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| author | Justin Stanley <molecuul@users.noreply.github.com> | 2019-01-30 18:55:59 -0600 |
|---|---|---|
| committer | Peter Scheibel <scheibel1@llnl.gov> | 2019-01-30 18:55:59 -0600 |
| commit | 993745b9190ece42426f70dc8538be402c370cd7 (patch) | |
| tree | 7b55453b0e3b853cf2c97cbc494ac0e25b6351a8 | |
| parent | 9bfcbcc1554ce6428b5b0cde5fa08a194df45cb7 (diff) | |
| download | spack-993745b9190ece42426f70dc8538be402c370cd7.tar.gz spack-993745b9190ece42426f70dc8538be402c370cd7.tar.bz2 spack-993745b9190ece42426f70dc8538be402c370cd7.tar.xz spack-993745b9190ece42426f70dc8538be402c370cd7.zip | |
redundans: add 0.14a (#10006)
Also update install to use globbing
| -rw-r--r-- | var/spack/repos/builtin/packages/redundans/package.py | 25 |
1 files changed, 15 insertions, 10 deletions
diff --git a/var/spack/repos/builtin/packages/redundans/package.py b/var/spack/repos/builtin/packages/redundans/package.py index 832b3f7d99..bf17cfb812 100644 --- a/var/spack/repos/builtin/packages/redundans/package.py +++ b/var/spack/repos/builtin/packages/redundans/package.py @@ -4,6 +4,7 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * +import glob class Redundans(Package): @@ -11,7 +12,9 @@ class Redundans(Package): homepage = "https://github.com/Gabaldonlab/redundans" url = "https://github.com/Gabaldonlab/redundans/archive/v0.13c.tar.gz" + git = "https://github.com/Gabaldonlab/redundans.git" + version('0.14a', commit='a20215a862aed161cbfc79df9133206156a1e9f0') version('0.13c', '2003fb7c70521f5e430553686fd1a594') depends_on('python', type=('build', 'run')) @@ -29,16 +32,18 @@ class Redundans(Package): def install(self, spec, prefix): sspace_location = join_path(spec['sspace-standard'].prefix, 'SSPACE_Standard_v3.0.pl') - mkdirp(prefix.bin) + filter_file(r'sspacebin = os.path.join(.*)$', 'sspacebin = \'' + sspace_location + '\'', 'redundans.py') - install('redundans.py', prefix.bin) - with working_dir('bin'): - install('fasta2homozygous.py', prefix.bin) - install('fasta2split.py', prefix.bin) - install('fastq2insert_size.py', prefix.bin) - install('fastq2mates.py', prefix.bin) - install('fastq2shuffled.py', prefix.bin) - install('fastq2sspace.py', prefix.bin) - install('filterReads.py', prefix.bin) + + binfiles = ['redundans.py', 'bin/filterReads.py'] + binfiles.extend(glob.glob('bin/fast?2*.py')) + + # new internal dep with 0.14a + if spec.satisfies('@0.14a:'): + binfiles.append('bin/denovo.py') + + mkdirp(prefix.bin) + for f in binfiles: + install(f, prefix.bin) |