From 1c0230f7d0add83c36daadcf88bda72500e49015 Mon Sep 17 00:00:00 2001 From: Desmond Orton Date: Tue, 6 Apr 2021 00:49:58 -0600 Subject: rnaquast: add new package (#22648) --- .../repos/builtin/packages/rnaquast/package.py | 37 ++++++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 var/spack/repos/builtin/packages/rnaquast/package.py diff --git a/var/spack/repos/builtin/packages/rnaquast/package.py b/var/spack/repos/builtin/packages/rnaquast/package.py new file mode 100644 index 0000000000..8ffc85a26c --- /dev/null +++ b/var/spack/repos/builtin/packages/rnaquast/package.py @@ -0,0 +1,37 @@ +# Copyright 2013-2021 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) + +import os +from spack import * + + +class Rnaquast(Package): + """Quality assessment of de novo transcriptome assemblies from RNA-Seq data + + rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome + and gene database. In addition, rnaQUAST is also capable of estimating gene + database coverage by raw reads and de novo quality assessment + using third-party software.""" + + homepage = "https://github.com/ablab/rnaquast" + url = "https://github.com/ablab/rnaquast/archive/refs/tags/v2.2.0.tar.gz" + + maintainers = ['dorton21'] + + version('2.2.0', sha256='117dff9d9c382ba74b7b0ff24bc7b95b9ca6aa701ebf8afd22943aa54e382334') + + depends_on('python@2.5:', type=('build', 'run')) + depends_on('py-matplotlib', type=('build', 'run')) + depends_on('py-joblib', type=('build', 'run')) + depends_on('py-gffutils', type=('build', 'run')) + depends_on('gmap-gsnap', type=('build', 'run')) + depends_on('blast-plus', type=('build', 'run')) + + def install(self, spec, prefix): + install_tree('.', prefix.bin) + os.rename('%s/rnaQUAST.py' % prefix.bin, '%s/rnaQUAST' % prefix.bin) + + def setup_run_environment(self, env): + env.prepend_path('PATH', prefix.bin) -- cgit v1.2.3-70-g09d2