From be679759be71177ed8df385dac8cf266e442f519 Mon Sep 17 00:00:00 2001 From: pabloaledo <112545720+pabloaledo@users.noreply.github.com> Date: Thu, 3 Aug 2023 14:04:37 +0200 Subject: ucsc-bedclip: add package (#39209) Signed-off-by: Pablo --- .../packages/mysql-connector-c/fix-cmake.patch | 12 ++++++ .../builtin/packages/mysql-connector-c/package.py | 23 +++++++++++ .../repos/builtin/packages/ucsc-bedclip/package.py | 46 ++++++++++++++++++++++ 3 files changed, 81 insertions(+) create mode 100644 var/spack/repos/builtin/packages/mysql-connector-c/fix-cmake.patch create mode 100644 var/spack/repos/builtin/packages/mysql-connector-c/package.py create mode 100644 var/spack/repos/builtin/packages/ucsc-bedclip/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/mysql-connector-c/fix-cmake.patch b/var/spack/repos/builtin/packages/mysql-connector-c/fix-cmake.patch new file mode 100644 index 0000000000..e9010c3a7b --- /dev/null +++ b/var/spack/repos/builtin/packages/mysql-connector-c/fix-cmake.patch @@ -0,0 +1,12 @@ +--- a/cmake/install_macros.cmake ++++ /dev/null +@@ -362,8 +362,8 @@ + CONFIGURATIONS Release RelWithDebInfo + COMPONENT ${ARG_COMPONENT} + OPTIONAL) +- ENDIF() + ENDFOREACH() ++ ENDIF() + + ENDFUNCTION() + diff --git a/var/spack/repos/builtin/packages/mysql-connector-c/package.py b/var/spack/repos/builtin/packages/mysql-connector-c/package.py new file mode 100644 index 0000000000..8b24b649d0 --- /dev/null +++ b/var/spack/repos/builtin/packages/mysql-connector-c/package.py @@ -0,0 +1,23 @@ +# 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 MysqlConnectorC(CMakePackage): + """MySQL Connector/C, the C interface for communicating with MySQL servers. + + Connector/C is a client library that implements the C API for client/server + communication. It is a standalone replacement for the MySQL client library + shipped with MySQL Server distributions.""" + + homepage = "https://dev.mysql.com/downloads/connector/c/" + url = "https://dev.mysql.com/get/Downloads/Connector-C/mysql-connector-c-6.1.11-src.tar.gz" + + depends_on("cmake") + + patch("fix-cmake.patch", when="@6.1.11") + + version("6.1.11", sha256="c8664851487200162b38b6f3c8db69850bd4f0e4c5ff5a6d161dbfb5cb76b6c4") 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) -- cgit v1.2.3-60-g2f50