diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/maker/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/maker/package.py | 91 |
1 files changed, 91 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/maker/package.py b/var/spack/repos/builtin/packages/maker/package.py new file mode 100644 index 0000000000..41363ec0a1 --- /dev/null +++ b/var/spack/repos/builtin/packages/maker/package.py @@ -0,0 +1,91 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * +import os + + +class Maker(Package): + """MAKER is a portable and easily configurable genome annotation pipeline. + It's purpose is to allow smaller eukaryotic and prokaryotic genomeprojects + to independently annotate their genomes and to create genome databases. + MAKER identifies repeats, aligns ESTs and proteins to a genome, produces + ab-initio gene predictions and automatically synthesizes these data into + gene annotations having evidence-based quality values. MAKER is also easily + trainable: outputs of preliminary runs can be used to automatically retrain + its gene prediction algorithm, producing higher quality gene-models on + subsequent runs. MAKER's inputs are minimal and its ouputs can be directly + loaded into a GMOD database. They can also be viewed in the Apollo genome + browser; this feature of MAKER provides an easy means to annotate, view and + edit individual contigs and BACs without the overhead of a database. MAKER + should prove especially useful for emerging model organism projects with + minimal bioinformatics expertise and computer resources. + + Note: MAKER requires registration. Fill out the form at + http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi to get a + download link. Spack will search your current directory for the download + file. Alternatively, add this file to a mirror so that Spack can find it. + For instructions on how to set up a mirror, see + http://spack.readthedocs.io/en/latest/mirrors.html""" + + homepage = "http://www.yandell-lab.org/software/maker.html" + + version('2.31.10', sha256='d3979af9710d61754a3b53f6682d0e2052c6c3f36be6f2df2286d2587406f07d') + + def url_for_version(self, version): + return "file://{0}/maker-{1}.tgz".format(os.getcwd(), version) + + variant('mpi', default=True, description='Build with MPI support') + + patch('install.patch') + patch('mpi.patch') + patch('MpiChunk.patch') + + depends_on('perl', type=('build', 'run')) + depends_on('perl-module-build', type='build') + depends_on('perl-dbi', type=('build', 'run')) + depends_on('perl-dbd-pg', type=('build', 'run')) + depends_on('perl-dbd-sqlite', type=('build', 'run')) + depends_on('perl-forks', type=('build', 'run')) + depends_on('perl-file-which', type=('build', 'run')) + depends_on('perl-perl-unsafe-signals', type=('build', 'run')) + depends_on('perl-bit-vector', type=('build', 'run')) + depends_on('perl-inline-c', type=('build', 'run')) + depends_on('perl-io-all', type=('build', 'run')) + depends_on('perl-io-prompt', type=('build', 'run')) + depends_on('perl-bio-perl', type=('build', 'run')) + depends_on('blast-plus') + depends_on('snap-korf') + depends_on('repeatmasker') + depends_on('exonerate') + depends_on('augustus') + depends_on('interproscan@:4.8') + depends_on('mpi', when='+mpi') + + def install(self, spec, prefix): + if '+mpi' in spec: + with working_dir('src'): + pattern = r'my \$go = 0;' + repl = 'my $go = 1;' + filter_file(pattern, repl, 'Build.PL', backup=False) + + perl = which('perl') + rm = which('rm') + with working_dir('src'): + perl('Build.PL', '--install_base', prefix) + perl('Build', 'install') + + install_tree('lib', join_path(prefix, 'perl', 'lib')) + + # Remove scripts that do not work. The 'mpi_evaluator' and + # 'mpi_iprscan' scripts depend on a custom perl module that is not + # shipped with maker. The 'maker2chado' script depends on setting up a + # CHADO database which is out of scope here. + for package in ('maker2chado', 'maker2jbrowse', 'maker2wap', + 'mpi_evaluator', 'mpi_iprscan'): + rm('-f', join_path(prefix.bin, package)) + + # Remove old IO::Prompt perl module + rm('-r', '-f', join_path(prefix, 'perl', 'lib', 'IO')) |