Rebuild Augustus recipe (#51641)

* Rebuild Augustus recipe

* add galaxy link

* simplify build.sh

* clean up recipe

* add make clean to reduce package size

* remove make clean

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

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
@@ -152,19 +154,22 @@ 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
     Stanke and Oliver Keller. 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 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."

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:

recipes/augustus/patches/utrrnaseq.patch

@@ -1,14 +1,25 @@
---- 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 ' '
 +	cp -f utrrnaseq ../../bin/utrrnaseq
 
  $(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 ' '