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>

7 files changed, 157 insertions, 0 deletions

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"))