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| author | Diego Alvarez S <dialvarezs@gmail.com> | 2024-06-03 18:30:00 -0300 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2024-06-03 14:30:00 -0700 |
| commit | 9428d999919a0fb218be3a5a8efb0e31dd2d30f1 (patch) | |
| tree | 2991c414de3f8d022894d9d86089fe2bae888907 | |
| parent | f3cf2e94c46bfc5a295863337fab719834c3b9d8 (diff) | |
| download | spack-9428d999919a0fb218be3a5a8efb0e31dd2d30f1.tar.gz spack-9428d999919a0fb218be3a5a8efb0e31dd2d30f1.tar.bz2 spack-9428d999919a0fb218be3a5a8efb0e31dd2d30f1.tar.xz spack-9428d999919a0fb218be3a5a8efb0e31dd2d30f1.zip | |
seqfu: new package (#44445)
* Add seqfu
---------
Co-authored-by: dialvarezs <dialvarezs@users.noreply.github.com>
| -rw-r--r-- | var/spack/repos/builtin/packages/seqfu/package.py | 32 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/seqfu/wno_incompatible_pointer_types.patch | 13 |
2 files changed, 45 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/seqfu/package.py b/var/spack/repos/builtin/packages/seqfu/package.py new file mode 100644 index 0000000000..99dcae672b --- /dev/null +++ b/var/spack/repos/builtin/packages/seqfu/package.py @@ -0,0 +1,32 @@ +# Copyright 2013-2024 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 Seqfu(Package): + """seqfu - Sequece Fastx Utilities""" + + homepage = "https://github.com/telatin/seqfu2" + url = "https://github.com/telatin/seqfu2/archive/refs/tags/v1.20.3.tar.gz" + + license("GPL-3.0", checked_by="dialvarezs") + + version("1.20.3", sha256="1b287b99f3f1ac7045f4d551e781d6780ce168ba8e0a7bfaa0f5490f32e15938") + + depends_on("nim@2", type="build") + depends_on("zlib", type="build") + + patch("wno_incompatible_pointer_types.patch", when="%gcc@14:") + + def setup_build_environment(self, env): + env.set("NIMBLE_DIR", ".nimble") + + def install(self, spec, prefix): + nimble = Executable("nimble") + nimble("install", "-y", "--depsOnly") + + make(parallel=False) + install_tree("bin", join_path(prefix, "bin")) diff --git a/var/spack/repos/builtin/packages/seqfu/wno_incompatible_pointer_types.patch b/var/spack/repos/builtin/packages/seqfu/wno_incompatible_pointer_types.patch new file mode 100644 index 0000000000..b8c2e93d7b --- /dev/null +++ b/var/spack/repos/builtin/packages/seqfu/wno_incompatible_pointer_types.patch @@ -0,0 +1,13 @@ +diff --git a/Makefile b/Makefile +index 287bb7c..7fb9434 100644 +--- a/Makefile ++++ b/Makefile +@@ -7,7 +7,7 @@ SCRIPTS=./scripts + SOURCE=./src + DATA=./data + VERSION := $(shell grep version seqfu.nimble | grep -o "[0-9]\\+\.[0-9]\\+\.[0-9]\\+") +-NIMPARAM := --gc:orc -d:NimblePkgVersion=$(VERSION) -d:release --opt:speed ++NIMPARAM := --gc:orc -d:NimblePkgVersion=$(VERSION) -d:release --opt:speed --passC:"-Wno-error=incompatible-pointer-types" + TARGETS=$(BIN)/seqfu $(BIN)/fu-msa $(BIN)/fu-primers $(BIN)/dadaist2-mergeseqs $(BIN)/fu-shred $(BIN)/fu-homocomp $(BIN)/fu-multirelabel $(BIN)/fu-index $(BIN)/fu-cov $(BIN)/fu-16Sregion $(BIN)/fu-nanotags $(BIN)/fu-orf $(BIN)/fu-sw $(BIN)/fu-virfilter $(BIN)/fu-tabcheck $(BIN)/byteshift $(BIN)/SeqCountHelper $(BIN)/fu-secheck + PYTARGETS=$(BIN)/fu-split $(BIN)/fu-pecheck $(BIN)/fu-readtope + |