From fee6f69b6a43cd94ac49350d487825c190e97360 Mon Sep 17 00:00:00 2001
From: Guoyi Zhang <kuoi@bioarchlinux.org>
Date: Thu, 6 Feb 2025 16:38:16 +1100
Subject: [PATCH] ipyrad: init

---
 BioArchLinux/ipyrad/PKGBUILD   | 35 ++++++++++++++++++++++++++++++++++
 BioArchLinux/ipyrad/lilac.yaml | 22 +++++++++++++++++++++
 2 files changed, 57 insertions(+)
 create mode 100644 BioArchLinux/ipyrad/PKGBUILD
 create mode 100644 BioArchLinux/ipyrad/lilac.yaml

diff --git a/BioArchLinux/ipyrad/PKGBUILD b/BioArchLinux/ipyrad/PKGBUILD
new file mode 100644
index 0000000000..294faa7a21
--- /dev/null
+++ b/BioArchLinux/ipyrad/PKGBUILD
@@ -0,0 +1,35 @@
+pkgname=ipyrad
+pkgver=0.9.104
+pkgrel=1
+pkgdesc="Interactive assembly and analysis of RAD-seq data sets."
+arch=('any')
+url="https://github.com/dereneaton/ipyrad"
+license=('GPL-3.0-or-later')
+depends=('python' 'python-pandas' 'python-scipy' 'python-numpy' 'python-numba' 'python-future' 'python-h5py' 'python-ipyparallel' 'python-requests' 'python-mpi4py' 
+		'cutadapt' 'python-pysam'  'bedtools' 'vsearch' 'bwa' 'samtools' 'python-toyplot')
+optdepends=('jupyter-notebook: for interactive')
+makedepends=('python-build' 'python-installer' 'python-wheel' 'gcc' 'make')
+source=("https://github.com/dereneaton/ipyrad/archive/${pkgver}.tar.gz"
+	"https://drive5.com/muscle/muscle_src_3.8.1551.tar.gz")
+sha256sums=('8da9e03569ee1bc0e84bafefd1204249091602a9caa732a79511f67ba81d96b1'
+            'c70c552231cd3289f1bad51c9bd174804c18bb3adcf47f501afec7a68f9c482e')
+provides=('muscle<5')
+conflicts=('muscle')
+build() {
+    # muscle v3
+    cd $srcdir
+    make CFLAGS=" -march=x86-64 -mtune=generic -O2 -pipe" LDLIBS=" -lm"
+
+    cd "${srcdir}/${pkgname}-${pkgver}"
+    python -m build --wheel --no-isolation
+}
+
+package() {
+    #muscle v3
+    cd "$srcdir"
+    install -D -m755 muscle "$pkgdir/usr/bin/muscle"
+
+    cd "${srcdir}/${pkgname}-${pkgver}"
+    python -m installer --destdir="${pkgdir}" dist/*.whl
+}
+
diff --git a/BioArchLinux/ipyrad/lilac.yaml b/BioArchLinux/ipyrad/lilac.yaml
new file mode 100644
index 0000000000..51e69c8e84
--- /dev/null
+++ b/BioArchLinux/ipyrad/lilac.yaml
@@ -0,0 +1,22 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: starsareintherose
+    email: kuoi@bioarchlinux.org
+pre_build_script: |
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+  run_cmd(['updpkgsums'])
+post_build_script: |
+  git_pkgbuild_commit()
+repo_depends:
+  - cutadapt
+  - python-pysam
+  - bedtools
+  - vsearch
+  - bwa
+  - samtools
+  - python-toyplot
+update_on:
+  - source: github
+    github: dereneaton/ipyrad
+    use_latest_release: true
+  - alias: python