From 7878654081a83cd29cd18e9f42d08dd61a93dc7f Mon Sep 17 00:00:00 2001
From: Kuoi <starsareintherose@outlook.com>
Date: Fri, 12 May 2023 20:45:56 +0800
Subject: [PATCH] abyss: fix

---
 BioArchLinux/abyss/PKGBUILD   | 17 +++++------------
 BioArchLinux/abyss/lilac.yaml |  2 ++
 2 files changed, 7 insertions(+), 12 deletions(-)

diff --git a/BioArchLinux/abyss/PKGBUILD b/BioArchLinux/abyss/PKGBUILD
index 215c597269..ce1301ac89 100644
--- a/BioArchLinux/abyss/PKGBUILD
+++ b/BioArchLinux/abyss/PKGBUILD
@@ -1,4 +1,5 @@
-# Maintainer: PolpOnline <aur at t0mmy dot anonaddy dot com>
+# Maintainer: Guoyi ZHang <myname at malacology dot net>
+# Contributor: PolpOnline <aur at t0mmy dot anonaddy dot com>
 # Contributor:  Eric Biggers <ebiggers3 at gmail dot com>
 
 pkgname=abyss
@@ -8,8 +9,8 @@ pkgdesc="Assembly By Short Sequences - a de novo, parallel, paired-end sequence
 arch=("i686" "x86_64")
 url="https://github.com/bcgsc/abyss"
 license=("GPL3")
-depends=("openmpi" "boost-libs" "btllib" "sqlite")
-makedepends=("boost" "sparsehash" "make")
+depends=("openmpi" "samtools")
+makedepends=("boost" "sparsehash" "make" "btllib")
 optdepends=(
   'pigz: for parallel gzip'
 )
@@ -18,19 +19,11 @@ sha512sums=('1853e2d4d577abf7d0e8ce70e944846e5ad67afcd1f0a1a4b9944047c7e8ebc1dbd
 
 build() {
   cd "${pkgname}-${pkgver}"
-
   ./autogen.sh
-  LDFLAGS="${LDFLAGS:-} -L/usr/lib/openmpi" \
-	  ./configure --prefix=/usr --disable-werror
+  ./configure --prefix=/usr --with-boost=/usr/lib --with-mpi=/usr/lib/openmpi --with-sparsehash=/usr/lib --without-sqlite --disable-werror
   make 
 }
 
-check() {
-  cd "${pkgname}-${pkgver}"
-
-  make check
-}
-
 package() {
   cd "${pkgname}-${pkgver}"
 
diff --git a/BioArchLinux/abyss/lilac.yaml b/BioArchLinux/abyss/lilac.yaml
index 4aa10943c3..a168e54350 100644
--- a/BioArchLinux/abyss/lilac.yaml
+++ b/BioArchLinux/abyss/lilac.yaml
@@ -7,8 +7,10 @@ pre_build_script: |
   run_cmd(['updpkgsums'])
 post_build_script: |
   git_pkgbuild_commit()
+  update_aur_repo()
 repo_depends:
   - btllib
+  - samtools
 update_on:
   - source: github
     github: bcgsc/abyss