Merge branch 'release-3.4'

EddyRivasLab · Aug 15, 2023 · 9acd8b6 · 9acd8b6
2 parents 03bf3c7 + a2f4db2
commit 9acd8b6
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Showing 178 changed files with 16,227 additions and 2,623 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,8 +1,10 @@
+build-*
 configure
 config.log
 config.status
 Makefile
 easel
+/TAGS
 *.o
 *.dSYM
 *.stamp

diff --git a/INSTALL b/INSTALL
@@ -1,10 +1,10 @@
 Brief installation instructions 
-HMMER 3.3.2 (Nov 2020)
+HMMER 3.4 (Aug 2023)
 
-Starting from a source distribution, hmmer-3.3.2.tar.gz:
-   uncompress hmmer-3.3.2.tar.gz  
-   tar xf hmmer-3.3.2.tar
-   cd hmmer-3.3.2
+Starting from a source distribution, hmmer-3.4.tar.gz:
+   uncompress hmmer-3.4.tar.gz  
+   tar xf hmmer-3.4.tar
+   cd hmmer-3.4
    ./configure
    make
    make check                        # optional: automated tests

diff --git a/LICENSE b/LICENSE
@@ -1,9 +1,9 @@
 HMMER - Biological sequence analysis with profile hidden Markov models
-Copyright (C) 1992-2020 Sean R. Eddy
-Copyright (C) 2000-2020 Howard Hughes Medical Institute
-Copyright (C) 2015-2020 President and Fellows of Harvard College
-Copyright (C) 1992-2004 Washington University School of Medicine
-Copyright (C) 1992-1994 MRC Laboratory of Molecular Biology
+Copyright (C) 1992-2023 Sean R. Eddy
+Copyright (C) 2015-2023 President and Fellows of Harvard College
+Copyright (C) 2000-2023 Howard Hughes Medical Institute
+Copyright (C) 1995-2006 Washington University School of Medicine
+Copyright (C) 1992-1995 MRC Laboratory of Molecular Biology
 -----------------------------------------------------------------------
 
 The code includes contributions and input from current and past
@@ -21,10 +21,12 @@ sources, including:
    Ian Holmes        
    Bjarne Knudsen    
    Diana Kolbe       
+   Martin Larralde
    Erik Lindahl      
    Graeme Mitchison  
    Eric Nawrocki     
    Lee Newberg       
+   Sam Petti
    Elena Rivas        
    Walt Shands  
    Travis Wheeler    

diff --git a/Makefile.in b/Makefile.in
@@ -1,5 +1,5 @@
 # Top level Makefile for HMMER3
-# 
+#
 # On most systems, to build H3 you should only need:
 #     % ./configure; make
 #
@@ -54,23 +54,24 @@ man1ext     = .1
 # Compiler configuration
 #
 CC             = @CC@
-CFLAGS         = @CFLAGS@ 
-PTHREAD_CFLAGS = @PTHREAD_CFLAGS@ 
+CFLAGS         = @CFLAGS@
+PTHREAD_CFLAGS = @PTHREAD_CFLAGS@
+NEON_CFLAGS    = @NEON_CFLAGS@
 SSE_CFLAGS     = @SSE_CFLAGS@
 VMX_CFLAGS     = @VMX_CFLAGS@
 LDFLAGS        = -static @LDFLAGS@
 CPPFLAGS       = @CPPFLAGS@
 
 # Other tools
 #
-AR        = @AR@ 
+AR        = @AR@
 RANLIB    = @RANLIB@
 INSTALL   = @INSTALL@
 
-# beautification magic stolen from git 
+# beautification magic stolen from git
 #
 QUIET_SUBDIR0 = +${MAKE} -C #space separator after -c
-QUIET_SUBDIR1 = 
+QUIET_SUBDIR1 =
 ifndef V
 	QUIET         = @
 	QUIET_CC      = @echo '    ' CC $@;
@@ -86,15 +87,15 @@ endif
 # all: Compile all documented executables.
 #      (Excludes test programs.)
 #
-all: 
+all:
 	${QUIET_SUBDIR0}${ESLDIR}     ${QUIET_SUBDIR1} all
 	${QUIET_SUBDIR0}${SADIR}      ${QUIET_SUBDIR1} all
 	${QUIET_SUBDIR0}src           ${QUIET_SUBDIR1} all
 	${QUIET_SUBDIR0}profmark      ${QUIET_SUBDIR1} all
 
 # dev: compile all executables, including drivers.
 #
-dev: 
+dev:
 	${QUIET_SUBDIR0}${ESLDIR}  ${QUIET_SUBDIR1} dev
 	${QUIET_SUBDIR0}${SADIR}   ${QUIET_SUBDIR1} all
 	${QUIET_SUBDIR0}src        ${QUIET_SUBDIR1} dev
@@ -111,7 +112,7 @@ tests:
 check:
 	@command -v python3 >/dev/null 2>&1 || { echo >&2 "python3 is required for 'make check', but is not in your PATH. Aborting."; exit 1; }
 	${QUIET_SUBDIR0}${ESLDIR}  ${QUIET_SUBDIR1} tests
-	${QUIET_SUBDIR0}${SADIR}   ${QUIET_SUBDIR1} all	
+	${QUIET_SUBDIR0}${SADIR}   ${QUIET_SUBDIR1} all
 	${QUIET_SUBDIR0}src        ${QUIET_SUBDIR1} tests
 	${QUIET_SUBDIR0}${ESLDIR}  ${QUIET_SUBDIR1} check
 	${QUIET_SUBDIR0}testsuite  ${QUIET_SUBDIR1} check
@@ -130,22 +131,22 @@ pdf:
 #
 #          Does not use quiet beautification magic; always verbose.
 install: all
-	${INSTALL} -d ${DESTDIR}${bindir}
-	${INSTALL} -d ${DESTDIR}${man1dir}
+	if [ ! -d ${DESTDIR}${bindir} ]; then ${INSTALL} -d ${DESTDIR}${bindir}; fi
+	if [ ! -d ${DESTDIR}${man1dir} ]; then ${INSTALL} -d ${DESTDIR}${man1dir}; fi
 	${MAKE} -C src install
 	${MAKE} -C documentation install
 
 # install-strip: same as install, but strip binaries
 #
 install-strip: all
-	${INSTALL} -d ${DESTDIR}${bindir}
-	${INSTALL} -d ${DESTDIR}${man1dir}
+	if [ ! -d ${DESTDIR}${bindir} ]; then ${INSTALL} -d ${DESTDIR}${bindir}; fi
+	if [ ! -d ${DESTDIR}${man1dir} ]; then ${INSTALL} -d ${DESTDIR}${man1dir}; fi
 	${MAKE} -C src install-strip
 	${MAKE} -C documentation install
 
 # uninstall: reverses the steps of "make install".
 #
-uninstall: 
+uninstall:
 	${MAKE} -C src uninstall
 	${MAKE} -C documentation uninstall
 
@@ -172,7 +173,7 @@ distclean:
 	${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} distclean
 	${QUIET_SUBDIR0}${ESLDIR}     ${QUIET_SUBDIR1} distclean
 	${QUIET_SUBDIR0}${SADIR}      ${QUIET_SUBDIR1} distclean
-	${QUIET}-rm config.log config.status
+	${QUIET}-rm -f config.log config.status
 	${QUIET}-rm -rf autom4te.cache
 	${QUIET}-rm -f *.o *~ Makefile.bak core TAGS TAGS.part gmon.out
 	${QUIET}-rm -f cscope.po.out cscope.out cscope.in.out cscope.files
@@ -184,6 +185,3 @@ endif
 
 TAGS:
 	./makeTAGS.sh
-
-
-
diff --git a/README.md b/README.md
@@ -1,21 +1,20 @@
 ## HMMER - biological sequence analysis using profile HMMs
 
-[![](https://travis-ci.org/EddyRivasLab/hmmer.svg?branch=develop)](https://travis-ci.org/EddyRivasLab/hmmer)
 ![](http://img.shields.io/badge/license-BSD-brightgreen.svg)
 
 [HMMER](http://hmmer.org) searches biological sequence databases for
 homologous sequences, using either single sequences or multiple
 sequence alignments as queries. HMMER implements a technology called
 "profile hidden Markov models" (profile HMMs). HMMER is used by many
 protein family domain databases and large-scale annotation pipelines,
-including [Pfam](http://pfam.xfam.org) and other members of the
-[InterPro Consortium](http://www.ebi.ac.uk/interpro/).
+including many members of the
+[InterPro Consortium](http://ebi.ac.uk/interpro/).
 
-To obtain HMMER releases, please visit [hmmer.org](http://hmmer.org).
+To obtain HMMER releases, visit [hmmer.org](http://hmmer.org).
 
 To participate in HMMER development, visit us at
 [github](https://github.com/EddyRivasLab/hmmer).  HMMER development
-depends on the Easel library, also at
+also depends on the lab's Easel library, at
 [github](https://github.com/EddyRivasLab/easel).
 
 
@@ -24,12 +23,12 @@ depends on the Easel library, also at
 ```
    % wget http://eddylab.org/software/hmmer/hmmer.tar.gz
    % tar zxf hmmer.tar.gz
-   % cd hmmer-3.3.2
-   % ./configure --prefix /your/install/path
+   % cd hmmer-3.4
+   % ./configure --prefix /your/install/path   # replace /your/install/path with what you want, obv 
    % make
-   % make check                 # optional: run automated tests
-   % make install               # optional: install HMMER programs, man pages
-   % (cd easel; make install)   # optional: install Easel tools
+   % make check                                # optional: run automated tests
+   % make install                              # optional: install HMMER programs, man pages
+   % (cd easel; make install)                  # optional: install Easel tools
 ``` 
 
 Executable programs will be installed in `/your/install/path/bin`. If
@@ -40,7 +39,7 @@ Files to read in the source directory:
 
    * INSTALL - brief installation instructions.
    * Userguide.pdf - the HMMER User's Guide.
- 
+
 To get started after installation, see the Tutorial section in the
 HMMER User's Guide (Userguide.pdf).
 
@@ -86,4 +85,3 @@ to send us a pull request on GitHub, please base your changes on our
 
 Visit our
 [issues tracking page at github](https://github.com/EddyRivasLab/hmmer/issues).
-