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bracken: added new version and removed depreciated version (#31904)

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Luke Diorio-Toth 2022-08-05 02:16:14 -05:00 committed by GitHub
parent 08f403146e
commit 901e6cb5e1
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1 changed files with 22 additions and 33 deletions
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55
var/spack/repos/builtin/packages/bracken/package.py
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@ -14,41 +14,30 @@ class Bracken(Package):
sequences from a metagenomics sample."""
homepage = "https://ccb.jhu.edu/software/bracken"
url = "https://github.com/jenniferlu717/Bracken/archive/1.0.0.tar.gz"
url = "https://github.com/jenniferlu717/Bracken/archive/v2.7.tar.gz"
version("1.0.0", sha256="8ee736535ad994588339d94d0db4c0b1ba554a619f5f96332ee09f2aabdfe176")
version("2.7", sha256="1795ecd9f9e5582f37549795ba68854780936110a2f6f285c3e626d448cd1532")
depends_on("perl", type=("build", "link", "run"))
depends_on("python@2.7:", type=("build", "link", "run"))
depends_on("perl-exporter-tiny")
depends_on("perl-list-moreutils")
depends_on("perl-parallel-forkmanager")
depends_on("python", type="run")
depends_on("kraken2", type="run")
def install(self, spec, prefix):
mkdirp(prefix.bin)
install_tree("sample_data", prefix.sample_data)
filter_file(r"#!/bin/env perl", "#!/usr/bin/env perl", "count-kmer-abundances.pl")
filter_file(
r"#!/usr/bin/python",
"#!/usr/bin/env {0}".format(os.path.basename(self.spec["python"].command.path)),
"est_abundance.py",
)
filter_file(
r"#!/usr/bin/python",
"#!/usr/bin/env {0}".format(os.path.basename(self.spec["python"].command.path)),
"generate_kmer_distribution.py",
)
files = (
"count-kmer-abundances.pl",
"est_abundance.py",
"generate_kmer_distribution.py",
)
mkdirp(prefix.bin.src)
# installer builds kmer2read_distr in src
chmod = which("chmod")
for name in files:
install(name, prefix.bin)
chmod("+x", join_path(self.prefix.bin, name))
chmod("+x", "./install_bracken.sh")
installer = Executable("./install_bracken.sh")
installer(self.stage.source_path)
# move main scripts to bin
install("bracken", prefix.bin)
install("bracken-build", prefix.bin)
install("./src/kmer2read_distr", prefix.bin)
install("./analysis_scripts/combine_bracken_outputs.py", prefix.bin)
chmod("+x", join_path(prefix.bin, "combine_bracken_outputs.py"))
# move scripts to src and create symlinks
files = ("est_abundance.py", "generate_kmer_distribution.py")
for file in files:
filepath = join_path("./src", file)
if os.path.isfile(filepath):
install(filepath, prefix.bin.src)
symlink(join_path(prefix.bin.src, file), join_path(prefix.bin, file))