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Adopts "git flow". This is an initial ur-commit on master. 

Merges 1.1 branch (f5feaab) into master. Updated release version to
1.1.1x, date to May 2016.

Changes to make it compile with new HMMER 3.1 master branch,
(h3-master) and Easel master branch (master):
- P7_MSVDATA => P7_SCOREDATA; p7_msvdata_*() => p7_scoredata_*().
- p7_MSVFilter_longtarget => SSV
- p7_domaindef_ByPosteriorHeuristics prototype changes; now has ntseq
  arg (pass NULL) and some trailing args (also pass NULL)
- p7_pli_ExtendAndMergeWindows() prototype change: remove <seqlen> arg
- p7_Builder() prototype change: adds two undocumented trailing args,
  pass NULL
- esl_sqio_ReadBlock() now takes max_residues and max_seqs args.
  CM_MAX_RESIDUE_COUNT for max_residues
- esl_composition_*() and esl_msaweight_*() calls require .h inclusion
- cm_tophits_RemoveOrMarkOverlaps adds do_clans arg; pass FALSE

revised how 'make check' copies easel miniapps. cp fails, because
files are identical; added if check for miniapps existing already.

in configure.ac, revised how the impl symlink is made. AC_CONFIG_LINKS
should not be used to link directories. Instead, do
AC_CONFIG_COMMANDS. (TODO: H3 configura.ac needs this too.)

Avoid zero mallocs; use ESL_MAX(1, size) as workaround. (cm_mx.c, cm_pipeline.c)

Fixed missing comma in --notrunc ESL_OPTIONS incomp list.

bug-i44.pl needed chmod +x
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2 parents be08dd7 + f5feaab commit a62a3809f30867ce9355fc79d336a8bba321e7fa @cryptogenomicon cryptogenomicon committed May 6, 2016
View
46 COPYRIGHT
@@ -0,0 +1,46 @@
+Infernal - inference of RNA secondary structural alignments
+@INFERNAL_COPYRIGHT@
+------------------------------------------------------------------
+
+Copyright (C) 2013 HHMI Janelia Farm Research Campus
+
+ Portions Copyright (C) 1991-2013 Sean R. Eddy
+ Portions Copyright (C) 2005-2013 Eric P. Nawrocki
+ Portions Copyright (C) 2005-2011 Diana L. Kolbe
+ Portions Copyright (C) 2004 Zasha Weinberg
+ Portions Copyright (C) 1990 Don G. Gilbert
+ Portions Copyright (C) 1995-2006 Washington University in St. Louis
+ Portions Copyright (C) 1992-1995 Medical Research Council, UK
+ Portions Copyright (C) 2004 University of Washington, Seattle
+ Portions Copyright (C) 1986,1993,1995 University of Toronto
+ Portions Copyright (C) 1989-2001 Free Software Foundation
+ Portions Copyright (C) 1991 Massachusetts Institute of Technology
+
+Infernal includes the HMMER software package, which has its own license and
+copyright information. See hmmer/COPYRIGHT and hmmer/LICENSE.
+
+Infernal uses the Easel software library, which has its own license and
+copyright information. See easel/COPYRIGHT and easel/LICENSE.
+
+Infernal is distributed under the terms of the GNU General Public
+License version 3 (GPLv3). See the file LICENSE for details.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or (at
+your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+A copy of the GNU General Public License is in the file LICENSE. You
+may also obtain a copy from <http://www.gnu.org/licenses/>.
+
+------------------------------------------------------------------
+The Infernal development team
+HHMI Janelia Farm Research Campus
+http://infernal.janelia.org/
+
+
View
8 Makefile.in
@@ -153,10 +153,10 @@ check:
${QUIET_SUBDIR0}${HMMERDIR} ${QUIET_SUBDIR1} tests
${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} tests
${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} check
- if test -d ${HMMERDIR}/easel; then cp ${ESLDIR}/miniapps/esl-afetch ${HMMERDIR}/easel/miniapps; fi
- if test -d ${HMMERDIR}/easel; then cp ${ESLDIR}/miniapps/esl-reformat ${HMMERDIR}/easel/miniapps; fi
- if test -d ${HMMERDIR}/easel; then cp ${ESLDIR}/miniapps/esl-sfetch ${HMMERDIR}/easel/miniapps; fi
- if test -d ${HMMERDIR}/easel; then cp ${ESLDIR}/miniapps/esl-shuffle ${HMMERDIR}/easel/miniapps; fi
+ if test -d ${HMMERDIR}/easel && ! test -e ${HMMERDIR}/easel/miniapps/esl-afetch; then cp ${ESLDIR}/miniapps/esl-afetch ${HMMERDIR}/easel/miniapps; fi
+ if test -d ${HMMERDIR}/easel && ! test -e ${HMMERDIR}/easel/miniapps/esl-reformat; then cp ${ESLDIR}/miniapps/esl-reformat ${HMMERDIR}/easel/miniapps; fi
+ if test -d ${HMMERDIR}/easel && ! test -e ${HMMERDIR}/easel/miniapps/esl-sfetch; then cp ${ESLDIR}/miniapps/esl-sfetch ${HMMERDIR}/easel/miniapps; fi
+ if test -d ${HMMERDIR}/easel && ! test -e ${HMMERDIR}/easel/miniapps/esl-sfetch; then cp ${ESLDIR}/miniapps/esl-shuffle ${HMMERDIR}/easel/miniapps; fi
if ! test -d ${HMMERDIR}/easel; then cd ${HMMERDIR}; @LN_S@ ../${ESLDIR} .; cd ..; fi
if ! test -d ${srcdir}/${HMMERDIR}/easel; then @LN_S@ ${srcdir}/${ESLDIR} ${srcdir}/${HMMERDIR}/easel; fi
${QUIET_SUBDIR0}${HMMERDIR}/testsuite ${QUIET_SUBDIR1} check
View
74 configure.ac
@@ -23,7 +23,7 @@
# w/ AC_CONFIG_HEADERS -- which means, easel.h.in
#
# SRE, Mon Oct 5 14:55:45 1998
-# SVN $Id$
+# SVN $Id: configure.ac 4708 2014-07-22 13:11:50Z nawrockie $
# xref autoconf macro archive: //www.gnu.org/software/ac-archive/
#
# GNU recommends the following order:
@@ -44,7 +44,7 @@
# Autoconf 2.61 has a bug in AC_FUNC_FSEEKO; don't use it.
AC_PREREQ(2.63)
-AC_INIT(Infernal, 1.1.1, nawrockie@janelia.hhmi.org, infernal)
+AC_INIT(Infernal, 1.1.1x, eric.nawrocki@nih.gov, infernal)
AC_MSG_NOTICE([Configuring Infernal for your system.])
# remember if the user is overriding CFLAGS
@@ -73,26 +73,26 @@ fi
#
################################################################
-INFERNAL_DATE="July 2014"
-INFERNAL_COPYRIGHT="Copyright (C) 2014 Howard Hughes Medical Institute."
-INFERNAL_LICENSE="Freely distributed under the GNU General Public License (GPLv3)."
+INFERNAL_DATE="May 2016"
+INFERNAL_COPYRIGHT="Copyright (C) 2016 Howard Hughes Medical Institute."
+INFERNAL_LICENSE="Freely distributed under a BSD open source license."
INFERNAL_VERSION=$PACKAGE_VERSION
INFERNAL_URL="http://infernal.janelia.org/"
INFERNAL_ESLDIR="easel"
INFERNAL_HMMERDIR="hmmer"
-INFERNAL_SADIR="hmmer/lib/libdivsufsort"
+INFERNAL_SADIR="hmmer/libdivsufsort"
-HMMER_DATE="July 2014"
-HMMER_COPYRIGHT="Copyright (C) 2014 Howard Hughes Medical Institute."
-HMMER_LICENSE="Freely distributed under the GNU General Public License (GPLv3)."
+HMMER_DATE="May 2016"
+HMMER_COPYRIGHT="Copyright (C) 2016 Howard Hughes Medical Institute."
+HMMER_LICENSE="Freely distributed under a BSD open source licence."
HMMER_VERSION=i$PACKAGE_VERSION
HMMER_URL="http://hmmer.org/"
HMMER_ESLDIR="../easel"
-HMMER_SADIR="lib/libdivsufsort"
+HMMER_SADIR="libdivsufsort"
EASEL_DATE="July 2014"
-EASEL_COPYRIGHT="Copyright (C) 2014 HHMI Janelia Farm Research Campus"
-EASEL_LICENSE="Freely distributed under the Janelia Software License."
+EASEL_COPYRIGHT="Copyright (C) 2016 Howard Hughes Medical Institute"
+EASEL_LICENSE="Freely distributed under a BSD open source license."
EASEL_VERSION="i$PACKAGE_VERSION"
EASEL_URL="http://bioeasel.org/"
@@ -697,37 +697,25 @@ AC_CONFIG_FILES([documentation/Makefile])
AC_CONFIG_FILES([documentation/manpages/Makefile])
AC_CONFIG_FILES([documentation/userguide/Makefile])
-# following from HMMER's configure.ac
-#################################################################
-AC_CONFIG_FILES([
- hmmer/documentation/Makefile
- hmmer/documentation/man/Makefile
- hmmer/documentation/userguide/Makefile
- hmmer/src/Makefile
- hmmer/src/Makefile-subdirs.mk
- hmmer/src/base/Makefile
- hmmer/src/build/Makefile
- hmmer/src/daemon/Makefile
- hmmer/src/dp_reference/Makefile
- hmmer/src/dp_sparse/Makefile
- hmmer/src/dp_vector/Makefile
- hmmer/src/experiments/Makefile
- hmmer/src/misc/Makefile
- hmmer/src/programs/Makefile
- hmmer/src/sandbox/Makefile
- hmmer/src/search/Makefile
- hmmer/src/utilities/Makefile
- hmmer/testsuite/Makefile
- hmmer/benchmarks/Makefile
- hmmer/benchmarks/profmark/Makefile
- hmmer/benchmarks/speed/Makefile
- hmmer/lib/libdivsufsort/Makefile
-])
-
-AC_CONFIG_HEADERS([
- hmmer/src/p7_config.h
- hmmer/lib/libdivsufsort/divsufsort.h
-])
+# HMMER files
+AC_CONFIG_FILES([hmmer/documentation/Makefile])
+AC_CONFIG_FILES([hmmer/documentation/man/Makefile])
+AC_CONFIG_FILES([hmmer/documentation/userguide/Makefile])
+AC_CONFIG_FILES([hmmer/src/Makefile hmmer/testsuite/Makefile hmmer/profmark/Makefile])
+AC_CONFIG_FILES([hmmer/src/impl_${impl_choice}/Makefile])
+AC_CONFIG_FILES([hmmer/libdivsufsort/Makefile])
+AC_CONFIG_HEADERS(hmmer/src/p7_config.h)
+AC_CONFIG_HEADERS(hmmer/libdivsufsort/divsufsort.h)
+
+# the following incantation establishes a symlink of
+# src/impl_{whatever} to src/impl in the *build* directory.
+# Testsuite sqc tests rely on it.
+# You can't use AC_CONFIG_LINKS, apparently, because it is only
+# designed to link files, not directories.
+# PORTABILITY: Beware: we're using a naked ln -sf here, which some systems may not support!
+AC_CONFIG_COMMANDS([hmmer/src/impl],
+ [cd hmmer/src; ln -sf impl_${impl_choice} impl],
+ [ac_top_build_prefix=${ac_top_build_prefix}; impl_choice=${impl_choice}])
# Finally, build the top-level HMMER makefile (note: this is *not* built by HMMER's configure)
AC_CONFIG_FILES([hmmer/Makefile])
View
1 documentation/userguide/cmbuild.tex
@@ -595,3 +595,4 @@ \subsubsection{Saving the model}
\prog{-F} option causes the new model to overwrite an existing
cmfile.
+
View
1 documentation/userguide/formats.tex
@@ -1331,3 +1331,4 @@ \subsection{Null model file format}
+
View
1 documentation/userguide/install.tex
@@ -5,7 +5,6 @@ \section{Installation}
\subsection{Quick installation instructions}
Download \prog{infernal-1.1.1.tar.gz} from \url{http://infernal.janelia.org/}, or
-
directly from
\url{ftp://selab.janelia.org/pub/software/infernal/infernal-1.1.1.tar.gz};
unpack it, configure, and make:
View
1 documentation/userguide/main.tex
@@ -2,6 +2,7 @@
%
% SVN $Id$
+
\documentclass[10pt]{article}
%\usepackage{helvetic}
\usepackage{times}
View
1 documentation/userguide/more.tex
@@ -201,3 +201,4 @@ \subsubsection{Reading from a stdin pipe using - (dash) as a filename argument}
can't read from pipes.
+
View
1 documentation/userguide/pipeline.tex
@@ -1437,3 +1437,4 @@ \subsection{HMM-only pipeline variant for models without structure}
turned off with the \ccode{--nohmmonly} option. When turned off, all
models will use the standard and truncated CM pipelines, even those
with no structure.
+
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