From b829f472d4d1f77e35e97fb9cb7502610fdd6d5b Mon Sep 17 00:00:00 2001 From: Kuoi Date: Sat, 16 Apr 2022 22:41:21 +0100 Subject: [PATCH] add abyss and afni --- BioArchLinux/abyss/PKGBUILD | 43 ++++++++++++++++++++++++++++ BioArchLinux/abyss/lilac.py | 10 +++++++ BioArchLinux/abyss/lilac.yaml | 8 ++++++ BioArchLinux/afni/Makefile.patch | 48 ++++++++++++++++++++++++++++++++ BioArchLinux/afni/PKGBUILD | 36 ++++++++++++++++++++++++ BioArchLinux/afni/lilac.py | 10 +++++++ BioArchLinux/afni/lilac.yaml | 9 ++++++ 7 files changed, 164 insertions(+) create mode 100644 BioArchLinux/abyss/PKGBUILD create mode 100644 BioArchLinux/abyss/lilac.py create mode 100644 BioArchLinux/abyss/lilac.yaml create mode 100644 BioArchLinux/afni/Makefile.patch create mode 100644 BioArchLinux/afni/PKGBUILD create mode 100644 BioArchLinux/afni/lilac.py create mode 100644 BioArchLinux/afni/lilac.yaml diff --git a/BioArchLinux/abyss/PKGBUILD b/BioArchLinux/abyss/PKGBUILD new file mode 100644 index 0000000000..276a957242 --- /dev/null +++ b/BioArchLinux/abyss/PKGBUILD @@ -0,0 +1,43 @@ +# Maintainer: PolpOnline +# Contributor: Eric Biggers + +pkgname=abyss +pkgver=2.3.4 +pkgrel=1 +pkgdesc="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" +arch=("i686" "x86_64") +url="https://github.com/bcgsc/abyss" +license=("GPL3") +depends=("make" "openmpi" "sqlite") +makedepends=("boost" "sparsehash") +optdepends=( + 'pigz: for parallel gzip' + 'samtools: to read BAM files' + 'zsh: to report time and memory usage' +) +source=("$pkgname-$pkgver.tar.gz::https://github.com/bcgsc/abyss/archive/$pkgver.tar.gz") +sha512sums=('9d4e418399dd62883b53e831f51a0bd2ba228da73eda6c6459cd729c002eb0487f9613fca1c9bd0f4fbb076eed8a9b952505ee97143ab7dde537c23e4a246cd4') + +build() { + cd "${pkgname}-${pkgver}" + + ./autogen.sh + LDFLAGS="${LDFLAGS:-} -L/usr/lib/openmpi" \ + ./configure --prefix=/usr --disable-werror + make +} + +check() { + cd "${pkgname}-${pkgver}" + + make check +} + +package() { + cd "${pkgname}-${pkgver}" + + make DESTDIR="${pkgdir}" install + install -Dm644 "LICENSE" "$pkgdir/usr/share/licenses/$pkgname/LICENSE" +} + + diff --git a/BioArchLinux/abyss/lilac.py b/BioArchLinux/abyss/lilac.py new file mode 100644 index 0000000000..fcbff72939 --- /dev/null +++ b/BioArchLinux/abyss/lilac.py @@ -0,0 +1,10 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + update_pkgver_and_pkgrel(_G.newver.lstrip('v')) + run_cmd(['updpkgsums']) + +def post_build(): + git_add_files('PKGBUILD') + git_commit() diff --git a/BioArchLinux/abyss/lilac.yaml b/BioArchLinux/abyss/lilac.yaml new file mode 100644 index 0000000000..21c1b18f9b --- /dev/null +++ b/BioArchLinux/abyss/lilac.yaml @@ -0,0 +1,8 @@ +build_prefix: extra-x86_64 +maintainers: + - github: starsareintherose + email: starsareintherose@outlook.com +update_on: + - source: github + github: bcgsc/abyss + use_latest_release: true diff --git a/BioArchLinux/afni/Makefile.patch b/BioArchLinux/afni/Makefile.patch new file mode 100644 index 0000000000..cd5f2086bf --- /dev/null +++ b/BioArchLinux/afni/Makefile.patch @@ -0,0 +1,48 @@ +--- Makefile.linux_openmp_64 2019-03-08 22:08:10.000000000 +0000 ++++ Makefile 2019-03-14 20:49:36.783847110 +0000 +@@ -6,7 +6,7 @@ + USE_ZLIB = -DHAVE_ZLIB + LZLIB = -lz + USE_GIFTI = -DHAVE_GIFTI +-LGIFTI = /usr/lib64/libexpat.a ++LGIFTI = /usr/lib/libexpat.so + + # ------------------------------ + # python from C (off for now) +@@ -17,7 +17,7 @@ + # X configuration + # + # uncomment to build using local /usr/local/afniX 'X' tree +-USE_LOCAL_X_TREE = 1 ++# USE_LOCAL_X_TREE = 1 + ifdef USE_LOCAL_X_TREE + XROOT = /usr/local/afniX + XROOT_I = -I$(XROOT)/include +@@ -37,7 +37,7 @@ + endif + + # in case user wants to override with system dynamic libs +-# XLIBS = -lXm -lXt ++XLIBS = -lXm -lXt + # ---------------------------------------------------------------------- + + CCDEBS = -DAFNI_DEBUG -DIMSEQ_DEBUG -DDISPLAY_DEBUG -DTHD_DEBUG +@@ -46,7 +46,8 @@ + CC = /usr/bin/gcc -O2 -m64 -fPIC -DREAD_WRITE_64 -DLINUX2 $(CEXTRA) + CCVOL = /usr/bin/gcc -O2 -m64 -fPIC -DREAD_WRITE_64 -DLINUX2 $(CEXTRA) + CCFAST = /usr/bin/gcc -O2 -m64 -fPIC -DREAD_WRITE_64 -DLINUX2 $(CEXTRA) +-CCOLD = /usr/bin/gcc -V 34 -O2 -m64 -fPIC -DREAD_WRITE_64 -DLINUX2 $(CEXTRA) ++#CCOLD = /usr/bin/gcc -V 34 -O2 -m64 -fPIC -DREAD_WRITE_64 -DLINUX2 $(CEXTRA) ++CCOLD = $(CCFAST) + + # The following line includes compiling for the SSE operations. + # However, I found that it actually makes things worse in some test code. +@@ -84,7 +85,7 @@ + + LINT = /usr/bin/lint -a -b -u -v -x $(IFLAGS) $(CCDEFS) + +-INSTALLDIR = ./linux_openmp_64 ++INSTALLDIR = ../../build + LIBDIR = $(INSTALLDIR) + + #INSTALL_PREREQ = suma diff --git a/BioArchLinux/afni/PKGBUILD b/BioArchLinux/afni/PKGBUILD new file mode 100644 index 0000000000..e992441eb7 --- /dev/null +++ b/BioArchLinux/afni/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Liam Timms +# Contributor: Chris +# Contributor: cornholio +# Contributor: martin +pkgname=afni +pkgver=22.0.11 +pkgrel=1 +pkgdesc="An open-source environment for processing and displaying functional MRI data" +arch=("x86_64") +url="http://afni.nimh.nih.gov" +license=(custom) +depends=("r" "tcsh" "python" "gcc-libs" "gsl" "libxpm" "glu" "openmotif" "libjpeg-turbo" "libxmu" "libxft" "freeglut") +source=("$pkgname-$pkgver.tar.gz::https://github.com/afni/afni/archive/AFNI_$pkgver.tar.gz" "Makefile.patch") +md5sums=('b7080c068fe57aa9d331f7fd7bdc8e1c' + '2cc1916ecd1e775f52d189f1dd5b0ed9') + +prepare() { + cd "$srcdir"/afni-AFNI_$pkgver/src + cp Makefile.linux_openmp_64 Makefile + patch -Np0 -i "$srcdir"/Makefile.patch +} + +build() { + cd "$srcdir"/afni-AFNI_$pkgver/src + CPPFLAGS="" + make -j1 vastness +} + +package(){ + mkdir -p "$pkgdir"/opt + cp -r "$srcdir"/build "$pkgdir"/opt/afni + find "$pkgdir"/opt/afni -name \*.a -delete + find "$pkgdir"/opt/afni -name \*.h -delete + mkdir -p "$pkgdir"/usr/share/licenses/afni + cp "$srcdir"/afni-AFNI_$pkgver/doc/README/README.copyright "$pkgdir"/usr/share/licenses/afni/LICENSE +} diff --git a/BioArchLinux/afni/lilac.py b/BioArchLinux/afni/lilac.py new file mode 100644 index 0000000000..fcbff72939 --- /dev/null +++ b/BioArchLinux/afni/lilac.py @@ -0,0 +1,10 @@ +#!/usr/bin/env python3 +from lilaclib import * + +def pre_build(): + update_pkgver_and_pkgrel(_G.newver.lstrip('v')) + run_cmd(['updpkgsums']) + +def post_build(): + git_add_files('PKGBUILD') + git_commit() diff --git a/BioArchLinux/afni/lilac.yaml b/BioArchLinux/afni/lilac.yaml new file mode 100644 index 0000000000..6313876212 --- /dev/null +++ b/BioArchLinux/afni/lilac.yaml @@ -0,0 +1,9 @@ +build_prefix: extra-x86_64 +maintainers: + - github: starsareintherose + email: starsareintherose@outlook.com +update_on: + - source: github + github: afni/afni + use_max_tag: true + prefix: 'AFNI_'