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authorLuke Diorio-Toth <ldioriototh@gmail.com>2022-08-05 02:16:14 -0500
committerGitHub <noreply@github.com>2022-08-05 09:16:14 +0200
commit901e6cb5e17d0a2df88554c454d5ec787828e37c (patch)
tree62e90bea7a3390351c81e89e53e1c4fe3e0afe78 /var
parent08f403146ea6f94f4869bbbfdcc6fc6367ac168f (diff)
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bracken: added new version and removed depreciated version (#31904)
Diffstat (limited to 'var')
-rw-r--r--var/spack/repos/builtin/packages/bracken/package.py55
1 files changed, 22 insertions, 33 deletions
diff --git a/var/spack/repos/builtin/packages/bracken/package.py b/var/spack/repos/builtin/packages/bracken/package.py
index 73e2ae1cd3..d2fa35e980 100644
--- a/var/spack/repos/builtin/packages/bracken/package.py
+++ b/var/spack/repos/builtin/packages/bracken/package.py
@@ -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))