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Repeatmodeler 2.0.4 (#38337)

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* perl-devel-size: adding new package
* repeatmodeler: adding new version 2.0.4
* perl-devel-size: adding proper description
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snehring 2023-06-14 10:10:50 -05:00 committed by GitHub
parent 40d6b84b4d
commit 9e3c3ae298
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GPG Key ID: 4AEE18F83AFDEB23
2 changed files with 69 additions and 31 deletions
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18
var/spack/repos/builtin/packages/perl-devel-size/package.py Normal file
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@ -0,0 +1,18 @@
# Copyright 2013-2023 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.package import *
class PerlDevelSize(PerlPackage):
"""Devel::Size - Perl extension for finding the memory usage of Perl variables"""
homepage = "https://metacpan.org/pod/Devel::Size"
url = "https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/Devel-Size-0.83.tar.gz"
maintainers("snehring")
version("0.83", sha256="757a67e0aa59ae103ea5ca092cbecc025644ebdc326731688ffab6f8823ef4b3")
version("0.82_51", sha256="189eb7c528c1fd21ab53675f4f9f75d4651980d72dff3dd01c8b2241bfe7b086")

82
var/spack/repos/builtin/packages/repeatmodeler/package.py
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@ -11,14 +11,23 @@ class Repeatmodeler(Package):
package."""
homepage = "https://www.repeatmasker.org/RepeatModeler/"
url = "https://www.repeatmasker.org/RepeatModeler/RepeatModeler-open-1.0.11.tar.gz"
url = "https://github.com/Dfam-consortium/RepeatModeler/archive/refs/tags/2.0.4.tar.gz"
version("1.0.11", sha256="7ff0d588b40f9ad5ce78876f3ab8d2332a20f5128f6357413f741bb7fa172193")
maintainers("snehring")
version("2.0.4", sha256="94aad46cc70911d48de3001836fc3165adb95b2b282b5c53ab0d1da98c27a6b6")
version(
"1.0.11",
sha256="7ff0d588b40f9ad5ce78876f3ab8d2332a20f5128f6357413f741bb7fa172193",
url="https://www.repeatmasker.org/RepeatModeler/RepeatModeler-open-1.0.11.tar.gz",
)
depends_on("perl", type=("build", "run"))
depends_on("perl-json", type=("build", "run"))
depends_on("perl-uri", type=("build", "run"))
depends_on("perl-libwww-perl", type=("build", "run"))
depends_on("perl-file-which", type=("build", "run"), when="@2.0.4:")
depends_on("perl-devel-size", type=("build", "run"), when="@2.0.4:")
depends_on("repeatmasker", type="run")
depends_on("recon+repeatmasker", type="run")
@ -27,36 +36,47 @@ class Repeatmodeler(Package):
depends_on("nseg", type="run")
depends_on("ncbi-rmblastn", type="run")
def install(self, spec, prefix):
# like repeatmasker, another interactive installer
# questions:
# 1. <enter to continue>
# 2. <perl path, default is OK>
# 3. <source path, default is OK>
# 4. RepeatMasker bin path
# 5. RECON bin path
# 6. RepeatScout bin path
# 7. Nseg bin path
# 8. trf bin path
# 9. Add a search engine:
# 1. RMBlast -> Path, Default? (Y/N)
# 2. WUBlast/ABBlast -> Path, Default? (Y/N)
# 3. Done
# "optional" dependencies that it still wants
depends_on("cdhit", type="run", when="@2.0.4:")
depends_on("genometools", type="run", when="@2.0.4:")
depends_on("mafft", type="run", when="@2.0.4:")
depends_on("ninja-phylogeny", type="run", when="@2.0.4:")
depends_on("blat", type="run", when="@2.0.4:")
depends_on("ltr-retriever", type="run", when="@2.0.4:")
config_answers = [
"",
"",
"",
spec["repeatmasker"].prefix.bin,
spec["recon"].prefix.bin,
spec["repeatscout"].prefix.bin,
spec["nseg"].prefix.bin,
spec["trf"].prefix.bin,
"1",
spec["ncbi-rmblastn"].prefix.bin,
"Y",
"3",
]
def install(self, spec, prefix):
# interactive configuration script
if spec.satisfies("@1.0.11"):
config_answers = [
"",
"",
"",
spec["repeatmasker"].prefix.bin,
spec["recon"].prefix.bin,
spec["repeatscout"].prefix.bin,
spec["nseg"].prefix.bin,
spec["trf"].prefix.bin,
"1",
spec["ncbi-rmblastn"].prefix.bin,
"Y",
"3",
]
elif spec.satisfies("@2.0.4:"):
config_answers = [
"",
spec["repeatmasker"].prefix.bin,
spec["recon"].prefix.bin,
spec["repeatscout"].prefix.bin,
spec["trf"].prefix.bin,
spec["cdhit"].prefix.bin,
spec["blat"].prefix.bin,
spec["ncbi-rmblastn"].prefix.bin,
"y",
spec["genometools"].prefix.bin,
spec["ltr-retriever"].prefix.bin,
spec["mafft"].prefix.bin,
spec["ninja-phylogeny"].prefix.bin,
]
config_filename = "spack-config.in"