autobuild/, release-notes/00CHECKLIST, documentation/

Identical changes as those made in trunk with revision 4135. I
realized after that commit that I should be making changes in the 1.1
release branch, then merging them to the trunk (as per 00CHECKLIST). 

release-notes/LICENSE.tag: another oversight in the 1.1rc1 - this was
identical to HMMER's LICENSE.tag (I had changed it in a working
directory, but never committed it!) So 1.1rc1 files have HMMER's
license instead of Infernal's. Ughh.


git-svn-id: https://svn.janelia.org/eddylab/eddys/src/infernal/branches/1.1@4136 db3e70e4-12e1-0310-b23f-81a6e3d09ba7

autobuild/infernal_autobuilds.pl

@@ -25,8 +25,8 @@
 # First we update in the source working directory.
 #
 chdir $srcdir ||    die "FAIL: couldn't cd to $srcdir"; 
-system("$svn update > autobuilds.log 2>&1");             if ($?) { die "FAIL: svn update"; }
-system("$autoconf  > autobuilds.log 2>&1 ");            if ($?) { die "FAIL: H3 $autoconf"; }
+system("$svn update > autobuilds.log 2>&1");            if ($?) { die "FAIL: svn update"; }
+system("$autoconf  > autobuilds.log 2>&1 ");            if ($?) { die "FAIL: inf $autoconf"; }
 system("(cd easel; $autoconf) > autobuilds.log 2>&1");  if ($?) { die "FAIL: esl $autoconf"; }
 
 # Then we try to build on everything

documentation/userguide/install.tex

@@ -4,14 +4,14 @@ \section{Installation}
 
 \subsection{Quick installation instructions}
 
-Download \prog{infernal-1.1.tar.gz} from \url{http://infernal.janelia.org/}, or
+Download \prog{infernal-1.1rc1.tar.gz} from \url{http://infernal.janelia.org/}, or
 directly from
-\url{ftp://selab.janelia.org/pub/software/infernal/infernal-1.1.tar.gz};
+\url{ftp://selab.janelia.org/pub/software/infernal/infernal-1.1rc1.tar.gz};
 unpack it, configure, and make:
 
-\user{wget ftp://selab.janelia.org/pub/software/infernal/infernal-1.1.tar.gz}\\
-\user{tar xf infernal-1.1.tar.gz}\\
-\user{cd infernal-1.1}\\
+\user{wget ftp://selab.janelia.org/pub/software/infernal/infernal-1.1rc1.tar.gz}\\
+\user{tar xf infernal-1.1rc1.tar.gz}\\
+\user{cd infernal-1.1rc1}\\
 \user{./configure}\\ 
 \user{make}
 

documentation/userguide/tutorial.tex

@@ -199,12 +199,12 @@ \subsubsection{Step 1: build a covariance model with cmbuild}
 
 \begin{sreoutput}
 # cmbuild :: covariance model construction from multiple sequence alignments
-# INFERNAL 1.1 (June 2012)
+# INFERNAL 1.1rc1 (June 2012)
 # Copyright (C) 2012 Howard Hughes Medical Institute.
 # Freely distributed under the GNU General Public License (GPLv3).
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 # CM file:                                            tRNA5.cm
-# alignment file:                                     ../tutorial/tRNA5.sto
+# alignment file:                                     tutorial/tRNA5.sto
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 #                                                                      rel entropy
 #                                                                      -----------
@@ -284,7 +284,7 @@ \subsubsection{Step 2: calibrate the model with cmcalibrate}
 
 \begin{sreoutput}
 # cmcalibrate :: fit exponential tails for CM E-values
-# INFERNAL 1.1 (June 2012)
+# INFERNAL 1.1rc1 (June 2012)
 # Copyright (C) 2012 Howard Hughes Medical Institute.
 # Freely distributed under the GNU General Public License (GPLv3).
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@@ -339,20 +339,19 @@ \subsubsection{Step 3: search a sequence database with cmsearch}
 
 \begin{sreoutput}
 # cmsearch :: search CM(s) against a sequence database
-# INFERNAL 1.1 (June 2012)
+# INFERNAL 1.1rc1 (June 2012)
 # Copyright (C) 2012 Howard Hughes Medical Institute.
 # Freely distributed under the GNU General Public License (GPLv3).
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 # query CM file:                         tRNA5.cm
-# target sequence database:              ../tutorial/mrum-genome.fa
+# target sequence database:              tutorial/mrum-genome.fa
 # number of worker threads:              2
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 \end{sreoutput}
 
 The second section is a list of ranked top hits (sorted by E-value,
 most significant hit first):
 
-% tutorial regression: tRNA5-search.out
 \begin{sreoutput}
  rank     E-value  score  bias  sequence      start     end   mdl trunc   gc  description
  ----   --------- ------ -----  ----------- ------- -------   --- ----- ----  -----------
@@ -795,7 +794,7 @@ \subsubsection{Step 3: search a sequence database with cmsearch}
 described above. In this search there were 56 such hits.
 
 Finally, the running time of the search is reported, in CPU time and
-elapsed time. This search took about 1.4 seconds of elapsed (wall
+elapsed time. This search took about 1.8 seconds of elapsed (wall
 %                                    ^^^
 clock time) (running on two cores). 
 
@@ -939,7 +938,7 @@ \subsubsection{Step 3: search the CM database with cmscan}
 
 \begin{sreoutput}
 # cmscan :: search sequence(s) against a CM database
-# INFERNAL 1.1 (June 2012)
+# INFERNAL 1.1rc1 (June 2012)
 # Copyright (C) 2012 Howard Hughes Medical Institute.
 # Freely distributed under the GNU General Public License (GPLv3).
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@@ -1032,6 +1031,7 @@ \subsubsection{Step 3: search the CM database with cmscan}
 %        ^^^^
 examined. The next line reports that the average number of residues
 re-searched for truncated hits per model was 992.0. An average is
+%                                            ^^^^^
 reported here because remember the number of residues re-searched per
 model depends on the expected maximum size of a hit, which varies per
 model, because only sequence terminii are examined for truncated hits
@@ -1165,7 +1165,7 @@ \subsection{Creating multiple alignments with cmalign}
 
 \begin{tinysreoutput}
 # STOCKHOLM 1.0
-#=GF AU Infernal 1.1
+#=GF AU Infernal 1.1rc1
 
 mrum-tRNA.1          GGAGCUAUAGCUCAAU..GGC..AGAGCGUUUGGCUGACAU........................................CCAAAAGGUUAUGGGUUCGAUUCCCUUUAGCCCCA
 #=GR mrum-tRNA.1  PP ****************..***..******************........................................***********************************
@@ -1294,7 +1294,7 @@ \subsubsection{cmalign assumes sequences may be truncated}
 \label{cmalign-cobalamin}
 \begin{sreoutput}
 # STOCKHOLM 1.0
-#=GF AU Infernal 1.1
+#=GF AU Infernal 1.1rc1
 
 Cobalamin.1         -------------------------------GUAGGCAAAAGGAAGAGGAAGgAUGGUGGAAAUCCUUCACGGGCCCGGCCA
 #=GR Cobalamin.1 PP ...............................44455566666899******989****************************
@@ -1393,7 +1393,7 @@ \subsection{Searching a sequence database for RNAs with unknown or no
 
 \begin{sreoutput}
 # cmbuild :: covariance model construction from multiple sequence alignments
-# INFERNAL 1.1 (June 2012)
+# INFERNAL 1.1rc1 (June 2012)
 # Copyright (C) 2012 Howard Hughes Medical Institute.
 # Freely distributed under the GNU General Public License (GPLv3).
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@@ -1651,11 +1651,11 @@ \subsection{Specifying and annotating match positions with cmbuild --hand}
 
 To build the hand-specified model from this alignment, do:
 
-\user{cmbuild --hand tRNA5-hand.cm tutorial/tRNA5.hand.sto}
+\user{cmbuild --hand tRNA5-hand.cm tutorial/tRNA5-hand.sto}
 
 \begin{sreoutput}
 # cmbuild :: covariance model construction from multiple sequence alignments
-# INFERNAL 1.1 (June 2012)
+# INFERNAL 1.1rc1 (June 2012)
 # Copyright (C) 2012 Howard Hughes Medical Institute.
 # Freely distributed under the GNU General Public License (GPLv3).
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -