME suite: motif based sequence analysis tools
 
-The MEME suite provides tools for discovering and using protein and
-DNA sequence motifs.  A motif is a pattern of nucleotides or amino acids
-that appears repeatedly in a group of related DNA or protein sequences.
+The MEME Suite allows the biologist to discover novel motifs in
+collections of unaligned nucleotide or protein sequences, and to perform
+a wide variety of other motif-based analyses. The Suite supports motif-
+based analysis of DNA, RNA and protein sequences. It provides motif
+discovery algorithms using both probabilistic (MEME) and discrete models
+(MEME), which have complementary strengths. It also allows discovery of
+motifs with arbitrary insertions and deletions (GLAM2). In addition to
+motif discovery, the MEME Suite provides tools for scanning sequences
+for matches to motifs (FIMO, MAST and GLAM2Scan), scanning for clusters
+of motifs (MCAST), comparing motifs to known motifs (Tomtom), finding
+preferred spacings between motifs (SpaMo), predicting the biological
+roles of motifs (GOMo), measuring the positional enrichment of sequences
+for known motifs (CentriMo), and analyzing ChIP-seq and other large
+datasets (MEME-ChIP).
 
-The MEME suite represents motifs as position-dependent scoring matrices.
-It consists of programs which allow you to:
+Check README.TESTS for runing the recommended tests on the compiled
+executables. Here, the tests *FAIL* on a 32bit system!
 
-- meme      - discovery of motifs shared by a group of sequences
-- mast      - search of databases for sequences containing these motifs
-- tomtom    - searching databases of motifs for similar motifs
-- gomo      - finding Gene Ontology terms linked to the motifs
-- glam2     - discovery of gapped motifs
-- glam2scan - scanning sequences with gapped motifs
-- fimo      - scanning sequences with motifs
-- mcast     - finding motif clusters
-- meme-chip - analysis of large DNA datasets like ChIPseq output
-- spamo     - finding motif complexes by analysing motif spacing
-- dreme     - discovery of short regular expression motifs
-
-Note: building on a 32bit architecture fails at the 'make test' step
-(check script). If the step is disabled, the suite builds, however it
-may or may NOT work properly. Therefore, 32bit is set as 'UNTESTED'.
-The 'make test' step will also fail if you don't build in a proper root
-environment.
+Check README.DATABASES for more info or if you want to install
+meme-suite without the databases present at build time.
 
 To cite the full MEME suite:
-Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin Frith,
-Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li,
-William S. Noble, "MEME SUITE: tools for motif discovery and searching",
-Nucleic Acids Research, 37:W202-W208, 2009.
+Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin Frith, Charles
+E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble, 
+"MEME SUITE: tools for motif discovery and searching", Nucleic Acids
+Research, 37:W202-W208, 2009.
 
 To cite individual tools, please check the citation page:
 http://meme-suite.org/doc/cite.html
diff --git a/academic/meme-suite/README.DATABASES b/academic/meme-suite/README.DATABASES
new file mode 100644
index 000000000000..3679a2f8f4ee
--- /dev/null
+++ b/academic/meme-suite/README.DATABASES
@@ -0,0 +1,15 @@
+At compile time, meme-suite checks if its database folder folder exists:
+
+/var/lib/meme-suite
+
+If you have installed any of the meme-db-* packages, this folder will be
+present. If you, however, want to install meme-suite first and later set
+the databases you need, just make sure that the folder is present before
+building meme-suite:
+
+mkdir -p /var/lib/meme-suite
+
+If you want to install the databases manually, they can be downloaded
+from here:
+
+http://meme-suite.org/doc/download.html
diff --git a/academic/meme-suite/README.TESTS b/academic/meme-suite/README.TESTS
new file mode 100644
index 000000000000..9a408ef4d45b
--- /dev/null
+++ b/academic/meme-suite/README.TESTS
@@ -0,0 +1,28 @@
+It is a good practice to run the series of tests provided by the MEME
+Suite developers once the executables are built. Unfortunatelly, they
+cannot be run properly as root (at least here).
+
+You can, however, run them once the package is built as a normal user.
+Just copy the folder where the meme suite was built as your normal user,
+navigate there and run 'make test'. So, do something like this (for meme
+version 5.1.0):
+
+1) cp -a /tmp/SBo/meme-5.1.0/ ~/
+2) cd ~/meme-5.1.0
+3) make test
+
+You should receive a summary, like this:
+
+========================================================================
+Testsuite summary for meme 5.1.0
+========================================================================
+# TOTAL: 152
+# PASS:  152
+# SKIP:  0
+# XFAIL: 0
+# FAIL:  0
+# XPASS: 0
+# ERROR: 0
+========================================================================
+
+Note that on my 32bit installation of Slackware in a VM, the tests fail.
diff --git a/academic/meme-suite/References b/academic/meme-suite/References
index 242a70d914e3..871bc591a775 100644
--- a/academic/meme-suite/References
+++ b/academic/meme-suite/References
@@ -1,22 +1,4 @@
-Authors
-
-The MEME Suite was developed by
-
-Timothy Bailey at the Institute for Molecular Bioscience at the University of Queensland,
-William Stafford Noble in the Department of Genome Sciences at the University of Washington and
-with input from
-
-Charles Elkan and
-Michael Gribskov.
-Development of portions of the MEME Suite have previously been supported by
-
-Columbia University,
-the Computational Biology Research Center at the National Institute of Advanced Industrial Science and Technology, Japan,
-the National Biomedical Computation Resource, and
-the San Diego Supercomputer Center.
-
 Citing MEME Suite Programs
-
 To cite the full MEME Suite
 Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble, "MEME SUITE: tools for motif discovery and searching", Nucleic Acids Research, 37:W202-W208, 2009. [full text]
 To cite individual tools
@@ -25,27 +7,31 @@ Fabian A. Buske, Mikael Bodén, Denis C. Bauer and Timothy L. Bailey, "Assigning
 AME
 Robert C. McLeay, Timothy L. Bailey, "Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data", BMC Bioinformatics, 11:165, 2010. [full text]
 CentriMo
-Timothy L. Bailey and Philip Machanick, "Inferring direct DNA binding from ChIP-seq", Nucleic Acids Research, 40:e128, 2012. [Abstract and Full Text]
+Timothy L. Bailey and Philip Machanick, "Inferring direct DNA binding from ChIP-seq", Nucleic Acids Research, 40:e128, 2012. [Full Text]
+T-Gene
+Timothy O'Connor, Charles E. Grant, Mikael Bodén, Timothy L. Bailey, "T-Gene: Improved target gene prediction", bioRxiv, preprint, 2019.
 DREME
 Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", Bioinformatics, 27(12):1653-1659, 2011. [full text]
 FIMO
-Charles E. Grant, Timothy L. Bailey, and William Stafford Noble, "FIMO: Scanning for occurrences of a given motif", Bioinformatics 27(7):1017–1018, 2011. [full text]
+Charles E. Grant, Timothy L. Bailey and William Stafford Noble, "FIMO: Scanning for occurrences of a given motif", Bioinformatics 27(7):1017–1018, 2011. [full text]
 GLAM2 and GLAM2SCAN
-Martin C. Frith, Neil F. W. Saunders, Bostjan Kobe, Timothy L. Bailey, "Discovering sequence motifs with arbitrary insertions and deletions", PLoS Computational Biology, 4(5):e1000071, 2008. [full text]
+Martin C. Frith, Neil F. W. Saunders, Bostjan Kobe and Timothy L. Bailey, "Discovering sequence motifs with arbitrary insertions and deletions", PLoS Computational Biology, 4(5):e1000071, 2008. [full text]
 GOMO
 Fabian A. Buske, Mikael Bodén, Denis C. Bauer and Timothy L. Bailey, "Assigning roles to DNA regulatory motifs using comparative genomics", Bioinformatics, 26(7), 860-866, 2010. [full text]
 MAST
 Timothy L. Bailey and Michael Gribskov, "Combining evidence using p-values: application to sequence homology searches", Bioinformatics, 14(1):48-54, 1998. [pdf]
+MCAST
+Timothy Bailey and William Stafford Noble, "Searching for statistically significant regulatory modules", Bioinformatics (Proceedings of the European Conference on Computational Biology), 19(Suppl. 2):ii16-ii25, 2003. [full text]
 MEME
-Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. [postscript] [pdf]
+Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. [pdf]
 MEME-ChIP
 Philip Machanick and Timothy L. Bailey, "MEME-ChIP: motif analysis of large DNA datasets", Bioinformatics 27(12):1696-1697, 2011. [full text]
+MoMo
+Alice Cheng, Charles Grant, Timothy L. Bailey and William Noble, "MoMo: Discovery of statistically significant post-translational modification motifs", Bioinformatics, 2018. [full text]
 PSPs
-Timothy L. Bailey, Mikael Bodén, Tom Whitington, and Philip Machanick, "The value of position-specific priors in motif discovery using MEME", BMC Bioinformatics, 11(1):179, 2010. [full text]
-MCAST
-Timothy Bailey and William Stafford Noble, "Searching for statistically significant regulatory modules", Bioinformatics (Proceedings of the European Conference on Computational Biology), 19(Suppl. 2):ii16-ii25, 2003. [full text]
+Timothy L. Bailey, Mikael Bodén, Tom Whitington and Philip Machanick, "The value of position-specific priors in motif discovery using MEME", BMC Bioinformatics, 11(1):179, 2010. [full text]
 SpaMo
-Tom Whitington, Martin C. Frith, James Johnson, and Timothy L. Bailey "Inferring transcription factor complexes from ChIP-seq data", Nucl. Acids Res. 39(15):e98, 2011. [full text]
+Tom Whitington, Martin C. Frith, James Johnson and Timothy L. Bailey "Inferring transcription factor complexes from ChIP-seq data", Nucl. Acids Res. 39(15):e98, 2011. [full text]
 Tomtom
 Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble, "Quantifying similarity between motifs", Genome Biology, 8(2):R24, 2007. [full text]
 Related papers
@@ -55,24 +41,24 @@ MAST related
 Timothy L. Bailey and Michael Gribskov, "Score distributions for simultaneous matching to multiple motifs" Journal of Computational Biology, Vol. 4, pp. 45-59, 1997. [pdf]
 Timothy L. Bailey and Michael Gribskov, "Methods and statistics for combining motif match scores" Journal of Computational Biology, Vol. 5, pp. 211-221, 1998. [pdf]
 MEME related
-Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. [postscript] [pdf]
+Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. [pdf]
 Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", UCSD Technical Report, CS94-351, March, 1994, University of California at San Diego. [pdf]
 Timothy L. Bailey, "Discovering motifs in DNA and protein sequences: The approximate common substring problem", Ph.D. dissertation, University of California at San Diego, 1995. [pdf]
 Timothy L. Bailey and Charles Elkan, "Unsupervised Learning of Multiple Motifs in Biopolymers using EM" Machine Learning, 21(1-2):51-80, October, 1995. [pdf]
 Timothy L. Bailey and Charles Elkan, "The value of prior knowledge in discovering motifs with MEME", Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, pp. 21-29, AAAI Press, Menlo Park, California, 1995. [pdf]
 Timothy L. Bailey and Michael Gribskov, "The megaprior heuristic for discovering protein sequence patterns"", Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, pp. 15-24 AAAI Press, Menlo Park, California, 1996. [pdf]
 William N. Grundy, Timothy L. Bailey and Charles P. Elkan, "ParaMEME: A Parallel Implementation and a Web Interface for a DNA and Protein Motif Discovery Tool", Computer Applications in the Biological Sciences (CABIOS), Vol. 12(4), pp. 303-310, 1996. [pdf]
-Timothy L. Bailey, Michael E. Baker and Charles P. Elkan, "An artificial intelligence approach to motif discovery in protein sequences: application to steriod dehydrogenases", Journal of steroid biochemistry and molecular biology, Vol. 62, 1997.
+Timothy L. Bailey, Michael E. Baker and Charles P. Elkan, "An artificial intelligence approach to motif discovery in protein sequences: application to steroid dehydrogenases", Journal of steroid biochemistry and molecular biology, Vol. 62, 1997.
 Martin Tompa, Nan Li, Timothy L. Bailey, George M. Church, Bart De Moor, Eleazar Eskin, Alexander V. Favorov, Martin C. Frith, Yutao Fu, W. James Kent, Vsevolod J. Makeev, Andrei A. Mironov,, William S. Noble, Giulio Pavesi, Graziano Pesole, Mireille Regnier, Nicolas Simonis, Saurabh Sinha, Gert Thijs, Jacques van Helden, Mathias Vandenbogaert, Zhiping Weng, Christopher Workman, Chun Ye and Zhou Zhu. "Assessing computational tools for the discovery of transcription factor binding sites." Nature Biotechnology, 23(1), 137-144, 2005. [full text]
-Timothy L. Bailey, Nadya Williams, Chris Misleh, and Wilfred W. Li, "MEME: discovering and analyzing DNA and protein sequence motifs" Nucleic Acids Research, Vol. 34, pp. W369-W373, 2006. [html] [pdf]
+Timothy L. Bailey, Nadya Williams, Chris Misleh and Wilfred W. Li, "MEME: discovering and analyzing DNA and protein sequence motifs" Nucleic Acids Research, Vol. 34, pp. W369-W373, 2006. [html] [pdf]
 Wenxiu Ma, William Stafford Noble and Timothy L. Bailey, "Motif-based analysis of large nucleotide datasets using MEME-ChIP" Nature Protocols, 9(6):1428-1450, 2014. [html]
 Tomtom related
-Emi Tanaka, Timothy L. Bailey, Charles E. Grant, William S. Noble, and Uri Keich, "Improved similarity scores for comparing motifs" Bioinformatics 27(12): 1603-1609, 2011. [full text]
+Emi Tanaka, Timothy L. Bailey, Charles E. Grant, William S. Noble and Uri Keich, "Improved similarity scores for comparing motifs" Bioinformatics 27(12): 1603-1609, 2011. [full text]
 Other
 William N. Grundy, Timothy L. Bailey, Charles P. Elkan and Michael E. Baker. "Hidden Markov Model Analysis of Motifs in Steroid Dehydrogenases and their Homologs" Biochemical and Biophysical Research Communications, Vol 231, pp. 760-766, 1997. [pdf]
 William N. Grundy, Timothy L. Bailey, Charles P. Elkan and Michael E. Baker. "Meta-MEME: Motif-based Hidden Markov Models of Protein Families" Computer Applications in the Biological Sciences (CABIOS), Vol. 13(4), pp. 397-406, 1997. [pdf]
-Michael E. Baker, William N. Grundy, and Charles P. Elkan, "Spinach CSP41, an mRNA-binding protein and ribonuclease, is homologous to nucleotide-sugar epimerases and hydroxysteroid dehydrogenases", Biochemical and Biophysical Research Communications 248(2), 250-254, 1998. [pdf]
-Michael E. Baker, William N. Grundy, and Charles P. Elkan, "A common ancestor for a subunit in the mitochondrial proton-translocating NADH:ubiquinone oxidoreductase (complex I) and short-chain dehydrogenases/reductases", Cellular and Molecular Life Sciences, Vol. 55(3), 450-455, 1999.
-John Hawkins, Charles Grant, William S. Noble, and Timothy L. Bailey, "Assessing phylogenetic motif models for predicting transcription factor binding sites" Bioinformatics (Proceedings of the Intelligent Systems for Molecular Biology Conference), 25(12), i339--347, 2009. [full text]
-Gabriel Cuellar-Partida, Fabian A. Buske, Robert C. McLeay, Tom Whitington, William Stafford Noble, and Timothy L. Bailey, "Epigenetic priors for identifying active transcription factor binding sites", Bioinformatics 28(1): 56-62, 2012 [pdf]
-Timothy L. Bailey, James Johnson, Charles E. Grant and William Stafford Noble, "The MEME Suite." Nucleic Acids Resesearch, 43(W1):W39-49, 2015 [full text]
+Michael E. Baker, William N. Grundy and Charles P. Elkan, "Spinach CSP41, an mRNA-binding protein and ribonuclease, is homologous to nucleotide-sugar epimerases and hydroxysteroid dehydrogenases", Biochemical and Biophysical Research Communications 248(2), 250-254, 1998. [pdf]
+Michael E. Baker, William N. Grundy and Charles P. Elkan, "A common ancestor for a subunit in the mitochondrial proton-translocating NADH:ubiquinone oxidoreductase (complex I) and short-chain dehydrogenases/reductases", Cellular and Molecular Life Sciences, Vol. 55(3), 450-455, 1999.
+John Hawkins, Charles Grant, William S. Noble and Timothy L. Bailey, "Assessing phylogenetic motif models for predicting transcription factor binding sites" Bioinformatics (Proceedings of the Intelligent Systems for Molecular Biology Conference), 25(12), i339--347, 2009. [full text]
+Gabriel Cuellar-Partida, Fabian A. Buske, Robert C. McLeay, Tom Whitington, William Stafford Noble and Timothy L. Bailey, "Epigenetic priors for identifying active transcription factor binding sites", Bioinformatics 28(1): 56-62, 2012 [pdf]
+Timothy L. Bailey, James Johnson, Charles E. Grant and William Stafford Noble, "The MEME Suite." Nucleic Acids Research, 43(W1):W39-49, 2015 [full text]
diff --git a/academic/meme-suite/meme-suite.SlackBuild b/academic/meme-suite/meme-suite.SlackBuild
index a21bb00ea193..acc62dc3a5e7 100644
--- a/academic/meme-suite/meme-suite.SlackBuild
+++ b/academic/meme-suite/meme-suite.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for meme-suite
 
-# Copyright 2017 Petar Petrov slackalaxy@gmail.com
+# Copyright 2017-2020 Petar Petrov slackalaxy@gmail.com
 # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
@@ -23,11 +23,12 @@
 #  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 PRGNAM=meme-suite
-SRCNAM=meme
-VERSION=${VERSION:-4.12.0}
+VERSION=${VERSION:-5.1.0}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
+SRCNAM=meme
+
 if [ -z "$ARCH" ]; then
   case "$( uname -m )" in
     i?86) ARCH=i586 ;;
@@ -60,9 +61,9 @@ 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}
+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 \
@@ -70,51 +71,49 @@ find -L . \
  \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
   -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
 
-# Fix a few paths
-sed -i "s:share/doc:doc/$PRGNAM-$VERSION/doc/:g" Makefile.in
-sed -i "s:share/doc:doc/$PRGNAM-$VERSION/doc/:g" doc/Makefile.*
-sed -i "s:share/doc:doc/$PRGNAM-$VERSION/doc/:g" doc/css/Makefile.*
-sed -i "s:share/doc:doc/$PRGNAM-$VERSION/doc/:g" doc/images/Makefile.*
-sed -i "s:share/doc:doc/$PRGNAM-$VERSION/doc/:g" doc/js/Makefile.*
-sed -i "s:share/doc:doc/$PRGNAM-$VERSION/doc/:g" doc/examples/Makefile.*
-sed -i "s:share/doc:doc/$PRGNAM-$VERSION/doc/:g" doc/examples/compute_prior_dist_example_output_files/Makefile.*
-sed -i "s:share/doc:doc/$PRGNAM-$VERSION/doc/:g" doc/examples/sample_opal_scripts/Makefile.*
-sed -i "s:\\$(libdir)/perl:&/vendor_perl:g"      scripts/Makefile.*
-sed -i "s:\\$(libdir)/python:$(libdir)/python2.7/site-packages:g" scripts/Makefile.*
+# Change name from "meme" to "meme-suite"
+sed -i "s:PACKAGE_NAME='meme':PACKAGE_NAME='meme-suite':" configure
+
+# Do not append the package version to folder names
+find . -name "Makefile.*" -exec \
+sed -i 's:${PACKAGE_NAME}-${PACKAGE_VERSION}:${PACKAGE_NAME}:g' {} \;
+
+# Sometimes the brackets are not curly
+find . -name "Makefile.*" -exec \
+sed -i 's:$(PACKAGE_NAME)-${PACKAGE_VERSION}:$(PACKAGE_NAME):g' {} \;
+
+# Documentation should go to docdir not datadir
+sed -i 's:${datadir}/${PACKAGE_NAME}:${docdir}:g' doc/Makefile.*
+
+# Make empty folders for the databases
+mkdir -p $PKG/var/lib/$PRGNAM/{fasta_databases,gomo_databases,motif_databases,tgene_databases}
 
 ./configure \
   --prefix=/usr \
   --libdir=/usr/lib${LIBDIRSUFFIX} \
   --docdir=/usr/doc/$PRGNAM-$VERSION \
   --with-url="http://meme-suite.org" \
-  --datarootdir=/usr/share/$PRGNAM/data \
-  --sysconfdir=/usr/share/$PRGNAM/etc \
+  --datarootdir=/usr/share \
+  --libexecdir=/usr/libexec \
   --localstatedir=/var \
+  --mandir=/usr/man \
   --with-db=/var/lib/$PRGNAM \
-  --with-logs=/var/log/$PRGNAM \
   --with-temp=/tmp
 
-# CFLAGS should be specified here, otherwise they are not accepted
 make CFLAGS="$SLKCFLAGS -std=gnu89"
-
-# The tests are recommended, but take quite some time. Be patient or comment out the line below.
-# Also, some tests fail on a 32bit system, therefore it is listed as unsupported. If you find a
-# fix, let me know.
-make test
 make install DESTDIR=$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
 
-# The databases directory should contain folders for motif, gomo and fasta databases
-mkdir -p $PKG/var/lib/$PRGNAM/{motif_databases,gomo_databases,fasta_databases}
-
 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
 cp -a \
   AUTHORS COPYING INSTALL README \
   $PKG/usr/doc/$PRGNAM-$VERSION
 cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
 cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
+cat $CWD/README.TESTS > $PKG/usr/doc/$PRGNAM-$VERSION/README.TESTS
+cat $CWD/README.DATABASES > $PKG/usr/doc/$PRGNAM-$VERSION/README.DATABASES
 
 mkdir -p $PKG/install
 cat $CWD/slack-desc > $PKG/install/slack-desc
diff --git a/academic/meme-suite/meme-suite.info b/academic/meme-suite/meme-suite.info
index 9f67bd2c7e41..4c8ad796e8ec 100644
--- a/academic/meme-suite/meme-suite.info
+++ b/academic/meme-suite/meme-suite.info
@@ -1,10 +1,10 @@
 PRGNAM="meme-suite"
-VERSION="4.12.0"
+VERSION="5.1.0"
 HOMEPAGE="http://meme-suite.org/"
-DOWNLOAD="UNSUPPORTED"
-MD5SUM=""
-DOWNLOAD_x86_64="http://meme-suite.org/meme-software/4.12.0/meme_4.12.0.tar.gz"
-MD5SUM_x86_64="40d282cc33f7dedb06b24b9f34ac15c1"
-REQUIRES="openmpi perl-HTML-Template perl-HTML-Tree perl-File-Which perl-JSON"
+DOWNLOAD="http://meme-suite.org/meme-software/5.1.0/meme-5.1.0.tar.gz"
+MD5SUM="71e357be7bce1686f516858957de3921"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+REQUIRES="openmpi perl-HTML-Template perl-JSON python3 meme-db-gomo meme-db-motif meme-db-tgene"
 MAINTAINER="Petar Petrov"
 EMAIL="slackalaxy@gmail.com"