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| author | snehring <7978778+snehring@users.noreply.github.com> | 2023-03-22 03:20:59 -0500 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2023-03-22 09:20:59 +0100 |
| commit | 8d2f08ae859b043a635b2dcbf0778b29ae971242 (patch) | |
| tree | 2d88fb7bc13d287ee5bf6a77712b0bc17820333d /var | |
| parent | d71ee98badbf365ba8d5688b6843183e193b2fc8 (diff) | |
| download | spack-8d2f08ae859b043a635b2dcbf0778b29ae971242.tar.gz spack-8d2f08ae859b043a635b2dcbf0778b29ae971242.tar.bz2 spack-8d2f08ae859b043a635b2dcbf0778b29ae971242.tar.xz spack-8d2f08ae859b043a635b2dcbf0778b29ae971242.zip | |
shapemapper: add new package (#36282)
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/bbmap/package.py | 2 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/shapemapper/package.py | 48 |
2 files changed, 50 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/bbmap/package.py b/var/spack/repos/builtin/packages/bbmap/package.py index bcdf9c760f..3a323a3663 100644 --- a/var/spack/repos/builtin/packages/bbmap/package.py +++ b/var/spack/repos/builtin/packages/bbmap/package.py @@ -12,7 +12,9 @@ class Bbmap(Package, SourceforgePackage): homepage = "https://sourceforge.net/projects/bbmap/" sourceforge_mirror_path = "bbmap/BBMap_38.63.tar.gz" + version("39.01", sha256="98608da50130c47f3abd095b889cc87f60beeb8b96169b664bc9d849abe093e6") version("38.63", sha256="089064104526c8d696164aefa067f935b888bc71ef95527c72a98c17ee90a01f") + version("37.78", sha256="f2da19f64d2bfb7db4c0392212668b425c96a27c77bd9d88d8f0aea90a193509") version("37.36", sha256="befe76d7d6f3d0f0cd79b8a01004a2283bdc0b5ab21b0743e9dbde7c7d79e8a9") depends_on("java") diff --git a/var/spack/repos/builtin/packages/shapemapper/package.py b/var/spack/repos/builtin/packages/shapemapper/package.py new file mode 100644 index 0000000000..1037f44b6b --- /dev/null +++ b/var/spack/repos/builtin/packages/shapemapper/package.py @@ -0,0 +1,48 @@ +# 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 Shapemapper(CMakePackage): + """ + ShapeMapper automates the calculation of RNA structure probing reactivities from mutational + profiling (MaP) experiments, in which chemical adducts on RNA are detected as internal + mutations in cDNA through reverse transcription and read out by massively parallel sequencing. + """ + + homepage = "https://github.com/Weeks-UNC/shapemapper2" + url = "https://github.com/Weeks-UNC/shapemapper2/releases/download/2.1.5/shapemapper-2.1.5-source-only.tar.gz" + + maintainers("snehring") + + version( + "2.1.5", + sha256="0846a5d8b5f01d2d039fad4b957df0b6220a8505463f1a410368a1b90d2b227c", + url="https://github.com/Weeks-UNC/shapemapper2/releases/download/2.1.5/shapemapper-2.1.5-source-only.tar.gz", + ) + + depends_on("bowtie2@2.3.0: ^perl+threads", type="run") + # hard version dep due to jni + depends_on("bbmap@37.78", type="run") + depends_on("boost+filesystem+program_options+iostreams+system") + depends_on("star@2.5.2:", type="run") + depends_on("pv@1.6.0:", type="run") + depends_on("python@3.7:", type="run") + depends_on("graphviz@2.38.0:", type="run") + depends_on("py-scikit-learn@0.18.1:", type="run") + depends_on("py-matplotlib@1.5.1:3.3", type="run") + + build_directory = "build" + + def install(self, spec, prefix): + for d in ["docs", "internals", "util"]: + mkdirp(join_path(prefix, d)) + install_tree(d, join_path(prefix, d)) + for f in ["shapemapper", "README.md"]: + install(f, prefix) + + def setup_run_environment(self, env): + env.prepend_path("PATH", self.prefix) |