add abyss and afni

BioArchLinux/abyss/PKGBUILD

@@ -0,0 +1,43 @@
+# Maintainer: PolpOnline <aur at t0mmy dot anonaddy dot com>
+# Contributor:  Eric Biggers <ebiggers3 at gmail dot com>
+
+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"
+}
+
+

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()

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

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

BioArchLinux/afni/PKGBUILD

@@ -0,0 +1,36 @@
+# Maintainer:  Liam Timms <timms5000@gmail.com>
+# Contributor: Chris <christopher.r.mullins g-mail>
+# Contributor: cornholio <vigo.the.unholy.carpathian@gmail.com>
+# Contributor: martin <martin pipegrep.co.uk>
+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
+}

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()

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_'