sci-biology/meme: Version bump to 4.11.2_p2

Gentoo-bug: 599860
* EAPI=6
* Install documentation and examples correctly
* Install perl and python modules correctly
* Add missing perl runtime dependencies

Package-Manager: portage-2.3.2

5 files changed, 872 insertions, 0 deletions

diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest
index 3ed08610b06e..4496d777cb23 100644
--- a/sci-biology/meme/Manifest
+++ b/sci-biology/meme/Manifest
@@ -1 +1,2 @@
+DIST meme_4.11.2.tar.gz 18004930 SHA256 6e3ff843366588ea13fa8060306be9e2c144521912dfb268f03638003bcdd581 SHA512 c97c3815e71e2fb5491548152f00688cdfbf4365f6027657e0ffc68e5d96cdd10a4708e0882ab7a5a61d78d93113c925cf5bb300fbe93fa4b2961becef497894 WHIRLPOOL 6b77d7832342658d5cf546af0b005b59664c811d25a0412df765a15a8c80a75d9618a1f9966c9a2824750eced6605b534d41199382a6f2641e7430540ba19fcf
 DIST meme_4.8.1.tar.gz 8703632 SHA256 c3ad3ca26bc2a7130c5eceb64e1745275c317a5469e98fc8759a9e56babccb8c SHA512 31833169ffa9bd82387d1872be40b0fc4312f4a05bb7abb84daf372244ce3f2a68c89c96722c0453f7bcd9eb4fc84fd3d66e1278af55d556715b94b0df5f87ba WHIRLPOOL 4b5e8968e6964479081d1fe036ff3aa7a50dc56bafc0031890d2e47dbdc8e0273e62ffe01800d8908b2fa9824a4766254bb0fd94003d9ca14784073d5357793e
diff --git a/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch b/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch
new file mode 100644
index 000000000000..0f3349c9583e
--- /dev/null
+++ b/sci-biology/meme/files/meme-4.11.2_p2-fix-build-system.patch
@@ -0,0 +1,323 @@
+Fix and modernise build system
+* Remove all *FLAGS setting, just append to the user-supplied ones
+* Add --enable-doc and --enable-examples configure flags
+* Install documentation and examples in correct directories
+* Discover libxml2 and libxslt dependencies using PKG_CHECK_MODULES
+* Install python and perl modules correctly
+
+--- a/configure.ac
++++ b/configure.ac
+@@ -76,61 +76,9 @@
+ AM_CONDITIONAL(WANT_STRLCPY, test ["$have_strlcpy" = no])
+ 
+ # Check for compiler-specific settings
+-LARGE_FILE_SUPPORT=`getconf LFS_CFLAGS`
+-if test "${GCC}" = "yes"; then
+-  ac_cc_opt="-O3"
+-  ac_cc_debug_opt="-O0"
+-  ac_cc_warn="-Wall -Wno-unused"
+-  ac_cc_debug="-ggdb"
+-  # Check for OS X llvm (clang) compiler
+-  if `gcc --version |grep llvm >/dev/null`; then
+-    ac_cc_debug="-g"
+-  fi
+-  CFLAGS="-std="gnu89" $ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT"
+-else
+-  ac_cc_opt="-O"
+-  ac_cc_debug_opt=""
+-  ac_cc_warn=""
+-  ac_cc_debug="-g"
+-  CFLAGS="$ac_cc_warn -DUNIX -D__USE_FIXED_PROTOTYPES__ $LARGE_FILE_SUPPORT"
+-fi
+-
+-# Set up default libxml2 settings
+-# check for installed copy of libxml2
+-build_libxml2="yes"
+-if test -n "$XML2_CONFIG"; then
+-  # Require at least version 2.6
+-  required_libxml2_version="2006000"
+-  LIBXML2_VERSION="`$XML2_CONFIG --version | \
+-    awk 'BEGIN { FS = "."; } { printf "%d", ($1 * 1000 + $2) * 1000 + $3;}'`"
+-  if test -n "$LIBXML2_VERSION" && \
+-     test "$LIBXML2_VERSION"  -ge "$required_libxml2_version"; then 
+-    build_libxml2="no"
+-    LIBXML2_LIBS="`$XML2_CONFIG --libs`"
+-    LIBXML2_CFLAGS="`$XML2_CONFIG --cflags`"
+-  fi
+-fi
+-if test -z "$LIBXML2_LIBS"; then
+-  AC_MSG_WARN([libxml2 library not found])
+-  LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la"
+-  LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include"
+-fi
+-
+-# Set up default libxslt settings
+-# check for installed copy of libxslt
+-build_libxslt="yes"
+-if test -n "$XSLT_CONFIG"; then
+-  build_libxslt="no"
+-  LIBXSLT_LIBS="`$XSLT_CONFIG --libs` -lexslt"
+-  LIBXSLT_CFLAGS="`$XSLT_CONFIG --cflags`"
+-fi
+-if test -z "$LIBXSLT_LIBS"; then
+-  AC_MSG_WARN([libxslt library not found])
+-  LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la"
+-  LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la"
+-  LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt"
+-  LIBXSLT_CFLAGS="-I\${top_srcdir}/src/"
+-fi
++AC_SYS_LARGEFILE
++CFLAGS="-std=gnu89 -Wall -Wno-unused ${CFLAGS}"
++CPPFLAGS="-DUNIX -D__USE_FIXED_PROTOTYPES__ ${CPPFLAGS}"
+ 
+ # who is installing 
+ USER=`whoami`
+@@ -279,6 +227,16 @@
+ AM_CONDITIONAL(PARALLEL, test ["$parallel" != no])
+ AM_CONDITIONAL(PARALLEL_IS_LAM, test -n ["$lammpi"]) 
+ 
++dnl Documentation
++AC_ARG_ENABLE([doc],
++	AS_HELP_STRING([--enable-doc], [Enable installation of documentation]))
++AM_CONDITIONAL([ENABLE_DOC], [test "x$enable_doc" = "xyes"])
++
++dnl Examples
++AC_ARG_ENABLE([examples],
++	AS_HELP_STRING([--enable-examples], [Enable installation of examples]))
++AM_CONDITIONAL([ENABLE_EXAMPLES], [test "x$enable_examples" = "xyes"])
++
+ AC_ARG_ENABLE(
+     webservice,
+     [  --enable-webservice=deploy_dir       Deploy the MEME service on an existing Opal 2.5+ installation],
+@@ -309,24 +267,35 @@
+ AM_CONDITIONAL(WEBEITHER, test ["x$OPAL_DEPLOY" != "x" -o "x$OPAL_URL" != "xno"])
+ 
+ # enable building of included libxml2
+-AC_ARG_ENABLE(
+-    build_libxml2,
+-    [  --enable-build-libxml2     Build included version of libxml2. Default is to use pre-existing locally installed copy.],
+-    build_libxml2=$enableval; \
+-    LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la"; \
+-    LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include" , )
+-AM_CONDITIONAL(BUILD_LIBXML2, test ["$build_libxml2" = yes])
++AC_ARG_ENABLE([build-libxml2],
++	AS_HELP_STRING([--enable-build-libxml2], [Build included version of libxml2. Default is to use pre-existing locally installed copy.]))
++AS_IF([test "x$enable_build_libxml2" = "xyes"], [
++	dnl Enable building of bundled libs
++	LIBXML2_CFLAGS="-I\${top_srcdir}/src/libxml2/include"
++	LIBXML2_LIBS="\${top_builddir}/src/libxml2/libxml2.la"
++	],[
++	dnl Use system libraries
++	PKG_CHECK_MODULES([LIBXML2], [libxml-2.0 >= 2.6])
++])
++AM_CONDITIONAL([BUILD_LIBXML2], [test "x$enable_build_libxml2" = "xyes"])
++
+ 
+ # enable building of included libxslt
+-AC_ARG_ENABLE(
+-    build_libxslt,
+-    [  --enable-build-libxslt     Build included version of libxslt. Default is to use pre-existing locally installed copy.],
+-    build_libxslt=$enableval; \
+-    LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la"; \
+-    LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la"; \
+-    LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt"; \
+-    LIBXSLT_CFLAGS="-I\${top_srcdir}/src/" , )
+-AM_CONDITIONAL(BUILD_LIBXSLT, test ["$build_libxslt" = yes])
++AC_ARG_ENABLE([build-libxslt],
++	AS_HELP_STRING([--enable-build-libxslt], [Build included version of libxslt. Default is to use pre-existing locally installed copy.]))
++AS_IF([test "x$enable_build_libxslt" = "xyes"], [
++	dnl Enable building of bundled libs
++	LIBXSLT_CFLAGS="-I\${top_srcdir}/src/"
++	LIBXSLT_LIBS="\${top_builddir}/src/libxslt/libxslt.la"
++
++	LIBEXSLT_CFLAGS="-I\${top_srcdir}/src/libexslt"
++	LIBEXSLT_LIBS="\${top_builddir}/src/libexslt/libexslt.la"
++	],[
++	dnl Use system libraries
++	PKG_CHECK_MODULES([LIBXSLT], [libxslt])
++	PKG_CHECK_MODULES([LIBEXSLT], [libexslt])
++])
++AM_CONDITIONAL([BUILD_LIBXSLT], [test "x$enable_build_libxslt" = "xyes"])
+ 
+ # set website url
+ AC_ARG_WITH(
+@@ -427,13 +396,13 @@
+     [AC_PATH_PROG(PERL, perl)])
+ AC_DEFINE_UNQUOTED(PERL, "$PERL", [Path to Perl] )
+ 
++AC_ARG_WITH([perl-dir],
++	AS_HELP_STRING([--with-perl-dir], [Perl modules directory]), [perlmoddir="$with_perl_dir"], [perlmoddir="lib/perl"])
++AC_SUBST([perlmoddir])
++
++
+ # set path to Python
+-AC_ARG_WITH(
+-    python,
+-    [  --with-python=NAME     Set path to Python. Default is to take from user's PATH.],
+-    [PYTHON=$withval],
+-    [AC_PATH_PROG(PYTHON, python)])
+-AC_DEFINE_UNQUOTED(PYTHON, "$PYTHON", [Path to Python] )
++AM_PATH_PYTHON
+ 
+ # set path to convert utility
+ AC_ARG_WITH(
+@@ -586,13 +555,15 @@
+         Configuration parameters
+         ========================
+ 
+-  Install path:               ${prefix}
++  Install path (prefix):      ${prefix}
+   Install UID:                ${MEME_USER}
+   Version:                    ${VERSION}
+-  C compiler:                 ${CC}
+-  C compiler flags:           ${CFLAGS}
+-  Linker:                     ${LD}
+-  Special Libs:               ${LIBS}
++  C compiler (CC):            ${CC}
++  C compiler flags (CFLAGS):  ${CFLAGS}
++  C preproc flags (CPPFLAGS): ${CPPFLAGS}
++  Linker (LD):                ${LD}
++  Linker flags (LDFLAGS):     ${LDFLAGS}
++  Special Libs (LIBS):        ${LIBS}
+   MPICC                       ${MPICC}
+   MPIRUN                      ${MPIRUN}
+   MPI_CMD                     ${MPI_CMD}
+--- a/doc/css/Makefile.am
++++ b/doc/css/Makefile.am
+@@ -5,7 +5,7 @@
+ 
+ EXTRA_DIST = $(NORMAL_FILES)
+ 
+-if ! WEBSITE
+-doccssdir = $(prefix)/doc/css
++if ENABLE_DOC
++doccssdir = $(htmldir)/css
+ doccss_DATA =  $(NORMAL_FILES)
+ endif
+--- a/doc/examples/compute_prior_dist_example_output_files/Makefile.am
++++ b/doc/examples/compute_prior_dist_example_output_files/Makefile.am
+@@ -7,8 +7,8 @@
+ EXAMPLES = \
+   prior.dist.txt
+ 
+-if ! WEBSITE
+-exdir = $(prefix)/doc/examples/compute_prior_dist_example_output_files
++if ENABLE_EXAMPLES
++exdir = $(docdir)/examples/compute_prior_dist_example_output_files
+ ex_DATA = $(EXAMPLES)
+ endif
+ 
+--- a/doc/examples/Makefile.am
++++ b/doc/examples/Makefile.am
+@@ -22,8 +22,8 @@
+ # load the EXAMPLE_OUTPUT_FILES variable
+ include examples.mk
+ 
+-if ! WEBSITE
+-exdir = $(prefix)/doc/examples
++if ENABLE_EXAMPLES
++exdir = $(docdir)/examples
+ nobase_dist_ex_DATA = $(EXAMPLES) $(EXAMPLE_OUTPUT_FILES)
+ endif
+ 
+--- a/doc/examples/sample_opal_scripts/Makefile.am
++++ b/doc/examples/sample_opal_scripts/Makefile.am
+@@ -15,8 +15,8 @@
+   MemeClient.pl \
+   MemeClient.py
+ 
+-if ! WEBSITE
+-exdir = $(prefix)/doc/examples/sample_opal_scripts
++if ENABLE_EXAMPLES
++exdir = $(docdir)/examples/sample_opal_scripts
+ ex_DATA = $(EXAMPLES)
+ endif
+ 
+--- a/doc/images/Makefile.am
++++ b/doc/images/Makefile.am
+@@ -30,8 +30,8 @@
+ 
+ MEME_IMAGES = $(PROGRAM_ICONS) $(OTHER_IMAGES)
+ 
+-if ! WEBSITE
+-memeimgdir = $(prefix)/doc/images
++if ENABLE_DOC
++memeimgdir = $(htmldir)/images
+ memeimg_DATA = $(MEME_IMAGES)
+ endif
+ 
+--- a/doc/js/Makefile.am
++++ b/doc/js/Makefile.am
+@@ -41,8 +41,8 @@
+ 
+ BUILT_SOURCES = $(BUILT_FILES)
+ 
+-if ! WEBSITE
+-docjsdir = $(prefix)/doc/js
++if ENABLE_DOC
++docjsdir = $(htmldir)/js
+ docjs_DATA =  $(NORMAL_FILES) $(BUILT_FILES) $(SYMLINK_FILES)
+ endif
+ 
+--- a/doc/Makefile.am
++++ b/doc/Makefile.am
+@@ -129,8 +129,8 @@
+   update-sequence-db.html \
+   ismb94.pdf
+ 
+-if ! WEBSITE
+-memedocdir = $(prefix)/doc
++if ENABLE_DOC
++memedocdir = $(htmldir)
+ memedoc_DATA =  $(NORMAL_FILES)
+ endif
+ 
+--- a/scripts/Makefile.am
++++ b/scripts/Makefile.am
+@@ -22,8 +22,8 @@
+   -e 's%@WHICHJAVA@%$(JAVA)%' \
+   -e 's%@WHICHCONVERT@%$(CONVERT)%' \
+   -e 's%@WHICHGHOSTSCRIPT@%$(GHOSTSCRIPT)%' \
+-  -e 's%@PERLLIBDIR@%$(libdir)/perl%' \
+-  -e 's%@PYTHONLIBDIR@%$(libdir)/python%' \
++  -e 's%@PERLLIBDIR@%$(perlmoddir)%' \
++  -e 's%@PYTHONLIBDIR@%$(pythondir)%' \
+   -e 's%@JAVALIBDIR@%$(libdir)/java%' \
+   -e 's%@LAM_BIN@%$(LAMBIN)%' \
+   -e 's%@APPCONFIGDIR@%$(sysconfdir)%' \
+@@ -62,7 +62,7 @@
+   DiffXML.pm \
+   HypergeometricDynProg.pm
+ 
+-perlmoddir=$(libdir)/perl
++perlmoddir = $(exec_prefix)/@perlmoddir@
+ perlmod_SCRIPTS = \
+   $(BUILT_PERL_MOD) \
+   $(NORMAL_PERL_MOD)
+@@ -76,8 +76,7 @@
+   hypergeometric.py \
+   sequence.py
+ 
+-pythonlibdir=$(libdir)/python
+-pythonlib_SCRIPTS = \
++python_PYTHON = \
+   $(BUILT_PYTHON_LIB) \
+   $(NORMAL_PYTHON_LIB)
+ 
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -19,7 +19,13 @@
+ ARCHIVE_REVISION = $(shell cat ../ARCHIVE_REVISION)
+ ARCHIVE_DATE = $(shell cat ../ARCHIVE_DATE)
+ 
+-SUBDIRS = filters libxml2 libxslt libexslt . parallel
++SUBDIRS = filters . parallel
++if BUILD_LIBXML2
++SUBDIRS += libxml2
++endif
++if BUILD_LIBXSLT
++SUBDIRS += libxslt libexslt
++endif
+ 
+ BUILT_SOURCES = dir.h projrel.h
+ 
diff --git a/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch b/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch
new file mode 100644
index 000000000000..30a182f8f43a
--- /dev/null
+++ b/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch
@@ -0,0 +1,383 @@
+--- a/doc/alphabet-format.html
++++ b/doc/alphabet-format.html
+@@ -233,7 +233,7 @@
+           providing a reference on the meaning of the symbols used. If present, the
+           symbol name must be the second field.</p>
+           <p>The &quot;<span class="pdat">name</span>&quot; follows the rules of
+-          <a href="qstr">quoted text</a>.</p>
++          <a href="#qstr">quoted text</a>.</p>
+         </div>
+         <h5>color</h5>
+         <div class="indent">
+--- a/doc/release-notes.html
++++ b/doc/release-notes.html
+@@ -14,8 +14,26 @@
+       <h2>Motif-based sequence analysis tools</h2>
+     </div>
+     <h2>MEME Suite Release Notes</h2>
++    <hr>
++      <b>MEME version 4.11.2 patch 1 -- June 16, 2016</b>
++      <ul>
++        <li>
++            <b>Bug fixes</b>
++            <ul>
++              <li>
++              Fixed bug in MCAST 4.11.2 that caused it to prematurely truncate
++              reading the sequence file.
++              </li>
++              <li>
++              Modified MEME to fall back to a simple Dirichlet prior when
++              using DNA or a custom alphabet with a prior that requires
++              a prior library, but no prior libray is specified.
++              </li>
++            </ul
++        </li>
++      </ul>
++      <p>
+       <hr>
+-      <p>
+         <b>MEME version 4.11.2 -- May 5 2016</b>
+       </p>
+       <ul>
+--- a/src/fasta-io.c
++++ b/src/fasta-io.c
+@@ -14,6 +14,7 @@
+ #include "alphabet.h"
+ #include "fasta-io.h"
+ #include "io.h"
++#include "seq-reader-from-fasta.h"
+ #include "prior-reader-from-psp.h"
+ #include "seq.h"
+ 
+@@ -159,61 +160,6 @@
+ }
+ 
+ /****************************************************************************
+- * Read raw sequence until a new sequence is encountered or too many letters
+- * are read.  The new sequence is appended to the end of the given
+- * sequence.
+- *
+- * Return: Was the sequence read completely?
+- ****************************************************************************/
+-static BOOLEAN_T read_raw_sequence_from_reader(
+-   DATA_BLOCK_READER_T *fasta_reader, // Sequence source
+-   char* name, // Sequence ID (used in error messages).
+-   ALPH_T* alph, // Alphabet in use
+-   unsigned int offset, // Current position in raw_sequence.
+-   unsigned int max_chars, // Maximum chars in raw_sequence.
+-   char* raw_sequence // Pre-allocated sequence.
+-) {
+-  // tlb; change a_char to integer so it will compile on SGI
+-  int a_char;
+-  int start_update;
+-  BOOLEAN_T return_value = TRUE;
+-
+-  // Start at the end of the given sequence.
+-  assert(offset < max_chars);
+-
+-  DATA_BLOCK_T *seq_block = new_sequence_block(max_chars - offset);
+-  return_value = !fasta_reader->get_next_block(fasta_reader, seq_block);
+-
+-  char *seq_buffer = get_sequence_from_data_block(seq_block);
+-  size_t seq_buffer_size = get_num_read_into_data_block(seq_block);
+-  int i;
+-  for (i = 0; i < seq_buffer_size; ++i) {
+-    a_char = seq_buffer[i];
+-    // Skip non-alphabetic characters.
+-    if (!isalnum(a_char) && a_char != '-' && a_char != '*' && a_char != '.') {
+-      if ((a_char != ' ') && (a_char != '\t') && (a_char != '\n') && (a_char != '\r')) {
+-        fprintf(stderr, "Warning: Skipping character %c in sequence %s.\n",
+-                a_char, name);
+-      }
+-    } else {
+-      // skip check if unknown alph
+-      if (alph != NULL && !alph_is_known(alph, a_char)) {
+-        fprintf(stderr, "Warning: Converting illegal character %c to %c ",
+-                a_char, alph_wildcard(alph));
+-        fprintf(stderr, "in sequence %s.\n", name);
+-        a_char = alph_wildcard(alph);
+-      }
+-      raw_sequence[offset] = (char) a_char;
+-      ++offset;
+-    }
+-  }
+-
+-  raw_sequence[offset] = '\0';
+-  free_data_block(seq_block);
+-  return(return_value);
+-}
+-
+-/****************************************************************************
+  * Read one sequence from a file in Fasta format.
+  *
+  * Return: Was a sequence successfully read?
+@@ -320,44 +266,6 @@
+ }
+ 
+ /****************************************************************************
+- * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder
+- * and copy them in to the raw sequence in the SEQ_T object starting at the
+- * given buffer offset. 
+- ****************************************************************************/
+-void read_one_fasta_segment_from_reader(
+-   DATA_BLOCK_READER_T *fasta_reader,
+-   size_t max_size,
+-   size_t buffer_offset,
+-   SEQ_T *sequence
+-) {
+-
+-  assert(sequence != NULL);
+-  assert(get_seq_length(sequence) <= max_size);
+-
+-  // Get the raw sequence buffer from the SEQ_T
+-  char *raw_sequence = get_raw_sequence(sequence);
+-  if (raw_sequence == NULL) {
+-    // Allocate space for raw sequence if not done yet.
+-    raw_sequence = mm_malloc(sizeof(char) * max_size + 1);
+-    raw_sequence[0] = 0;
+-  }
+-
+-  // Read a block of sequence charaters into the
+-  // raw sequence buffer for the SEQ_T.
+-  char *name = get_seq_name(sequence);
+-  BOOLEAN_T is_complete = read_raw_sequence_from_reader(
+-    fasta_reader,
+-    name,
+-    NULL, //FIXME this is dodgy, need a proper way of getting the alphabet. The fasta_reader has it but it is not accessable!
+-    buffer_offset,
+-    max_size,
+-    raw_sequence
+-  );
+-  set_raw_sequence(raw_sequence, is_complete, sequence);
+-
+-}
+-
+-/****************************************************************************
+  * Read all the sequences from a FASTA file at once.
+    Multiple files can be appended by calling this more than once.
+  ****************************************************************************/
+--- a/src/fasta-io.h
++++ b/src/fasta-io.h
+@@ -43,19 +43,6 @@
+ );
+ 
+ /****************************************************************************
+- * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder
+- * and copy them in to the raw sequence in the SEQ_T object starting at the
+- * given buffer offset. 
+- ****************************************************************************/
+-void read_one_fasta_segment_from_reader(
+-  DATA_BLOCK_READER_T *fasta_reader,
+-  size_t max_size,
+-  size_t buffer_offset,
+-  SEQ_T* sequence
+-);
+-
+-
+-/****************************************************************************
+  * Read all the sequences from a file in Fasta format.
+  ****************************************************************************/
+ void read_many_fastas
+--- a/src/init.c
++++ b/src/init.c
+@@ -767,10 +767,16 @@
+       if (alph_is_builtin_protein(alph)) { // default mixture prior for proteins
+         plib_name = make_path_to_file(get_meme_etc_dir(), PROTEIN_PLIB);
+       } else {
+-        fprintf(stderr, "The prior library must be specified for DNA or custom "
+-            "alphabets when specifiying a prior type of 'dmix', 'mega' "
+-            "or 'megap'.");
+-        exit(1);
++        fprintf(
++          stderr, 
++          "WARNING: When using DNA or a custom alphabet, "
++          "and specifiying a prior type of\n"
++          "'dmix', 'mega' or 'megap', a prior library must be provided.\n"
++          "No prior library was provided, so a simple Dirichlet prior will be used.\n"
++        );
++        prior = "dirichlet";
++        ptype = Dirichlet;
++        if (beta <= 0) beta = 0.01; // default b = 0.01 for simple Dirichlet
+       }
+     }
+   }
+--- a/src/seq-reader-from-fasta.c
++++ b/src/seq-reader-from-fasta.c
+@@ -639,11 +639,140 @@
+   return fasta_reader->current_position;
+ }
+ 
++
++/****************************************************************************
++ * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder
++ * and copy them in to the raw sequence in the SEQ_T object starting at the
++ * given buffer offset. 
++ ****************************************************************************/
++void read_one_fasta_segment_from_reader(
++   DATA_BLOCK_READER_T *fasta_reader,
++   size_t max_size,
++   size_t offset,
++   SEQ_T *sequence
++) {
++
++
++  assert(sequence != NULL);
++  assert(offset < max_size);
++
++  // Get the raw sequence buffer from the SEQ_T
++  char *raw_sequence = get_raw_sequence(sequence);
++  if (raw_sequence == NULL) {
++    // Allocate space for raw sequence if not done yet.
++    raw_sequence = mm_malloc(sizeof(char) * max_size + 1);
++    raw_sequence[0] = 0;
++  }
++
++  // Read a block of sequence charaters into the
++  // raw sequence buffer for the SEQ_T, starting at offset.
++  BOOLEAN_T is_complete = read_raw_sequence_from_reader(
++    fasta_reader,
++    max_size - offset,
++    raw_sequence + offset
++  );
++  set_raw_sequence(raw_sequence, is_complete, sequence);
++}
++
++/****************************************************************************
++ * Read raw sequence until a new sequence is encountered or too many letters
++ * are read.
++ *
++ * Return: Was the sequence read completely?
++ ****************************************************************************/
++BOOLEAN_T read_raw_sequence_from_reader(
++   DATA_BLOCK_READER_T *reader, // Sequence source
++   unsigned int max_chars, // Maximum chars in raw_sequence.
++   char* raw_sequence // Pre-allocated sequence buffer.
++) {
++
++  SEQ_READER_FROM_FASTA_T *fasta_reader 
++    = (SEQ_READER_FROM_FASTA_T *) get_data_block_reader_data(reader);
++
++  // Read sequence into temp. buffer from the sequence file.
++  char buffer[max_chars];
++  long start_file_pos = ftell(fasta_reader->fasta_file);
++  size_t seq_index = 0;
++  size_t total_read = 0;
++  while (seq_index < max_chars) {
++
++    size_t num_char_read = fread(
++      buffer,
++      sizeof(char), 
++      max_chars - seq_index,
++      fasta_reader->fasta_file
++    );
++    fasta_reader->current_position += num_char_read;
++    total_read += num_char_read;
++
++    if (feof(fasta_reader->fasta_file)) {
++       fasta_reader->at_end_of_file = TRUE;
++    }
++    else if (num_char_read < (max_chars - seq_index)) {
++      die(
++        "Error while reading sequence from file:%s.\nError message: %s\n", 
++        fasta_reader->filename,
++        strerror(ferror(fasta_reader->fasta_file))
++      );
++    }
++
++    size_t i;
++    for(i = 0; i < num_char_read; ++i) {
++      char c = buffer[i];
++      assert(c != 0);
++      if (isspace(c)) {
++        // Skip over white space
++        fasta_reader->at_start_of_line = (c == '\n');
++      }
++      else if (c == '>' && fasta_reader->at_start_of_line == TRUE) {
++        // We found the start of a new sequence while trying
++        // to fill the buffer. Leave the buffer incomplete.
++        // and wind back the file
++        fseek(fasta_reader->fasta_file, start_file_pos + i - 1, SEEK_SET);
++        fasta_reader->current_position = start_file_pos + i - 1;
++        fasta_reader->at_end_of_seq = TRUE;
++        fasta_reader->at_start_of_line = FALSE;
++        fasta_reader->at_end_of_file = FALSE;
++        break;
++      }
++      else {
++        fasta_reader->at_start_of_line = FALSE;
++        // Check that character is legal in alphabet. 
++        // If not, replace with wild card character.
++        if (alph_is_known(fasta_reader->alphabet, c)) {
++          raw_sequence[seq_index] = c;
++        }
++        else {
++          raw_sequence[seq_index] = alph_wildcard(fasta_reader->alphabet);
++          fprintf(
++            stderr, 
++            "Warning: %c is not a valid character in %s alphabet.\n"
++            "         Converting %c to %c.\n",
++            c,
++            alph_name(fasta_reader->alphabet),
++            c,
++            raw_sequence[i]
++          );
++        }
++        ++seq_index;
++      }
++    }
++    if (fasta_reader->at_end_of_seq | fasta_reader->at_end_of_file) {
++      break;
++    }
++  }
++
++  raw_sequence[seq_index] = '\0';
++  return(fasta_reader->at_end_of_seq | fasta_reader->at_end_of_file);
++}
++
+ /******************************************************************************
+- * Fills in the next data block for the sequence. 
+- * During the first call for the sequence it fills in the full data block.
+- * On successive calls, shifts the sequence in the block down one position
+- * and reads one more character.
++ * Populates the data block for the with the next block of sequence. 
++ *
++ * During the first call for the sequence it fills in a buffer from a file,
++ * The sequence pointer in the data block is set to point at the start of the buffer.
++ * On successive calls, the sequence pointer in the block is shifted down one position
++ * in the buffer. When the end of the buffer is reached, it is filled again from the file.
+  * 
+  * Returns TRUE if it was able to completely fill the block, FALSE if 
+  * the next sequence or EOF was reached before the block was filled.
+--- a/src/seq-reader-from-fasta.h
++++ b/src/seq-reader-from-fasta.h
+@@ -37,5 +37,30 @@
+   int * end_ptr           // end position of sequence (chr:\d+-(\d+))
+ );
+ 
++/****************************************************************************
++ * Read raw sequence until a new sequence is encountered or too many letters
++ * are read.
++ *
++ * Return: Was the sequence read completely?
++ ****************************************************************************/
++BOOLEAN_T read_raw_sequence_from_reader(
++   DATA_BLOCK_READER_T *fasta_reader, // Sequence source
++   unsigned int max_chars, // Maximum chars in raw_sequence.
++   char* raw_sequence // Pre-allocated sequence.
++);
++
++/****************************************************************************
++ * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder
++ * and copy them in to the raw sequence in the SEQ_T object starting at the
++ * given buffer offset. 
++ ****************************************************************************/
++void read_one_fasta_segment_from_reader(
++   DATA_BLOCK_READER_T *reader,
++   size_t max_size,
++   size_t offset,
++   SEQ_T *sequence
++);
++
++
+ size_t get_current_pos_from_seq_reader_from_fasta(DATA_BLOCK_READER_T *reader);
+ #endif
diff --git a/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch b/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch
new file mode 100644
index 000000000000..498d1df7b664
--- /dev/null
+++ b/sci-biology/meme/files/meme-4.11.2_p2-patch2.patch
@@ -0,0 +1,54 @@
+--- a/doc/release-notes.html
++++ b/doc/release-notes.html
+@@ -15,6 +15,21 @@
+     </div>
+     <h2>MEME Suite Release Notes</h2>
+     <hr>
++      <b>MEME version 4.11.2 patch 2 -- October 24, 2016</b>
++      <ul>
++        <li>
++            <b>Bug fixes</b>
++            <ul>
++              <li>
++              Fixed bug in handling of RNA-like custom alphabets.
++              </li>
++              <li>
++              Fixed bug in MAST -comp option.
++              </li>
++            </ul
++        </li>
++      </ul>
++      <hr>
+       <b>MEME version 4.11.2 patch 1 -- June 16, 2016</b>
+       <ul>
+         <li>
+--- a/src/alph-in.c
++++ b/src/alph-in.c
+@@ -1044,7 +1044,7 @@
+           lookup[0] = sym->complement;
+           comp2 = (ALPH_SYM_T*)rbtree_get(reader->merged, lookup);
+         }
+-        if (comp1 != comp2) {
++        if (comp1 && (comp1 != comp2)) {
+           add_msg(reader, parmsg_create(SEVERITY_ERROR, -1, -1, -1, 
+                 "not like %s alphabet as %c complement rules are incorrect",
+                 ext_name, req_syms[i]));
+--- a/src/mast-util.c
++++ b/src/mast-util.c
+@@ -740,14 +740,14 @@
+ 
+   // create the frequency array  
+   alph = xlate ? xlate_dest_alph(xlate) : alph;
+-  freq = allocate_array(alph_size_core(alph));
++  freq = allocate_array(alph_size_full(alph));
+   init_array(0, freq);
+ 
+   // count the number of letters of each type 
+   if (xlate) {
+     for (n=0; sequence[n]; n++) {
+       i = xlate_index(xlate, false, sequence+n);
+-      if (i > 0 && i < alph_size_core(alph)) incr_array_item(i, 1, freq);
++      if (i > 0 && i < alph_size_full(alph)) incr_array_item(i, 1, freq);
+     }
+   } else {
+     for (n=0; sequence[n]; n++) {
diff --git a/sci-biology/meme/meme-4.11.2_p2.ebuild b/sci-biology/meme/meme-4.11.2_p2.ebuild
new file mode 100644
index 000000000000..4eb826065500
--- /dev/null
+++ b/sci-biology/meme/meme-4.11.2_p2.ebuild
@@ -0,0 +1,111 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit autotools perl-functions python-single-r1 versionator
+
+MY_PV=$(get_version_component_range 1-3)
+MY_P=${PN}_${MY_PV}
+
+DESCRIPTION="The MEME/MAST system - Motif discovery and search"
+HOMEPAGE="http://meme-suite.org/tools/meme"
+SRC_URI="http://meme-suite.org/meme-software/${MY_PV}/${MY_P}.tar.gz"
+
+LICENSE="meme"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="debug doc examples mpi"
+
+RDEPEND="
+	${PYTHON_DEPS}
+	app-shells/tcsh
+	dev-libs/libxml2:2
+	dev-libs/libxslt
+	sys-libs/zlib
+	app-text/ghostscript-gpl
+	media-gfx/imagemagick
+	dev-lang/perl:=
+	dev-perl/HTML-Parser
+	dev-perl/HTML-Template
+	dev-perl/Log-Log4perl
+	dev-perl/Math-CDF
+	dev-perl/XML-Compile-SOAP
+	dev-perl/XML-Compile-WSDL11
+	dev-perl/XML-Parser
+	dev-perl/XML-Simple
+	virtual/perl-Data-Dumper
+	virtual/perl-Exporter
+	virtual/perl-File-Path
+	virtual/perl-File-Spec
+	virtual/perl-File-Temp
+	virtual/perl-Getopt-Long
+	virtual/perl-Scalar-List-Utils
+	virtual/perl-Time-HiRes
+	mpi? ( virtual/mpi )"
+DEPEND="${RDEPEND}"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+S="${WORKDIR}/${MY_P}"
+PATCHES=(
+	"${FILESDIR}"/${PN}-4.11.2_p2-patch1.patch
+	"${FILESDIR}"/${PN}-4.11.2_p2-patch2.patch
+	"${FILESDIR}"/${PN}-4.11.2_p2-fix-build-system.patch
+)
+
+pkg_setup() {
+	python-single-r1_pkg_setup
+	perl_set_version
+}
+
+src_prepare() {
+	default
+	eautoreconf
+}
+
+src_configure() {
+	econf \
+		--sysconfdir="${EPREFIX}"/etc/${PN} \
+		--with-logs="${EPREFIX}"/var/log/${PN} \
+		--with-perl=perl \
+		--with-convert=convert \
+		--with-gs=gs \
+		--disable-build-libxml2 \
+		--disable-build-libxslt \
+		$(use_enable debug) \
+		$(use_enable doc) \
+		$(use_enable examples) \
+		$(use_enable !mpi serial) \
+		--with-perl-dir="${VENDOR_LIB#${EPREFIX}/usr}" \
+		PYTHON="${EPYTHON}"
+
+	# delete bundled libs, just to be sure. These need
+	# to be removed after econf, else AC_OUTPUT will fail
+	rm -r src/{libxml2,lib{,e}xslt} || die
+}
+
+src_test() {
+	# bug #297070
+	emake -j1 test
+}
+
+src_install() {
+	default
+	docompress -x /usr/share/doc/${PF}/examples
+
+	# prefix all binaries with 'meme-', in order
+	# to prevent collisions, bug 455010
+	cd "${ED%/}"/usr/bin/ || die
+	local i
+	for i in *; do
+		if [[ $i != meme-* ]]; then
+			mv {,meme-}"${i}" || die
+		fi
+	done
+
+	diropts -m ugo+rwxt -o root
+	keepdir /var/log/meme
+}