diff --git a/recipes/augustus/build.sh b/recipes/augustus/build.sh
index 6c55e6ebfea54..d0126d902f5b8 100644
--- a/recipes/augustus/build.sh
+++ b/recipes/augustus/build.sh
@@ -2,34 +2,39 @@
 
 set -x -e
 
-#export CXXFLAGS="${CXXFLAGS} -std=c++11 -stdlib=libstdc++ -stdlib=libc++ -DUSE_BOOST"
-export CXXFLAGS="${CXXFLAGS} -std=c++11  -DUSE_BOOST -I${PREFIX}/include"
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -std=c++14 -DUSE_BOOST -I${PREFIX}/include"
 
 mkdir -p ${PREFIX}/bin
 mkdir -p ${PREFIX}/scripts
 mkdir -p ${PREFIX}/config
 
 ## Make the software
-
-if [ "$(uname)" = Darwin ] ; then
-    # SQLITE disabled due to compile issue, see: https://svn.boost.org/trac10/ticket/13501
-    sqlite=
+if [[ "$(uname)" = Darwin ]]; then
+	# SQLITE disabled due to compile issue, see: https://svn.boost.org/trac10/ticket/13501
+	sqlite=
 else
-    sqlite='SQLITE=true'
+	sqlite='SQLITE=true'
 fi
-make \
-    CC="${CC}" \
-    CXX="${CXX}" \
-    INCLUDE_PATH_BAMTOOLS="-I${PREFIX}/include/bamtools" \
-    LIBRARY_PATH_BAMTOOLS="-L${PREFIX}/lib" \
-    INCLUDE_PATH_LPSOLVE="-I${PREFIX}/include/lpsolve" \
-    LIBRARY_PATH_LPSOLVE="-L${PREFIX}/lib" \
-    INCLUDE_PATH_HTSLIB="-I${PREFIX}/include/htslib" \
-    LIBRARY_PATH_HTSLIB="-L${PREFIX}/lib" \
-    COMPGENPRED=true \
-    MYSQL=false \
-    $sqlite
 
+make \
+	CC="${CC}" \
+	CXX="${CXX}" \
+	INCLUDE_PATH_BAMTOOLS="-I${PREFIX}/include/bamtools" \
+	LIBRARY_PATH_BAMTOOLS="-L${PREFIX}/lib" \
+	INCLUDE_PATH_LPSOLVE="-I${PREFIX}/include/lpsolve" \
+	LIBRARY_PATH_LPSOLVE="-L${PREFIX}/lib" \
+	INCLUDE_PATH_HTSLIB="-I${PREFIX}/include/htslib" \
+	LIBRARY_PATH_HTSLIB="-L${PREFIX}/lib" \
+	COMPGENPRED=true \
+	MYSQL=false \
+	"${sqlite}" -j"${CPU_COUNT}"
+
+# Fix perl shebang
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${SRC_DIR}/scripts/*.pl
+rm -rf ${SRC_DIR}/scripts/*.bak
 
 ## Build Perl
 
@@ -39,7 +44,7 @@ cd perl-build
 # affects tests for Augustus 3.3:
 # https://github.com/Gaius-Augustus/Augustus/commit/7ca3ab
 #sed -i'' -e '1s/perl -w/perl/' *.pl
-cp ${RECIPE_DIR}/Build.PL ./
+cp -f ${RECIPE_DIR}/Build.PL ./
 perl ./Build.PL
 perl ./Build manifest
 perl ./Build install --installdirs site
@@ -49,11 +54,11 @@ cd ..
 
 ## End build perl
 
+chmod 0755 bin/augustus
 mv bin/* $PREFIX/bin/
 mv scripts/* $PREFIX/bin/
 mv config/* $PREFIX/config/
 
-
 ## Set AUGUSTUS variables on env activation
 
 mkdir -p ${PREFIX}/etc/conda/activate.d ${PREFIX}/etc/conda/deactivate.d
diff --git a/recipes/augustus/meta.yaml b/recipes/augustus/meta.yaml
index 7faa39e763a44..6eec34c826555 100644
--- a/recipes/augustus/meta.yaml
+++ b/recipes/augustus/meta.yaml
@@ -1,28 +1,31 @@
+{% set name = "augustus" %}
 {% set version = "3.5.0" %}
 {% set sha256 = "5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686" %}
 
 package:
-  name: augustus
+  name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://github.com/Gaius-Augustus/Augustus/archive/v{{ version }}.tar.gz
   sha256: {{ sha256 }}
   patches:
+    - patches/0001-Makefile.patch
     - patches/homGeneMapping.src.makefile.patch
     - patches/utrrnaseq.patch
 
 build:
-  number: 4
+  number: 5
+  run_exports:
+    - {{ pin_subpackage('augustus', max_pin="x") }}
 
 requirements:
   build:
     - make
-    - {{ compiler('c') }}
     - {{ compiler('cxx') }}
   host:
     - zlib
-    - samtools ==0.1.19
+    - samtools
     - bamtools
     - htslib
     - gsl
@@ -35,7 +38,6 @@ requirements:
     - perl
     - perl-module-build
   run:
-    - zlib
     - boost-cpp
     - gsl
     - lp_solve
@@ -152,8 +154,8 @@ test:
     - fix_in_frame_stop_codon_genes.py --help | grep -Fq 'fix_in_frame_stop_codon_genes.py'
 
 about:
-  home: http://bioinf.uni-greifswald.de/augustus/
-  license: Artistic Licence
+  home: "https://bioinf.uni-greifswald.de/augustus"
+  license: "Artistic Licence"
   license_family: Other
   license_file: "src/LICENSE.TXT"
   summary: 'AUGUSTUS is a gene prediction program for eukaryotes written by Mario
@@ -161,10 +163,13 @@ about:
     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 synthenic genomic alignments.'
+  dev_url: "https://github.com/Gaius-Augustus/Augustus"
+  doc_url: "https://github.com/Gaius-Augustus/Augustus/blob/v{{ version }}/docs/RUNNING-AUGUSTUS.md"
 
 extra:
   identifiers:
     - biotools:augustus
     - doi:10.1093/bioinformatics/btr010
     - usegalaxy-eu:augustus
+    - usegalaxy-eu:augustus_training
   notes: "Builds with sqlite support are currently only available on Linux due to compile issues with macOS."
diff --git a/recipes/augustus/patches/0001-Makefile.patch b/recipes/augustus/patches/0001-Makefile.patch
new file mode 100644
index 0000000000000..29177a5f9654f
--- /dev/null
+++ b/recipes/augustus/patches/0001-Makefile.patch
@@ -0,0 +1,40 @@
+diff --git a/Makefile b/Makefile
+index a26b40c..b2ccb6a 100644
+--- a/Makefile
++++ b/Makefile
+@@ -26,20 +26,26 @@ clean:
+ 		cd .. && ./pyclean.sh; \
+ 	fi
+ 
+-PREFIX = /usr/local
+-INSTALLDIR = /opt/augustus-$(AUGVERSION)
++# DESTDIR is usually the empty string but can be set for staging
++prefix ?= $(PREFIX)
++bindir = $(DESTDIR)$(prefix)/bin
++INSTALLDIR = $(prefix)/share/augustus-$(AUGVERSION)
+ 
+ install:
+-	if [ ! $(PWD) -ef $(INSTALLDIR) ] ; then \
++	@echo Installing augustus executables into $(bindir)
++# two main ways:
++# 1) make install is executed from anywhere but in INSTALLDIR. Then INSTALLDIR is created if it does not exist and config data is copied.
++# 2) make install is executed in INSTALLDIR. This is done by the singularity file.
++	if [ ! $(CURDIR) -ef $(INSTALLDIR) ] ; then \
+ 		install -d $(INSTALLDIR) && \
+ 		cp -a config bin scripts $(INSTALLDIR) ; \
+ 	fi
+-	ln -sf $(INSTALLDIR)/bin/augustus $(PREFIX)/bin/augustus
+-	ln -sf $(INSTALLDIR)/bin/etraining $(PREFIX)/bin/etraining
+-	ln -sf $(INSTALLDIR)/bin/prepareAlign $(PREFIX)/bin/prepareAlign
+-	ln -sf $(INSTALLDIR)/bin/fastBlockSearch $(PREFIX)/bin/fastBlockSearch
+-	if [ -f $(INSTALLDIR)/bin/load2db ] ; then ln -sf $(INSTALLDIR)/bin/load2db $(PREFIX)/bin/load2db ; fi
+-	if [ -f $(INSTALLDIR)/bin/getSeq ] ; then ln -sf $(INSTALLDIR)/bin/getSeq $(PREFIX)/bin/getSeq ; fi
++	ln -sf $(INSTALLDIR)/bin/augustus $(bindir)/augustus
++	ln -sf $(INSTALLDIR)/bin/etraining $(bindir)/etraining
++	ln -sf $(INSTALLDIR)/bin/prepareAlign $(bindir)/prepareAlign
++	ln -sf $(INSTALLDIR)/bin/fastBlockSearch $(bindir)/fastBlockSearch
++	if [ -f $(INSTALLDIR)/bin/load2db ] ; then ln -sf $(INSTALLDIR)/bin/load2db $(bindir)/load2db ; fi
++	if [ -f $(INSTALLDIR)/bin/getSeq ] ; then ln -sf $(INSTALLDIR)/bin/getSeq $(bindir)/getSeq ; fi
+ 
+ # for internal purposes:
+ release:
diff --git a/recipes/augustus/patches/utrrnaseq.patch b/recipes/augustus/patches/utrrnaseq.patch
index 33ed805d73488..4befbfaf97c85 100644
--- a/recipes/augustus/patches/utrrnaseq.patch
+++ b/recipes/augustus/patches/utrrnaseq.patch
@@ -1,6 +1,17 @@
---- a/auxprogs/utrrnaseq/Makefile	2022-09-23 10:06:14.000000000 -0700
-+++ b/auxprogs/utrrnaseq/Makefile	2022-10-08 10:15:31.359607884 -0700
-@@ -29,6 +29,7 @@
+diff --git a/auxprogs/utrrnaseq/Makefile b/auxprogs/utrrnaseq/Makefile
+index 134c5c5..63fa103 100644
+--- a/auxprogs/utrrnaseq/Makefile
++++ b/auxprogs/utrrnaseq/Makefile
+@@ -3,7 +3,7 @@
+ include ../../common.mk
+ 
+ CXX ?= g++
+-CXXFLAGS := -Wall -O0 -pedantic -fmessage-length=0 ${CXXFLAGS}
++CXXFLAGS := -Wall -O3 -pedantic -fmessage-length=0 -std=c++14 ${CXXFLAGS}
+ INCLS   += $(INCLUDE_PATH_BOOST) # set boost include path in INCLUDE_PATH_BOOST, if boost is not installed system-wide
+ LDFLAGS += $(LIBRARY_PATH_BOOST) # set boost library path in LIBRARY_PATH_BOOST, if boost is not installed system-wide
+ 
+@@ -29,6 +29,7 @@ utrrnaseq: $(OBJS)
  	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS)
  	@echo 'Finished building target: $@'
  	@echo ' '
@@ -8,7 +19,7 @@
  
  $(OBJS): $(OBJ_DIR)/%.o: $(SRC_DIR)/%.cpp
  	@echo 'Building file: $<'
-@@ -55,5 +56,6 @@
+@@ -55,5 +56,6 @@ clean_test:
  clean: clean_test
  	rm -rf $(OBJS) $(DEPS) $(OBJ_DIR) utrrnaseq
  	@echo ' '