HISTORY.TXT

+List of changes from version 3.3 to 3.3.1 (until May 8th, 2018)
+     - new species pisaster (Pisaster ochraceus, ochre starfish)
+     - bugfixes of sampling error in intron model and in check of
+       frame-compatibility of CDSpart hints without frame
+     - new auxiliary program utrrnaseq to find training UTRs
+     - new script setStopCodonFreqs.pl
 List of changes from version 3.2.3 to 3.3 (until July 11th, 2017)
      - new program ESPOCA to estimate selective pressure on codon alignments
      - gene finding on ancestral genomes is enabled

Makefile

@@ -32,6 +32,8 @@ release:
 	rm -f src/makedepend.pl
 	rm -r augustus-training
 	cd docs/tutorial2015/results; ls | grep -v do.sh | grep -v README | xargs rm; cd -
+	rm -r auxprogs/utrrnaseq/input/human-chr19
+	rm -r docs/tutorial-cgp/results/cactusout
 	make clean all
 	make clean
 	cd config/species; rm -rf tobacco xeno1 bombus_terrestris{1,3} symsag xenoturbella meara pavar newest elegans maker2_* lizard

README.TXT

@@ -2,15 +2,15 @@
 %                                                                                                %
 %           Gene Prediction with the Command-Line Version of AUGUSTUS                            %
 %                                                                                                %
-%           Authors: Lizzy Gerischer, Oliver Keller, Stefanie König, Lars Romoth, Mario Stanke   %
-%             Mario Stanke                                                                       %
+%           Authors: Lizzy Gerischer, Oliver Keller, Stefanie König, Lars Romoth, Katharina Hoff %
+%             and Mario Stanke                                                                   %
 %             Universitaet Greifswald                                                            %
 %             Institut fuer Mathematik und Informatik                                            %
 %             17497 Greifswald                                                                   %
-%             Fon: +49 3834 864642                                                               %
+%             Fon: +49 3834 4204642                                                              %
 %             mario.stanke@uni-greifswald.de                                                     %
 %                                                                                                %
-%             Date: July 11th, 2017                                                              %
+%             Date: May 8th, 2018                                                                %
 %                                                                                                %
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
@@ -30,8 +30,7 @@
 
               1. INTRODUCTION
               ---------------
-AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke, Oliver Keller, Stefanie König
-and Lizzy Gerischer. It can be used as an ab initio program, which means it bases its prediction purely on the
+AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke, Oliver Keller, Stefanie König, Lizzy Gerischer and Katharina Hoff. It can be used as an ab initio program, which means it bases its prediction purely on the
 sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources
 such as EST, MS/MS, protein alignments and syntenic genomic alignments. Since version 3.0 AUGUSTUS
 can also predict the genes simultaneously in several aligned genomes (see README-cgp.txt).
@@ -102,6 +101,7 @@ Currently, AUGUSTUS has been trained for predicting genes in:
   - Nematostella vectensis (Cnidaria)
   - Ciona intestinalis (Chordata)
   - Strongylocentrotus purpuratus (Echinodermata)
+  - Pisaster ochraceus (starfish)
   
 The training annotation files of the following species are a courtesy of Jason Stajich (see also http://fungal.genome.duke.edu/): 
 Aspergillus fumigatus, Aspergillus nidulans, Aspergillus oryzae, Aspergillus terreus, Botrytis cinerea, Candida albicans
@@ -140,9 +140,9 @@ Parameters for Mnemiopsis leidyi, Nematostella vectensis, Ciona intestinalis and
 
 1. unpack
 
->tar -xzf augustus-3.3.tar.gz
+>tar -xzf augustus-3.3.1.tar.gz
 
-The tar-archive contains one directory 'augustus-3.3' with the following sub-directories:
+The tar-archive contains one directory 'augustus-3.3.1' with the following sub-directories:
 bin
 src
 include
@@ -182,6 +182,21 @@ Compiling bam2hints and filterBam requires:
       to your /etc/apt/sources.list, first: 
       deb http://us.archive.ubuntu.com/ubuntu vivid main universe)
 
+Compiling bam2wig requires:
+
+   -htslib
+   -bcftools
+   -tabix
+   -samtools
+   For bam2wig, these four packages must be installed from github. An installation via Ubuntu packages is not sufficient.
+   See detailed installation & compilation instructions at auxprogs/bam2wig/README.TXT
+   Also, the environment variable TOOLDIR (directory in which htslib, bcftools, tabix and samtools reside) must be exported:
+
+   export TOOLDIR=/path/where/dependencies/reside
+
+   Compiling utrrnaseq requires Boost library >Boost_1_49_0.  For Ubuntu e.g. install with
+      sudo apt-get install libboost-all-dev
+
 > make
 
 After compilation has finished, the command bin/augustus should be executable and print a usage message.
@@ -710,7 +725,7 @@ HS04636	blat2hints	exonpart	500	599	.	+	.	priority=2; source=E
 HS04636	blat2hints	intron		550	650	.	+	.	priority=5; source=mRNA
 
 When two hints or hint groups contradict each other then the hints with the lower priority number
-are ignored. This is especially usefull if for a genome several sources of hints are available,
+are ignored. This is especially useful if for a genome several sources of hints are available,
 where one source should be trusted when in doubt. For example, the rhesus macaque currently has few native ESTs
 but human ESTs often also align to rhesus. Giving the hints from native ESTs a higher priority means
 that AUGUSTUS uses only them for genes with support by native ESTs and uses the alien EST alignments

auxprogs/Makefile

@@ -9,9 +9,13 @@ all:
 	cd filterBam; make;
 	cd homGeneMapping; make;
 	cd joingenes; make;
+	cd bam2wig; make;
+	cd utrrnaseq/Debug; make all;
 clean:
 	cd bam2hints; make clean;
 	cd compileSpliceCands; make clean;
 	cd filterBam; make clean;
 	cd homGeneMapping; make clean;
 	cd joingenes; make clean;
+	cd bam2wig; make clean;
+	cd utrrnaseq/Debug; make clean;

auxprogs/bam2wig/Makefile

 # Makefile of bam2wig
 #
-# NOTE: Modify the variable SAMTOOLS according to where your samtools software has been installed
+# NOTE: Modify the variable TOOLDIR according to where your samtools/htslib/bcftools/tabix software has been installed
 #
 # Created: 12-June-2012
-# Last modified: 07-April-2014
+# Last modified: 10-NOV-2017
 #
 
+ifndef TOOLDIR
+	TOOLDIR=$(HOME)/tools
+# replace with your own parent directory of samtools, htslib, bcftools, tabix
+# if TOOLDIR is not specified as environment variable
+endif
+
 PROGRAM = bam2wig
 SOURCES = $(PROGRAM)
 OBJECTS = $(SOURCES:.c=.o)
-TOOLDIR=/home/mario/tools
 SAMTOOLS=$(TOOLDIR)/samtools/
 HTSLIB=$(TOOLDIR)/htslib/
-BCFTOOLS=$(TOOLDIR)/bcftools-1.2/
+BCFTOOLS=$(TOOLDIR)/bcftools/
 TABIX=$(TOOLDIR)/tabix/
 INCLUDES=-I$(SAMTOOLS) -I. -I$(HTSLIB) -I$(BCFTOOLS) -I$(TABIX)
 VPATH=$(SAMTOOLS)
@@ -21,10 +26,12 @@ CFLAGS=-Wall -O2 $(INCLUDES)
 CC=gcc
 
 $(PROGRAM) : bam2wig.o
-	$(CC) $(CFLAGS) $^ -o $@ $(LIBS)
+	$(CC) $(CFLAGS) $^ -o $@ $(LIBS) -lbz2 -llzma
+	cp bam2wig ../../bin/bam2wig
 
 bam2wig.o : bam2wig.c
-	$(CC) $(CFLAGS) -c $^ -o $@ $(INCLUDES)
+	$(CC) $(CFLAGS) -c $^ -o $@
 
 clean:
 	rm -f $(OBJECTS) bam2wig.o
+	rm -f ../../bin/bam2wig

auxprogs/bam2wig/README.txt

@@ -7,7 +7,45 @@ Installation instructions:
    * tabix
   You find those tools at https://github.com/samtools . bam2wig has been tested with samtools 0.2.0-rc7
 
-1. Edit Makefile and modify the value of SAMTOOLS variable
+  We recommend that you install all four tools into one directory that we will further refer to as the
+  TOOLDIR. For example, you can install all tools into your home directory, which will result into
+  four folders in your home directory: bcftools, htslib, samtools and tabix.
+
+  Installation example:
+
+  git clone https://github.com/samtools/htslib.git
+  cd htslib
+  autoheader
+  autoconf
+  ./configure
+  make
+  sudo make install
+  cd ..
+  git clone https://github.com/samtools/bcftools.git
+  cd bcftools
+  autoheader
+  autoconf
+  ./configure
+  make
+  sudo make install
+  cd ..
+  git clone https://github.com/samtools/tabix.git
+  cd tabix
+  make
+  cd ..
+  git clone https://github.com/samtools/samtools.git
+  cd samtools
+  autoheader
+  autoconf -Wno-syntax
+  ./configure
+  make
+  sudo make install
+  cd ..
+
+1. Export TOOLDIR path
+
+  export TOOLDIR=/path/where/four/dependencies/reside
+
 2. Type
 
  make
@@ -15,7 +53,7 @@ Installation instructions:
 on command prompt
 
 Examples:
-A file test.bam has ben included. You can try bam2wig by trying out
+A file test.bam has been included. You can try bam2wig by trying out
 the following examples,
 
 a) ./bam2wig test.bam 
@@ -24,5 +62,5 @@ b) ./bam2wig -t "my_specified_track" -r chr3L test.s.bam
 Example (b) can only be done if an index file for test.s.bam exists. 
 Do "samtools index test.s.bam" and a file "test.s.bam.bai" will be generated.
 
-Tonatiuh Pena
-17-June-2012
+Tonatiuh Pena Centeno, Katharina Hoff
+29 November 2017