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authorGlenn Johnson <glenn-johnson@uiowa.edu>2021-04-23 08:56:22 -0500
committerGitHub <noreply@github.com>2021-04-23 15:56:22 +0200
commita276f9405c5c3a124d6d7b0ae0dd3ba08d09f18b (patch)
treee936e4441c31fa8797a08a24d01a259251a8a8a6 /var
parentce6a617706d2462e882d3ad49c0b0cc89b5a3de9 (diff)
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augustus: add v3.4.0 and update package (#22879)
- add version 3.4.0 - add patch for bam2wig when version 3.4.0 - url format changed again, hopefully stable now - added missing python dependency when version >3.3.1 - have older version compile with htslib, samtools ,bcftools - new dependencies for version 3.4.0 - sqlite - mysql-client - mysqlpp - lp-solve - suite-sparse - refactored filtering code - set python interpreter in scripts
Diffstat (limited to 'var')
-rw-r--r--var/spack/repos/builtin/packages/augustus/bam2wig_Makefile.patch23
-rw-r--r--var/spack/repos/builtin/packages/augustus/package.py127
2 files changed, 112 insertions, 38 deletions
diff --git a/var/spack/repos/builtin/packages/augustus/bam2wig_Makefile.patch b/var/spack/repos/builtin/packages/augustus/bam2wig_Makefile.patch
new file mode 100644
index 0000000000..bbd5bfeef6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/augustus/bam2wig_Makefile.patch
@@ -0,0 +1,23 @@
+--- a/auxprogs/bam2wig/Makefile 2020-12-11 09:40:21.000000000 -0600
++++ b/auxprogs/bam2wig/Makefile 2021-04-07 15:20:59.573957969 -0500
+@@ -19,18 +19,8 @@
+ SOURCES = $(PROGRAM)
+ OBJECTS = $(SOURCES:.c=.o)
+
+-ifneq ($(wildcard ${TOOLDIR}/htslib/htslib/.),) # if TOOLDIR exists and contains htslib
+- INCLUDES=-I$(TOOLDIR)/htslib -I$(TOOLDIR)/htslib/htslib
+- HTSLIBS=-L$(TOOLDIR)/htslib -Wl,-rpath,$(TOOLDIR)/htslib -lhts -lcurses -lm -lz -lpthread -lcurl -lssl -lcrypto -lbz2 -llzma
+- HTSERRHINT="Check if the installed HTSlib is of version 1.10 or higher - see README.txt"
+-else
+- INCLUDES=-I/usr/include/htslib
+- HTSLIBS=-lhts -lz -lpthread
+- ifdef DEF_TOOLDIR
+- HTSERRHINT="There is no htslib folder in directory $(TOOLDIR) \n"
+- endif
+- HTSERRHINT:=$(HTSERRHINT)"Check if HTSlib is installed and of version 1.10 or higher - see README.txt"
+-endif
++INCLUDES=-I$(HTSLIBDIR)/include/htslib
++HTSLIBS=-L$(HTSLIBDIR)/lib -Wl,-rpath,$(HTSLIBDIR)/lib -lhts -lcurses -lm -lz -lpthread -lcurl -lssl -lcrypto -lbz2 -llzma
+
+ CFLAGS:=-Wall -O2 $(CFLAGS)
+ CC?=gcc
diff --git a/var/spack/repos/builtin/packages/augustus/package.py b/var/spack/repos/builtin/packages/augustus/package.py
index f8da4eb502..4ad9991493 100644
--- a/var/spack/repos/builtin/packages/augustus/package.py
+++ b/var/spack/repos/builtin/packages/augustus/package.py
@@ -12,9 +12,10 @@ class Augustus(MakefilePackage):
genomic sequences"""
homepage = "http://bioinf.uni-greifswald.de/augustus/"
- url = "https://github.com/Gaius-Augustus/Augustus/archive/3.3.2.tar.gz"
- # Releases have moved to github
+ url = "https://github.com/Gaius-Augustus/Augustus/archive/v3.3.4.tar.gz"
+ # Releases have moved to github
+ version('3.4.0', sha256='2c06cf5953da5afdce1478fa10fcd3c280a3b050f1b2367bf3e731d7374d9bb8')
version('3.3.2', sha256='d09f972cfd88deb34b19b69878eb8af3bbbe4f1cde1434b69cedc2aa6247a0f2')
version('3.3.1-tag1', sha256='011379606f381ee21b9716f83e8a1a57b2aaa01aefeebd2748104efa08c47cab',
url='https://github.com/Gaius-Augustus/Augustus/archive/v3.3.1-tag1.tar.gz')
@@ -24,14 +25,24 @@ class Augustus(MakefilePackage):
url='http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.2.3.tar.gz')
depends_on('perl', type=('build', 'run'))
+ depends_on('python', when='@3.3.1:', type=('build', 'run'))
depends_on('bamtools')
depends_on('gsl')
depends_on('boost')
depends_on('zlib')
- depends_on('htslib', when='@3.3.1:')
- depends_on('bcftools', when='@3.3.1:')
- depends_on('samtools', when='@3.3.1:')
+ depends_on('htslib')
+ depends_on('bcftools')
+ depends_on('samtools')
depends_on('curl', when='@3.3.1:')
+ depends_on('sqlite', when='@3.4.0:')
+ depends_on('mysql-client', when='@3.4.0:')
+ depends_on('mysqlpp', when='@3.4.0:')
+ depends_on('lp-solve', when='@3.4.0:')
+ depends_on('suite-sparse', when='@3.4.0:')
+
+ # Trying to use filter_file here got too complicated so use a patch with a
+ # corresponding environment variable
+ patch('bam2wig_Makefile.patch', when='@3.4.0:')
def edit(self, spec, prefix):
# Set compile commands for each compiler and
@@ -44,30 +55,42 @@ class Augustus(MakefilePackage):
self.spec['boost'].prefix.include),
'src/subdir.mk', string=True)
- # Set compile commands to all makefiles.
+ # Makefiles to set spack compiler over gcc/g++
makefiles = [
'auxprogs/aln2wig/Makefile',
'auxprogs/bam2hints/Makefile',
'auxprogs/bam2wig/Makefile',
- 'auxprogs/checkTargetSortedness/Makefile',
'auxprogs/compileSpliceCands/Makefile',
'auxprogs/homGeneMapping/src/Makefile',
'auxprogs/joingenes/Makefile',
- 'src/Makefile'
+ 'src/Makefile',
]
+ if self.version < Version('3.4.0'):
+ makefiles.append('auxprogs/checkTargetSortedness/Makefile')
+
+ if self.version >= Version('3.4.0'):
+ makefiles.extend([
+ 'auxprogs/filterBam/src/Makefile',
+ 'src/unittests/Makefile',
+ ])
+
for makefile in makefiles:
filter_file('gcc', spack_cc, makefile, string=True)
filter_file('g++', spack_cxx, makefile, string=True)
+ bamtools = self.spec['bamtools'].prefix
+ bcftools = self.spec['bcftools'].prefix
+ htslib = self.spec['htslib'].prefix
+ samtools = self.spec['samtools'].prefix
+
with working_dir(join_path('auxprogs', 'filterBam', 'src')):
makefile = FileFilter('Makefile')
- makefile.filter('BAMTOOLS = .*', 'BAMTOOLS = %s' % self.spec[
- 'bamtools'].prefix)
+ makefile.filter('BAMTOOLS = .*', 'BAMTOOLS = {0}'.format(bamtools))
makefile.filter('INCLUDES = *',
'INCLUDES = -I$(BAMTOOLS)/include/bamtools ')
if 'bamtools@2.5:' in spec:
makefile.filter('LIBS = -lbamtools -lz',
- 'LIBS = $(BAMTOOLS)/lib64/'
+ 'LIBS = $(BAMTOOLS)/lib64'
'/libbamtools.a -lz')
if 'bamtools@:2.4' in spec:
makefile.filter('LIBS = -lbamtools -lz',
@@ -75,39 +98,57 @@ class Augustus(MakefilePackage):
'/libbamtools.a -lz')
with working_dir(join_path('auxprogs', 'bam2hints')):
makefile = FileFilter('Makefile')
- makefile.filter('# Variable definition',
- 'BAMTOOLS = %s' % self.spec['bamtools'].prefix)
- makefile.filter('INCLUDES = /usr/include/bamtools',
- 'INCLUDES = $(BAMTOOLS)/include/bamtools')
+ makefile.filter('/usr/include/bamtools',
+ '{0}/include/bamtools'.format(bamtools))
if 'bamtools@2.5:' in spec:
makefile.filter('LIBS = -lbamtools -lz',
- 'LIBS = $(BAMTOOLS)/lib64/'
- '/libbamtools.a -lz')
+ 'LIBS = {0}/lib64'
+ '/libbamtools.a -lz'.format(bamtools))
if 'bamtools@:2.4' in spec:
makefile.filter('LIBS = -lbamtools -lz',
- 'LIBS = $(BAMTOOLS)/lib/bamtools'
- '/libbamtools.a -lz')
- with working_dir(join_path('auxprogs', 'bam2wig')):
- makefile = FileFilter('Makefile')
- # point tools to spack installations
- if 'bcftools' in spec:
- bcftools = self.spec['bcftools'].prefix.include
+ 'LIBS = {0}/lib/bamtools'
+ '/libbamtools.a -lz'.format(bamtools))
+
+ if self.version < Version('3.4.0'):
+ with working_dir(join_path('auxprogs', 'bam2wig')):
+ makefile = FileFilter('Makefile')
+ # point tools to spack installations
makefile.filter('BCFTOOLS=.*$',
- 'BCFTOOLS=%s' % bcftools)
- if 'samtools' in spec:
- samtools = self.spec['samtools'].prefix.include
+ 'BCFTOOLS={0}/include'.format(bcftools))
makefile.filter('SAMTOOLS=.*$',
- 'SAMTOOLS=%s' % samtools)
- if 'htslib' in spec:
- htslib = self.spec['htslib'].prefix.include
+ 'SAMTOOLS={0}/include'.format(samtools))
makefile.filter('HTSLIB=.*$',
- 'HTSLIB=%s' % htslib)
+ 'HTSLIB={0}/include'.format(htslib))
+
+ # fix bad linking dirs
+ makefile.filter('$(SAMTOOLS)/libbam.a',
+ '$(SAMTOOLS)/../lib/libbam.a', string=True)
+ makefile.filter('$(HTSLIB)/libhts.a',
+ '$(HTSLIB)/../lib/libhts.a', string=True)
+ with working_dir(join_path('auxprogs', 'checkTargetSortedness')):
+ makefile = FileFilter('Makefile')
+ makefile.filter('SAMTOOLS.*=.*$',
+ 'SAMTOOLS={0}/include'.format(samtools))
+ makefile.filter('LIBS=-lbam',
+ 'LIBS=$(SAMTOOLS)/../lib/libbam.a',
+ string=True)
+ else:
+ mysql = self.spec['mysql-client'].prefix
+ mysqlpp = self.spec['mysqlpp'].prefix
+ lpsolve = self.spec['lp-solve'].prefix
- # fix bad linking dirs
- makefile.filter('$(SAMTOOLS)/libbam.a',
- '$(SAMTOOLS)/../lib/libbam.a', string=True)
- makefile.filter('$(HTSLIB)/libhts.a',
- '$(HTSLIB)/../lib/libhts.a', string=True)
+ with working_dir('src'):
+ makefile = FileFilter('Makefile')
+ makefile.filter(r'/usr/include/mysql\+\+',
+ '{0}/include/mysql++'.format(mysqlpp))
+ if '^mariadb-c-client' in spec:
+ makefile.filter('/usr/include/mysql',
+ '{0}/include/mariadb'.format(mysql))
+ else:
+ makefile.filter('/usr/include/mysql',
+ '{0}/include/mysql'.format(mysql))
+ makefile.filter('/usr/include/lpsolve',
+ '{0}/include/lpsolve'.format(lpsolve))
def install(self, spec, prefix):
install_tree('bin', join_path(self.spec.prefix, 'bin'))
@@ -117,12 +158,22 @@ class Augustus(MakefilePackage):
@run_after('install')
def filter_sbang(self):
with working_dir(self.prefix.scripts):
- pattern = '^#!.*/usr/bin/perl'
+ pattern = '^#!.*'
repl = '#!{0}'.format(self.spec['perl'].command.path)
- files = glob.iglob("*.pl")
+ files = glob.glob("*.pl")
for file in files:
filter_file(pattern, repl, *files, backup=False)
+ repl = '#!{0}'.format(self.spec['python'].command.path)
+ files = glob.glob("*.py")
+ for file in files:
+ filter_file(pattern, repl, *files, backup=False)
+
+ def setup_build_environment(self, env):
+ if self.version >= Version('3.4.0'):
+ htslib = self.spec['htslib'].prefix
+ env.set('HTSLIBDIR', htslib)
+
def setup_run_environment(self, env):
env.set('AUGUSTUS_CONFIG_PATH', join_path(
self.prefix, 'config'))