Userguide is ready for 1.1.2 release.

Bugs/BUGTRAX

@@ -1342,6 +1342,9 @@ an optimally accurate parsetree, if it's not a legal local begin
 state, then don't allow a local begin.
 
 //
+#### 
+####  1.1.1 release: 23 July 2014
+####
 
 ID              i44
 TITLE		cmalign --mapstr allows broken basepairs
@@ -1374,3 +1377,6 @@ checks that both a broken non-pseudoknotted basepair and a
 pseudoknotted broken basepair are both correctly removed.
 
 //
+#### 
+####  1.1.2 release: June 2014
+####

LICENSE

@@ -1,6 +1,6 @@
 Infernal - inference of RNA secondary structural alignments
 @INFERNAL_COPYRIGHT@
-Copyright (C) 1991-2013      Sean R. Eddy
+Copyright (C) 1991-2016      Sean R. Eddy
 Copyright (C) 2005-2016      Eric P. Nawrocki
 Copyright (C) 2005-2011      Diana L. Kolbe
 Copyright (C) 2004           Zasha Weinberg

documentation/manpages/cmscan.man

@@ -68,8 +68,8 @@ option saves output in a simple tabular format that is concise and
 easier to parse. The
 .BI --fmt " 2"
 option modifies the format of the tabular output by adding several
-fields, including markup of overlapping hits, as described in the
-Infernal user guide. 
+fields, including markup of overlapping hits, as described in section
+6 of the Infernal user guide. 
 The 
 .B -o
 option allows redirecting the main output, including throwing it away
@@ -176,7 +176,7 @@ instead of the default stdout.
 .BI --tblout " <f>"
 Save a simple tabular (space-delimited) file summarizing the
 hits found, with one data line per hit. 
-The format of this file is described in the Infernal user guide.
+The format of this file is described in section 6 of the Infernal user guide.
 
 .TP 
 .BI --fmt " <n>"
@@ -196,7 +196,7 @@ With
 .BI --fmt " 2"
 nine additional fields are added to the tabular output file, most of
 which pertain to the annotation of overlapping hits. 
-See the Infernal user guide for a description of both formats.
+See section 6 the Infernal user guide for a description of both formats.
 
 .TP 
 .B --acc
@@ -726,7 +726,7 @@ and
 .B --tblout
 because clan annotation is only output in format 2 of the tabular
 output file. 
-See the Infernal user guide for specifications on the format of the 
+See section 9 of the Infernal user guide for specifications on the format of the 
 clan input file
 .I <f>.
 

documentation/manpages/cmsearch.man

@@ -167,7 +167,7 @@ to the file
 .BI --tblout " <f>"
 Save a simple tabular (space-delimited) file summarizing the
 hits found, with one data line per hit. The format of this file is
-described in the Infernal user guide.
+described in section 6 of the Infernal user guide.
 
 .TP 
 .B --acc

documentation/userguide/Makefile.in

@@ -41,6 +41,7 @@ MANPAGES = \
 
 TEXFILES =\
 	cmbuild.tex\
+	copyright.tex\
 	filter.tex\
 	format_prior.tex\
 	formats.tex\
@@ -57,7 +58,7 @@ TEXFILES =\
 
 pdf:    Userguide.pdf
 
-Userguide.pdf: symlinks.stamp titlepage.tex copyright.tex manpages.tex
+Userguide.pdf: symlinks.stamp titlepage.tex manpages.tex
 	@for prog in pdflatex bibtex; do \
 	  command -v $$prog >/dev/null 2>&1 || { echo >&2 "The $$prog program is required to build the Userguide, but it's not installed. Aborting."; exit 1; } \
 	done
@@ -83,10 +84,6 @@ titlepage.tex: ${srcdir}/titlepage.tex.in
 	@cp -f ${srcdir}/titlepage.tex.in titlepage.tex
 	@${SEDITION} INFERNAL_VERSION ${INFERNAL_VERSION} INFERNAL_DATE ${INFERNAL_DATE} titlepage.tex
 
-copyright.tex: ${srcdir}/copyright.tex.in
-	@cp -f ${srcdir}/copyright.tex.in copyright.tex
-	@${SEDITION} INFERNAL_COPYRIGHT ${INFERNAL_COPYRIGHT} copyright.tex
-
 # manpages: convert man pages to LaTeX chapter in User Guide.
 #    uses PolyglotMan 3.2 "rman", and rmanprocess.pl script in easel's devkit
 manpages.tex: ${MANPAGES}
@@ -114,7 +111,7 @@ distclean: clean
 	   done ;\
 	fi
 	-rm -f symlinks.stamp
-	-rm -f titlepage.tex copyright.tex manpages.tex
+	-rm -f titlepage.tex manpages.tex
 	-rm -f Userguide.pdf
 	-rm -f Makefile
 

documentation/userguide/ack.tex

@@ -34,9 +34,8 @@ \section{Acknowledgements}
 
 Infernal testing requires \emph{a lot} of compute power, and we are
 extremely fortunate to have access to a highly reliable and
-state-of-the-art computing cluster, thanks to Goran Ceric, Rob Lines,
-Peter Bukowinski, Ken Carlile, Patrick Yeboah, and others here at
-Janelia.
+state-of-the-art computing cluster, thanks to Jesse Becker, Ron
+Patterson and others at NCBI.
 
 Infernal is primarily developed on GNU/Linux and Apple Macintosh
 machines, but is tested on a variety of hardware. Over the years,

documentation/userguide/cmbuild.tex

@@ -524,9 +524,7 @@ \subsubsection{Architecture construction}
 an insertion. Importantly though this frequency is determined using
 the relative weights from the sequence weighting step, instead of
 absolute gaps (e.g. a residue in a sequence with weight $0.8$ will count
-as $0.8$ residues)\footnote{This behavior is new in Infernal 1.1, in all
-previous versions of Infernal, absolute weights, not relative weights
-were used at this step.}.
+ as $0.8$ residues).
 
 The threshold defaults to 0.5. It can be changed to another number
 \otext{<x>} (from 0 to 1.0) by the \prog{--symfrac <x>} option.  The

documentation/userguide/copyright.tex.in

@@ -1,18 +0,0 @@
-\vspace*{\fill}
-\begin{flushleft}
-@INFERNAL_COPYRIGHT@\vspace{5mm}
-
-\vspace{5mm}
-Permission is granted to make and distribute verbatim copies of this
-manual provided the copyright notice and this permission notice are
-retained on all copies.\vspace{5mm}
-
-\vspace{5mm} Infernal is licensed and freely distributed under the GNU
-General Public License version 3 (GPLv3). For a copy of the License,
-see \url{http://www.gnu.org/licenses/}.
-
-\vspace{5mm}
-\end{flushleft}
-
-
-

documentation/userguide/formats.tex

@@ -129,9 +129,6 @@ \subsection{Infernal CM files}
 The CM format is described in more detail below, followed by a
 description of the HMMER3 HMM format for the CM's mandatory filter HMM
 filter.
-%The HMM format is similar but is not described in detail here. See the
-%HMMER user guide for more information
-%(\url{http://hmmer.janelia.org}{http://hmmer.janelia.org}).
 
 \subsubsection{CM header section}
 

documentation/userguide/install.tex

@@ -4,14 +4,14 @@ \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};
+Download \prog{infernal-1.1.2.tar.gz} from \url{http://eddylab.org/infernal/}, or
+directly from \\
+\url{eddylab.org/infernal/infernal-1.1.2.tar.gz};
 unpack it, configure, and make:
 
-\user{wget ftp://selab.janelia.org/pub/software/infernal/infernal-1.1.1.tar.gz}\\
-\user{tar xf infernal-1.1.1.tar.gz}\\
-\user{cd infernal-1.1.1}\\
+\user{wget eddylab.org/infernal/infernal-1.1.2.tar.gz}\\
+\user{tar xf infernal-1.1.2.tar.gz}\\
+\user{cd infernal-1.1.2}\\
 \user{./configure}\\ 
 \user{make}
 
@@ -77,9 +77,11 @@ \subsection{System requirements}
 
 \paragraph{Compiler:} The source code is C conforming to POSIX and ANSI
 C99 standards. It should compile with any ANSI C99 compliant compiler,
-including the GNU C compiler \prog{gcc}. We test the code using both
-the \prog{gcc} and \prog{icc} compilers. We find that \prog{icc}
-produces somewhat faster code at present.
+including the GNU C compiler \prog{gcc}. 
+% as of 1.1.2, I don't test on icc anymore:
+%We test the code using both
+%the \prog{gcc} and \prog{icc} compilers. We find that \prog{icc}
+%produces somewhat faster code at present.
 
 \paragraph{Libraries and other installation requirements:} Infernal includes
 two software libraries, HMMER and Easel, which it will automatically
@@ -134,8 +136,7 @@ \subsection{MPI parallelization for clusters is optional}
 The \prog{cmalign}, \prog{cmcalibrate}, \prog{cmsearch} and
 \prog{cmscan} programs also support MPI (Message Passing Interface)
 parallelization on clusters.  To use MPI, you first need to have an
-MPI library installed, such as OpenMPI (\url{www.open-mpi.org}). We
-use Intel MPI at Janelia.
+MPI library installed, such as OpenMPI (\url{www.open-mpi.org}). 
 
 MPI support is not enabled by default, and it is not compiled into the
 precompiled binaries that we supply with Infernal. To enable MPI support

documentation/userguide/introduction.tex

@@ -8,7 +8,7 @@ \section{Introduction}
 structurally annotated multiple sequence alignment of an RNA family
 with a position-specific scoring system for substitutions, insertions,
 and deletions. Positions in the profile that are basepaired in the
-consensus secondary structure of the alignment are modeled as
+  h consensus secondary structure of the alignment are modeled as
 dependent on one another, allowing Infernal's scoring system to
 consider the secondary structure, in addition to the primary sequence,
 of the family being modeled. Infernal profiles are probabilistic
@@ -239,7 +239,7 @@ \subsection{How to learn more about CMs and profile HMMs}
 book chapters \citep{Eddy06b,NawrockiEddy09}, and a few doctoral
 theses \citep{Klein03,Nawrocki09b,Kolbe10} related to
 CMs\footnote{Eddy lab publications are available from
-\url{http://selab.janelia.org/publications.html}}. The book
+\url{http://eddylab.org/publications.html}}. The book
 \emph{Biological Sequence Analysis: Probabilistic Models of Proteins
 and Nucleic Acids} \citep{Durbin98} has several chapters devoted to
 HMMs and CMs. Profile HMM filtering for CMs was introduced by Weinberg
@@ -269,7 +269,7 @@ \subsection{How to learn more about CMs and profile HMMs}
 searches, EP Nawrocki and SR Eddy. Bioinformatics, 29:2933-2935,
 2013.) is the most appropriate paper to cite. If you’re writing for an
 enlightened (url-friendly) journal, you may want to cite the webpage
-\url{infernal.janelia.org} because it is kept up-to-date.
+\url{http://eddylab.org/infernal/} because it is kept up-to-date.
 \end{srefaq}
 
 

documentation/userguide/main.tex

@@ -47,7 +47,7 @@
 \newpage
 \input{tabular}
 
-% Changes in options between 1.0 and 1.1 are omitted from the 1.2 user guide.
+% Changes in options between 1.0 and 1.1 are omitted from the 1.1.2 user guide.
 %\newpage
 %\input{diffoptions}
 

documentation/userguide/more.tex

@@ -12,28 +12,28 @@ \subsection{How do I cite Infernal?}
 Bioinformatics, 29:2933-2935, 2013.
 
 The most appropriate citation is to the web site,
-\url{infernal.janelia.org}. You should also cite what version of the
-software you used. We archive all old versions, so anyone should be
-able to obtain the version you used, when exact reproducibility of an
-analysis is an issue.
+\url{http://eddylab.org/infernal/}. You should also cite what version
+of the software you used. We archive all old versions, so anyone
+should be able to obtain the version you used, when exact
+reproducibility of an analysis is an issue.
 
 The version number is in the header of most output files. To see it
 quickly, do something like \prog{cmscan -h} to get a help page, and
 the header will say:
 
 \begin{sreoutput}
 # cmscan :: search sequence(s) against a CM database
-# INFERNAL 1.1.1 (July 2014)
-# Copyright (C) 2014 Howard Hughes Medical Institute.
-# Freely distributed under the GNU General Public License (GPLv3).
+# INFERNAL 1.1.2 (June 2016)
+# Copyright (C) 2016 Howard Hughes Medical Institute.
+# Freely distributed under a BSD open source license.
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 \end{sreoutput}
 
-So (from the second line there) this is from Infernal 1.1.1.
+So (from the second line there) this is from Infernal 1.1.2.
 
 \subsection{How do I report a bug?}
 
-Email us, at \url{infernal@janelia.hhmi.org}.
+Email us, at \url{sean@eddylab.org}.
 
 Before we can see what needs fixing, we almost always need to
 reproduce a bug on one of our machines. This means we want to have a

documentation/userguide/tabular.tex

@@ -9,7 +9,7 @@ \subsection{Target hits tables}
 different formats of target hits table, which are both described
 below. By default, both \prog{cmsearch} and \prog{cmscan} produce the
 target hits table in \emph{format 1}. Format 1 is the only format that
-was used by Infernal versions 1.1rc1 through 1.1.1. As of version 1.2,
+was used by Infernal versions 1.1rc1 through 1.1.1. As of version 1.1.2,
 with \prog{cmscan}, the \ccode{--fmt 2} option can be used in
 combination with \ccode{--tblout} to produce a target hits table in
 the alternative \emph{format 2}.  Both formats 1 and 2 target hits

documentation/userguide/titlepage.tex.in

@@ -18,11 +18,9 @@ Version @INFERNAL_VERSION@; @INFERNAL_DATE@ \\
 \vspace*{\fill}
 
 Eric Nawrocki and Sean Eddy\\
-for the INFERNAL Development Team\\
-Janelia Farm Research Campus\\
-19700 Helix Drive\\
-Ashburn VA 20147 USA\\
-\url{http://eddylab.org/} \\
+for the INFERNAL development team\\
+\url{github.com/EddyRivasLab/infernal/}
+\url{http://eddylab.org/infernal}
 \end{center}
 
 \vspace*{\fill}