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Diffstat (limited to 'var/spack/repos/builtin/packages/ucsc-bedclip/package.py')
-rw-r--r-- | var/spack/repos/builtin/packages/ucsc-bedclip/package.py | 46 |
1 files changed, 46 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/ucsc-bedclip/package.py b/var/spack/repos/builtin/packages/ucsc-bedclip/package.py new file mode 100644 index 0000000000..d1ea52d32c --- /dev/null +++ b/var/spack/repos/builtin/packages/ucsc-bedclip/package.py @@ -0,0 +1,46 @@ +# 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 UcscBedclip(Package): + """Remove lines from bed file that refer to off-chromosome locations.""" + + homepage = "http://hgdownload.cse.ucsc.edu/admin/exe/" + url = "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v449.src.tgz" + + version("377", sha256="932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676") + version("449", sha256="b5a86863d6cfe2120f6c796a13b1572ad05b22622f6534b95c9d26ccbede09b7") + + depends_on("libpng") + depends_on("libuuid") + depends_on("gmake") + depends_on("mysql-connector-c") + depends_on("openssl") + depends_on("zlib") + + def setup_build_environment(self, env): + env.set("MYSQLLIBS", "-lmysqlclient") + env.set("L", "-lssl") + env.set("BINDIR", "bin") + + def install(self, spec, prefix): + with working_dir("kent/src/lib"): + make() + with working_dir("kent/src/htslib"): + make() + with working_dir("kent/src/jkOwnLib"): + make() + with working_dir("kent/src/hg/lib"): + make() + with working_dir("kent/src/hg/lib"): + make() + with working_dir("kent/src/utils/bedClip"): + mkdirp("bin") + mkdirp(prefix.bin) + make() + make("install") + install("bin/bedClip", prefix.bin) |