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| author | pabloaledo <112545720+pabloaledo@users.noreply.github.com> | 2023-08-03 14:16:30 +0200 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2023-08-03 14:16:30 +0200 |
| commit | 85e5fb9ab76e39bf1b7b0a7ff36237e3941626d6 (patch) | |
| tree | 4d7bf585d5a1fb8009179b4bfc259a3309f7c530 /var | |
| parent | c0c300d7735c25cc521d85277f7287fbd20bcd48 (diff) | |
| download | spack-85e5fb9ab76e39bf1b7b0a7ff36237e3941626d6.tar.gz spack-85e5fb9ab76e39bf1b7b0a7ff36237e3941626d6.tar.bz2 spack-85e5fb9ab76e39bf1b7b0a7ff36237e3941626d6.tar.xz spack-85e5fb9ab76e39bf1b7b0a7ff36237e3941626d6.zip | |
ucsc-bedgraphtobigwig: add package (#39208)
Signed-off-by: Pablo <pablo.aledo@seqera.io>
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/ucsc-bedgraphtobigwig/package.py | 50 |
1 files changed, 50 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/ucsc-bedgraphtobigwig/package.py b/var/spack/repos/builtin/packages/ucsc-bedgraphtobigwig/package.py new file mode 100644 index 0000000000..ccb84f38ea --- /dev/null +++ b/var/spack/repos/builtin/packages/ucsc-bedgraphtobigwig/package.py @@ -0,0 +1,50 @@ +# 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 UcscBedgraphtobigwig(Package): + """Convert a bedGraph file to bigWig format.""" + + homepage = "http://hgdownload.cse.ucsc.edu/admin/exe/" + url = "https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v445.src.tgz" + + version("449", sha256="b5a86863d6cfe2120f6c796a13b1572ad05b22622f6534b95c9d26ccbede09b7") + version("445", sha256="c7abb5db6a5e16a79aefcee849d2b59dbc71ee112ca1e41fea0afb25229cf56c") + + depends_on("libpng") + depends_on("libuuid") + depends_on("gmake") + depends_on("openssl") + depends_on("zlib") + # This package has known issues installing with the latest MySQL because + # MySQL removed the type my_bool, while mariadb didn't. + # https://groups.google.com/a/soe.ucsc.edu/g/genome/c/mIT6fe9l99g + depends_on("mysql-client") + conflicts("mysql@8.0.0:") + + 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/bedGraphToBigWig"): + mkdirp(prefix.bin) + mkdirp("bin") + make() + make("install") + install("bin/bedGraphToBigWig", prefix.bin) |