From 7b053fde892d236dd6f3ece849b0258a2ec53557 Mon Sep 17 00:00:00 2001 From: Luke Diorio-Toth Date: Tue, 25 Oct 2022 18:08:56 -0500 Subject: New packages: mlst, any2fasta, perl-carp, perl-class-method-modifiers, perl-role-tiny, perl-moo, perl-sub-quote (#33274) * added mlst and deps * added install() to any2fasta * added script dependencies, builds OK * fixed style * Update var/spack/repos/builtin/packages/any2fasta/package.py Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> --- .../repos/builtin/packages/any2fasta/package.py | 24 +++++++++++++++ var/spack/repos/builtin/packages/mlst/package.py | 36 ++++++++++++++++++++++ .../repos/builtin/packages/perl-carp/package.py | 19 ++++++++++++ .../perl-class-method-modifiers/package.py | 19 ++++++++++++ .../repos/builtin/packages/perl-moo/package.py | 23 ++++++++++++++ .../builtin/packages/perl-role-tiny/package.py | 18 +++++++++++ .../builtin/packages/perl-sub-quote/package.py | 18 +++++++++++ 7 files changed, 157 insertions(+) create mode 100644 var/spack/repos/builtin/packages/any2fasta/package.py create mode 100644 var/spack/repos/builtin/packages/mlst/package.py create mode 100644 var/spack/repos/builtin/packages/perl-carp/package.py create mode 100644 var/spack/repos/builtin/packages/perl-class-method-modifiers/package.py create mode 100644 var/spack/repos/builtin/packages/perl-moo/package.py create mode 100644 var/spack/repos/builtin/packages/perl-role-tiny/package.py create mode 100644 var/spack/repos/builtin/packages/perl-sub-quote/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/any2fasta/package.py b/var/spack/repos/builtin/packages/any2fasta/package.py new file mode 100644 index 0000000000..4b9428767d --- /dev/null +++ b/var/spack/repos/builtin/packages/any2fasta/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2022 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 Any2fasta(Package): + """any2fasta: Convert various sequence formats to FASTA""" + + homepage = "https://github.com/tseemann/any2fasta" + url = "https://github.com/tseemann/any2fasta/archive/refs/tags/v0.4.2.tar.gz" + + version("0.4.2", sha256="e4cb2ddccda6298f5b0aee0c10184a75307a08b584d2abbfbf0d59d37b197e73") + version("0.2.3", sha256="197cd1e18adebe28b71a1448c5107804b7093b2aa83c4bcfd8edd3fc4ed485df") + version("0.1.2", sha256="ef035595756df7dca1f8a503ee26f8479393953bc67d8870c9965b6d5ade2674") + + depends_on("perl@5.10:", type=("build", "run")) + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install("any2fasta", prefix.bin) diff --git a/var/spack/repos/builtin/packages/mlst/package.py b/var/spack/repos/builtin/packages/mlst/package.py new file mode 100644 index 0000000000..fb2b7b585c --- /dev/null +++ b/var/spack/repos/builtin/packages/mlst/package.py @@ -0,0 +1,36 @@ +# Copyright 2013-2022 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 Mlst(Package): + """Scan contig files against traditional PubMLST typing schemes""" + + homepage = "https://github.com/tseemann/mlst" + url = "https://github.com/tseemann/mlst/archive/refs/tags/v2.22.1.tar.gz" + + version("2.22.1", sha256="a8f64d7cb961a8e422e96a19309ad8707f8792d9f755a9e5a1f5742986d19bca") + + depends_on("perl@5.26:", type="run") + depends_on("perl-moo", type="run") + depends_on("perl-list-moreutils", type="run") + depends_on("perl-json", type="run") + depends_on("perl-file-which", type="run") + depends_on("blast-plus@2.9.0:", type="run") + depends_on("any2fasta", type="run") + # dependencies for scripts + depends_on("parallel", type="run") + depends_on("curl", type="run") + + def install(self, spec, prefix): + mkdirp(prefix.bin) + mkdirp(prefix.db) + mkdirp(prefix.perl5) + install_tree("bin", prefix.bin) + install_tree("scripts", prefix.bin) + install_tree("db", prefix.db) + install_tree("perl5", prefix.perl5) diff --git a/var/spack/repos/builtin/packages/perl-carp/package.py b/var/spack/repos/builtin/packages/perl-carp/package.py new file mode 100644 index 0000000000..3b0dd441cd --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-carp/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2022 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 PerlCarp(PerlPackage): + """Carp - alternative warn and die for modules""" + + homepage = "https://metacpan.org/pod/Carp" + url = "https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX/Carp-1.50.tar.gz" + + version("1.50", sha256="f5273b4e1a6d51b22996c48cb3a3cbc72fd456c4038f5c20b127e2d4bcbcebd9") + + depends_on("perl-extutils-makemaker", type=("build", "run")) + depends_on("perl-test-more", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/perl-class-method-modifiers/package.py b/var/spack/repos/builtin/packages/perl-class-method-modifiers/package.py new file mode 100644 index 0000000000..a67a0c4c19 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-class-method-modifiers/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2022 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 PerlClassMethodModifiers(PerlPackage): + """Class::Method::Modifiers - Provides Moose-like method modifiers""" + + homepage = "https://metacpan.org/pod/Class::Method::Modifiers" + url = "https://cpan.metacpan.org/authors/id/E/ET/ETHER/Class-Method-Modifiers-2.13.tar.gz" + + version("2.13", sha256="ab5807f71018a842de6b7a4826d6c1f24b8d5b09fcce5005a3309cf6ea40fd63") + + depends_on("perl-carp", type=("build", "run")) + depends_on("perl-exporter-tiny", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/perl-moo/package.py b/var/spack/repos/builtin/packages/perl-moo/package.py new file mode 100644 index 0000000000..188ff7361b --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-moo/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2022 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 PerlMoo(PerlPackage): + """Moo - Minimalist Object Orientation (with Moose compatibility)""" + + homepage = "https://metacpan.org/pod/Moo" + url = "https://cpan.metacpan.org/authors/id/H/HA/HAARG/Moo-2.005004.tar.gz" + + version("2.005004", sha256="e3030b80bd554a66f6b3c27fd53b1b5909d12af05c4c11ece9a58f8d1e478928") + + depends_on("perl-carp", type=("build", "run")) + depends_on("perl-class-method-modifiers", type=("build", "run")) + depends_on("perl-exporter-tiny", type=("build", "run")) + depends_on("perl-role-tiny", type=("build", "run")) + depends_on("perl-scalar-list-utils", type=("build", "run")) + depends_on("perl-sub-quote", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/perl-role-tiny/package.py b/var/spack/repos/builtin/packages/perl-role-tiny/package.py new file mode 100644 index 0000000000..96868dbb3a --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-role-tiny/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2022 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 PerlRoleTiny(PerlPackage): + """Role::Tiny - Roles: a nouvelle cuisine portion size slice of Moose""" + + homepage = "https://metacpan.org/pod/Role::Tiny" + url = "https://cpan.metacpan.org/authors/id/H/HA/HAARG/Role-Tiny-2.002004.tar.gz" + + version("2.002004", sha256="d7bdee9e138a4f83aa52d0a981625644bda87ff16642dfa845dcb44d9a242b45") + + depends_on("perl-exporter-tiny", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/perl-sub-quote/package.py b/var/spack/repos/builtin/packages/perl-sub-quote/package.py new file mode 100644 index 0000000000..382afc3140 --- /dev/null +++ b/var/spack/repos/builtin/packages/perl-sub-quote/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2022 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 PerlSubQuote(PerlPackage): + """Sub::Quote - Efficient generation of subroutines via string eval""" + + homepage = "https://metacpan.org/pod/Sub::Quote" + url = "https://cpan.metacpan.org/authors/id/H/HA/HAARG/Sub-Quote-2.006006.tar.gz" + + version("2.006006", sha256="6e4e2af42388fa6d2609e0e82417de7cc6be47223f576592c656c73c7524d89d") + + depends_on("perl-scalar-list-utils", type=("build", "run")) -- cgit v1.2.3-60-g2f50