From dcf13af459f39ae1002f830e1790b8748156db7e Mon Sep 17 00:00:00 2001
From: Teague Sterling <teaguesterling@users.noreply.github.com>
Date: Tue, 2 Jul 2024 23:40:02 -0700
Subject: kentutils: add v455, v460, v464, v465 + package updates (#44413)
This addresses a few issues in the kentutils package:
- Issue #44372
- Cleaning up formattting and styles
- Removing old versions that are not avaialble anymore
- Removing newer versions that are also not available anymore
- The installer does not install the static libs
that are expected by packages that depend on kentutils
- There are conflicts and less-than-desirable dependencies
that can be addressed via variants
Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
---
.../kentutils/fix-mysql-options-gcc13.patch | 13 ++
.../packages/kentutils/mysql-zlib-workaround.patch | 13 ++
.../repos/builtin/packages/kentutils/package.py | 147 ++++++++++++++++++---
3 files changed, 157 insertions(+), 16 deletions(-)
create mode 100644 var/spack/repos/builtin/packages/kentutils/fix-mysql-options-gcc13.patch
create mode 100644 var/spack/repos/builtin/packages/kentutils/mysql-zlib-workaround.patch
diff --git a/var/spack/repos/builtin/packages/kentutils/fix-mysql-options-gcc13.patch b/var/spack/repos/builtin/packages/kentutils/fix-mysql-options-gcc13.patch
new file mode 100644
index 0000000000..f0a799d306
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kentutils/fix-mysql-options-gcc13.patch
@@ -0,0 +1,13 @@
+diff --git a/jksql.c.orig b/jksql.c
+index bf38b3b..69b2c42 100644
+--- a/kent/src/hg/lib/jksql.c
++++ b/kent/src/hg/lib/jksql.c
+@@ -1129,7 +1129,7 @@ mysql_options(conn, MYSQL_OPT_LOCAL_INFILE, NULL);
+ if (sp->verifyServerCert && !sameString(sp->verifyServerCert,"0"))
+ {
+ #if !defined(MARIADB_VERSION_ID) && MYSQL_VERSION_ID >= 80000
+- mysql_options(conn, MYSQL_OPT_SSL_MODE, SSL_MODE_REQUIRED);
++ mysql_options(conn, MYSQL_OPT_SSL_MODE, (void*) SSL_MODE_REQUIRED);
+ #else
+ my_bool flag = TRUE;
+ mysql_options(conn, MYSQL_OPT_SSL_VERIFY_SERVER_CERT, &flag);
diff --git a/var/spack/repos/builtin/packages/kentutils/mysql-zlib-workaround.patch b/var/spack/repos/builtin/packages/kentutils/mysql-zlib-workaround.patch
new file mode 100644
index 0000000000..10a460d781
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kentutils/mysql-zlib-workaround.patch
@@ -0,0 +1,13 @@
+diff --git a/kent/src/inc/common.mk.orig b/kent/src/inc/common.mk
+index 83803ad..8c90e3a 100644
+--- a/kent/src/inc/common.mk
++++ b/kent/src/inc/common.mk
+@@ -226,6 +226,8 @@ ifeq (${ZLIB},)
+ ZLIB=-lz
+ endif
+
++MYSQLLIBS := $(subst -lzlib,, ${MYSQLLIBS})
++
+ # on hgwdev, use the static libraries
+ ifeq (${IS_HGWDEV},yes)
+ FULLWARN = yes
diff --git a/var/spack/repos/builtin/packages/kentutils/package.py b/var/spack/repos/builtin/packages/kentutils/package.py
index c6bb2c29e7..47bbfb9700 100644
--- a/var/spack/repos/builtin/packages/kentutils/package.py
+++ b/var/spack/repos/builtin/packages/kentutils/package.py
@@ -3,39 +3,154 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+import os
+
from spack.package import *
class Kentutils(MakefilePackage):
- """Jim Kent command line bioinformatic utilities"""
+ """
+ Jim Kent command line bioinformatic utilities and libraries
+
+ This bundles a custom version of htslib, but can be overridden with ~htslib.
+ Consider adding the ^mysql+client_only dependency to avoid building all mysql/mariadb.
+ """
homepage = "https://genome.cse.ucsc.edu/"
url = "https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v453.src.tgz"
- version("459", sha256="0b6e89a183e6385c713cf010a7aeead9da6626d8d2f78c363a4f1bc56ccccebb")
- # The above archive only goes back to v305. v302 is left for now but deprecated. Suggest
- # this is dropped on next update (v302 is from 2014!) and the `requires()` removed.
+ maintainers("teaguesterling")
+
+ version("465", sha256="eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0")
+ version("464", sha256="24e20fe68e2a2894d802c87662f69a62f71b3c15fafb2e4d6c3c425c63638bb2")
+ version("460", sha256="b955e56ee880074521ef1ab1371491f47e66dc6fdd93b05328386dd675a635fa")
+ version("455", sha256="e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db")
+ # This version isn't present in the archive any more
+ # Might be worth changing url to: https://github.com/ucscGenomeBrowser/kent-core/tags/...
version(
- "302.1",
- commit="d8376c5d52a161f2267346ed3dc94b5dce74c2f9",
- git="https://github.com/ENCODE-DCC/kentUtils.git",
+ "459",
+ sha256="0b6e89a183e6385c713cf010a7aeead9da6626d8d2f78c363a4f1bc56ccccebb",
deprecated=True,
)
- depends_on("libpng")
- depends_on("openssl")
- depends_on("uuid")
- depends_on("mariadb")
- depends_on("zlib-api")
- depends_on("freetype")
- depends_on("libiconv")
+ # The bundled version of kentlib has some custom changes that are used by parts of
+ # kentlib. See https://github.com/spack/spack/pull/44501#issuecomment-2162789410
+ # for some additional details. A built-in version SHOULD work for most things though.
+ variant(
+ "builtin_htslib",
+ default=False,
+ description="Build with bundled htslib (using an external htslib may lead to errors)",
+ sticky=True,
+ )
+
+ with default_args(type=("build", "link", "run")):
+ depends_on("libpng")
+ depends_on("openssl")
+ depends_on("uuid")
+ depends_on("mysql-client")
+ depends_on("zlib-api")
+ depends_on("freetype")
+ depends_on("libiconv")
+ depends_on("htslib+pic", when="~builtin_htslib")
- requires("%gcc", when="@302.1")
+ # The bgzip.c bug present in other packages is present in kent/src/htslib/bgzf.c
+ # Conflicting line: assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE);
+ # We can patch this by removing the assertion, but there are still performance issues
+ # See: https://github.com/samtools/htslib/issues/1257
+ conflicts("zlib-ng")
+
+ # Does not add a link to mysql_config, which is required for compilation
+ conflicts("mariadb-c-client")
+
+ # MySQL pointer/integer conversion issue (https://github.com/ucscGenomeBrowser/kent/pull/87)
+ patch("fix-mysql-options-gcc13.patch", when="%gcc@13: ^mysql")
+ # MySQL build flags from `mysql_config` are not compatible with Spack's method of building
+ # and includes zlib when it's not needed/available, leading to a linking failure.
+ patch("mysql-zlib-workaround.patch", when="%gcc ^mysql")
def flag_handler(self, name, flags):
- if name == "ldflags":
+ if name == "cflags":
+ flags.append(self.compiler.cc_pic_flag)
+ elif name == "ldflags":
flags.append(f'{self.spec["libiconv"].libs.ld_flags}')
return (flags, None, None)
+ @property
+ def machtype(self):
+ # This is hard-coded in the Makefile and included here for reference
+ # and to make it adjustable if we need to adjust this in the future
+ return "local"
+
+ @property
+ def headers(self):
+ headers = []
+ headers.extend(find_headers("*", self.prefix.inc, recursive=True))
+ if self.spec.satisfies("+builtin_htslib"):
+ headers.extend(find_headers("*", self.prefix.htslib, recursive=True))
+ return HeaderList(headers)
+
+ @property
+ def libs(self):
+ return LibraryList([join_path(self.prefix, lib) for lib in self.local_libs])
+
+ @property
+ def local_libs(self):
+ libs = [
+ f"lib/{self.machtype}/jkweb.a",
+ f"lib/{self.machtype}/jkOwnLib.a",
+ f"lib/{self.machtype}/jkhgap.a",
+ f"lib/{self.machtype}/jkhgapcgi.a",
+ f"hg/altSplice/lib/{self.machtype}/libSpliceGraph.a",
+ ]
+ if self.spec.satisfies("+builtin_htslib"):
+ libs.append("htslib/libhts.a")
+ return LibraryList(libs)
+
+ @property
+ def lib_dir(self):
+ return join_path(self.prefix.lib, self.machtype)
+
+ @property
+ def htslib_include_dir(self):
+ if self.spec.satisfies("~builtin_htslib"):
+ # If we're not using the bundled version, just defer to htslib
+ return self.spec["htslib"].prefix.include
+ else:
+ # In the event we're using the bundled htslib, the htslib
+ # headers live in a different part of the installed tree
+ return self.prefix.htslib
+
+ # Packages that link to kentlib (and potential, htslib) often have
+ # idiosyncratic ways of setting up their includes and linker paths.
+ # Having these paths available will make things cleaner downstream.
+ def setup_dependent_package(self, module, dep_spec):
+ setattr(module, "kentutils_include_dir", self.prefix.inc)
+ setattr(module, "kentutils_lib_dir", self.lib_dir)
+ setattr(module, "kentutils_htslib_include_dir", self.htslib_include_dir)
+
+ def install_libs_from_stage(self, spec, prefix):
+ # Dependent packages expect things in the source tree, but we don't
+ # want to copy all of the compilation artifacts in so we'll do them
+ # manually instead of leaving the build directory around
+
+ src_prefix = "kent/src"
+
+ def install_kent(path, tree):
+ src = join_path(src_prefix, path)
+ dest = join_path(prefix, path)
+ mkdirp(os.path.dirname(dest))
+ if tree:
+ install_tree(src, dest)
+ else:
+ install(src, dest)
+
+ install_kent("inc", tree=True)
+ if spec.satisfies("+builtin_htslib"):
+ install_kent("htslib/htslib", tree=True)
+
+ for lib in self.local_libs:
+ install_kent(lib, tree=False)
+
def install(self, spec, prefix):
install_tree("bin", prefix.bin)
+ self.install_libs_from_stage(spec, prefix)
--
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