diff options
Diffstat (limited to 'var')
-rw-r--r-- | var/spack/repos/builtin/packages/libbigwig/package.py | 26 | ||||
-rw-r--r-- | var/spack/repos/builtin/packages/methyldackel/package.py | 40 |
2 files changed, 66 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/libbigwig/package.py b/var/spack/repos/builtin/packages/libbigwig/package.py new file mode 100644 index 0000000000..9b6819b7a7 --- /dev/null +++ b/var/spack/repos/builtin/packages/libbigwig/package.py @@ -0,0 +1,26 @@ +# 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 Libbigwig(CMakePackage): + """A C library for reading/parsing local and remote bigWig and bigBed files.""" + + homepage = "https://github.com/dpryan79/libBigWig" + url = "https://github.com/dpryan79/libBigWig/archive/refs/tags/0.4.7.tar.gz" + maintainers = ["snehring"] + + version("0.4.7", sha256="8e057797011d93fa00e756600898af4fe6ca2d48959236efc9f296abe94916d9") + + variant("curl", default=True, description="Build with curl support") + + depends_on("curl", when="+curl") + + def cmake_args(self): + args = [] + if self.spec.satisfies("~curl"): + args.append("-DWITH_CURL=OFF") + return args diff --git a/var/spack/repos/builtin/packages/methyldackel/package.py b/var/spack/repos/builtin/packages/methyldackel/package.py new file mode 100644 index 0000000000..6e943c4c3d --- /dev/null +++ b/var/spack/repos/builtin/packages/methyldackel/package.py @@ -0,0 +1,40 @@ +# 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 Methyldackel(MakefilePackage): + """MethylDackel (formerly named PileOMeth, which was a temporary name + derived due to it using a PILEup to extract METHylation metrics) will + process a coordinate-sorted and indexed BAM or CRAM file containing + some form of BS-seq alignments and extract per-base methylation + metrics from them. + """ + + homepage = "https://github.com/dpryan79/MethylDackel" + url = "https://github.com/dpryan79/MethylDackel/archive/refs/tags/0.6.1.tar.gz" + maintainers = ["snehring"] + + version("0.6.1", sha256="eeb1da4c830bcd9f3e6663a764947d957c41337643069524a4b545812fcf4819") + + depends_on("htslib@1.11:") + depends_on("libbigwig") + depends_on("curl") + + def edit(self, spec, prefix): + filter_file(r"^prefix \?=.*$", "prefix = " + spec.prefix, "Makefile") + filter_file( + "$(LIBBIGWIG)", + join_path(spec["libbigwig"].prefix.lib64, "libBigWig.a"), + "Makefile", + string=True, + ) + filter_file( + "-IlibBigWig", + "-I" + spec["libbigwig"].prefix.include.libbigwig, + "Makefile", + string=True, + ) |