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| author | Justin Stanley <molecuul@users.noreply.github.com> | 2019-02-04 10:36:10 -0600 |
|---|---|---|
| committer | Levi Baber <baberlevi@gmail.com> | 2019-02-04 10:36:10 -0600 |
| commit | 478c3f5e8b143998b64b6218d39dbf0ec3943b10 (patch) | |
| tree | 0bde28cae90f43bbb1a65442d3c711155f6f0161 | |
| parent | bca72036a84f5622c5ce83275721a43455d63e85 (diff) | |
| download | spack-478c3f5e8b143998b64b6218d39dbf0ec3943b10.tar.gz spack-478c3f5e8b143998b64b6218d39dbf0ec3943b10.tar.bz2 spack-478c3f5e8b143998b64b6218d39dbf0ec3943b10.tar.xz spack-478c3f5e8b143998b64b6218d39dbf0ec3943b10.zip | |
augustus: fix bam2wig auxprog build (#10362)
* augustus: fix bam2wig auxprog build
* augustus: few more changes to make new versions work
| -rw-r--r-- | var/spack/repos/builtin/packages/augustus/package.py | 40 |
1 files changed, 35 insertions, 5 deletions
diff --git a/var/spack/repos/builtin/packages/augustus/package.py b/var/spack/repos/builtin/packages/augustus/package.py index 1e65c495bc..3b9cac0555 100644 --- a/var/spack/repos/builtin/packages/augustus/package.py +++ b/var/spack/repos/builtin/packages/augustus/package.py @@ -11,17 +11,26 @@ class Augustus(MakefilePackage): genomic sequences""" homepage = "http://bioinf.uni-greifswald.de/augustus/" - url = "http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.3.1.tar.gz" - list_url = "http://bioinf.uni-greifswald.de/augustus/binaries/old" + url = "https://github.com/Gaius-Augustus/Augustus/archive/3.3.2.tar.gz" + # Releases have moved to github - version('3.3.1', '8363ece221c799eb169f47e545efb951') - version('3.3', '93691d9aafc7d3d0e1adf31ec308507f') - version('3.2.3', 'b8c47ea8d0c45aa7bb9a82626c8ff830') + version('3.3.2', sha256='d09f972cfd88deb34b19b69878eb8af3bbbe4f1cde1434b69cedc2aa6247a0f2') + version('3.3.1', sha256='011379606f381ee21b9716f83e8a1a57b2aaa01aefeebd2748104efa08c47cab', + url='https://github.com/Gaius-Augustus/Augustus/archive/v3.3.1-tag1.tar.gz') + version('3.3', '93691d9aafc7d3d0e1adf31ec308507f', + url='http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.3.tar.gz') + version('3.2.3', 'b8c47ea8d0c45aa7bb9a82626c8ff830', + url='http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.2.3.tar.gz') 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('tabix', when='@3.3.1:') + depends_on('curl', when='@3.3.1:') def edit(self, spec, prefix): with working_dir(join_path('auxprogs', 'filterBam', 'src')): @@ -52,6 +61,27 @@ class Augustus(MakefilePackage): makefile.filter('LIBS = -lbamtools -lz', 'LIBS = $(BAMTOOLS)/lib/bamtools' '/libbamtools.a -lz') + with working_dir(join_path('auxprogs', 'bam2wig')): + makefile = FileFilter('Makefile') + # point tools to spack installations + bcftools = self.spec['bcftools'].prefix.include + samtools = self.spec['samtools'].prefix.include + htslib = self.spec['htslib'].prefix.include + tabix = self.spec['tabix'].prefix.include + + makefile.filter('SAMTOOLS=.*$', + 'SAMTOOLS=%s' % samtools) + makefile.filter('HTSLIB=.*$', + 'HTSLIB=%s' % htslib) + makefile.filter('BCFTOOLS=.*$', + 'BCFTOOLS=%s' % bcftools) + makefile.filter('TABIX=.*$', + 'TABIX=%s' % tabix) + # fix bad linking dirs + makefile.filter('$(SAMTOOLS)/libbam.a', + '$(SAMTOOLS)/../lib/libbam.a', string=True) + makefile.filter('$(HTSLIB)/libhts.a', + '$(HTSLIB)/../lib/libhts.a', string=True) def install(self, spec, prefix): install_tree('bin', join_path(self.spec.prefix, 'bin')) |