Merge pull request #18 from BioArchLinux/mick

new packages in mick branch

BioArchLinux/bayesass/PKGBUILD

@@ -0,0 +1,28 @@
+# Maintainer:  Mick Elliot <m.g.elliot@rug.nl>
+# Contributor: Mick Elliot <m.g.elliot@rug.nl>
+
+pkgname=bayesass
+_pkgname=BA3
+pkgver=3.0.4.2
+pkgrel=1
+pkgdesc="Software for inferring proportions of recent migrants among populations using multilocus genotype data."
+arch=('x86_64')
+url="https://github.com/brannala/${_pkgname}"
+license=('GPL')
+depends=(gsl cblas gcc-libs)
+source=("${url}/archive/refs/tags/${pkgver}.tar.gz")
+
+sha256sums=('6f808241da430a4554510870c381b646f4655bf461641c9f18feedda7b88889a')
+
+build() {
+  cd "${_pkgname}-${pkgver}"
+  make
+}
+
+package() {
+  cd "${_pkgname}-${pkgver}"
+  install -Dm755 BA3MSAT "${pkgdir}/usr/bin/BA3MSAT"
+  install -Dm755 BA3SNP "${pkgdir}/usr/bin/BA3SNP"
+}
+
+

BioArchLinux/bayesass/lilac.py

@@ -0,0 +1,11 @@
+#!/usr/bin/env python3
+
+from lilaclib import *
+
+def pre_build():
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+
+def post_build():
+  git_add_files('PKGBUILD')
+  git_commit()
+

BioArchLinux/bayesass/lilac.yaml

@@ -0,0 +1,9 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: michael.g.elliot
+    email: m.g.elliot@rug.nl
+update_on:
+  - source: regex
+    regex: (\d+.\d+.\d+.\d+)
+    url: https://github.com/brannala/BA3/tags
+

BioArchLinux/lastz/PKGBUILD

@@ -0,0 +1,35 @@
+# Maintainer:  Mick Elliot <m.g.elliot@rug.nl>
+# Contributor: Mick Elliot <m.g.elliot@rug.nl>
+
+pkgname=lastz
+pkgver=1.04.15
+pkgrel=1
+pkgdesc="Pairwise DNA sequence aligner"
+arch=('x86_64')
+url="https://lastz.github.io/lastz/"
+license=('MIT')
+depends=(glibc)
+makedepends=()
+provides=(lastz)
+source=("https://github.com/${pkgname}/${pkgname}/archive/refs/tags/${pkgver}.tar.gz")
+sha256sums=('46a5cfb1fd41911a36fce5d3a2721ebfec9146952943b302e78b0dfffddd77f8')
+
+build() {
+  cd "${pkgname}-${pkgver}"
+  make -f Makefile.warnings
+  make -f Makefile.warnings lastz_32
+}
+
+check() {
+  cd "${pkgname}-${pkgver}"
+  make test
+}
+
+package() {
+  cd "${pkgname}-${pkgver}"
+  export LASTZ_INSTALL="${pkgdir}/usr/bin" && make install
+  export LASTZ_INSTALL="${pkgdir}/usr/bin" && make install_32
+  install -Dm644 LICENSE "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
+}
+
+

BioArchLinux/lastz/lilac.py

@@ -0,0 +1,11 @@
+#!/usr/bin/env python3
+
+from lilaclib import *
+
+def pre_build():
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+
+def post_build():
+  git_add_files('PKGBUILD')
+  git_commit()
+

BioArchLinux/lastz/lilac.yaml

@@ -0,0 +1,10 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: michaelgelliot
+    email: m.g.elliot@rug.nl
+update_on:
+  - source: github
+    github: lastz/lastz
+    use_max_tag: true
+
+

BioArchLinux/lastz_backtobackgaps/PKGBUILD

@@ -0,0 +1,36 @@
+# Maintainer:  Mick Elliot <m.g.elliot@rug.nl>
+# Contributor: Mick Elliot <m.g.elliot@rug.nl>
+
+pkgname=lastz_backtobackgaps
+_pkgname=lastz
+pkgver=1.04.15
+pkgrel=1
+pkgdesc="Pairwise DNA sequence aligner. This version allows back to back gaps (adjacent indels) but might break backward compatibility with lastZ and BLASTZ."
+arch=('x86_64')
+url="https://lastz.github.io/lastz/"
+license=('MIT')
+depends=(glibc)
+makedepends=()
+provides=(lastz)
+source=("https://github.com/${_pkgname}/${_pkgname}/archive/refs/tags/${pkgver}.tar.gz")
+sha256sums=('46a5cfb1fd41911a36fce5d3a2721ebfec9146952943b302e78b0dfffddd77f8')
+
+build() {
+  cd "${_pkgname}-${pkgver}"
+  make -f Makefile.warnings allowBackToBackGaps=ON
+  make -f Makefile.warnings lastz_32 allowBackToBackGaps=ON
+}
+
+check() {
+  cd "${_pkgname}-${pkgver}"
+  make test
+}
+
+package() {
+  cd "${_pkgname}-${pkgver}"
+  export LASTZ_INSTALL="${pkgdir}/usr/bin" && make install
+  export LASTZ_INSTALL="${pkgdir}/usr/bin" && make install_32
+  install -Dm644 LICENSE "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
+}
+
+

BioArchLinux/lastz_backtobackgaps/lilac.py

@@ -0,0 +1,11 @@
+#!/usr/bin/env python3
+
+from lilaclib import *
+
+def pre_build():
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+
+def post_build():
+  git_add_files('PKGBUILD')
+  git_commit()
+

BioArchLinux/lastz_backtobackgaps/lilac.yaml

@@ -0,0 +1,10 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: michaelgelliot
+    email: m.g.elliot@rug.nl
+update_on:
+  - source: github
+    github: lastz/lastz
+    use_max_tag: true
+
+

BioArchLinux/libarmadillo/PKGBUILD

@@ -0,0 +1,31 @@
+# Maintainer:  Mick Elliot <m.g.elliot@rug.nl>
+# Contributor: Mick Elliot <m.g.elliot@rug.nl>
+
+pkgname=libarmadillo
+_pkgname=armadillo
+sfname=arma
+pkgver=10.8.0
+pkgrel=1
+pkgdesc="C++ library for linear algebra & scientific computing"
+arch=('x86_64')
+url="http://${sfname}.sourceforge.net/"
+license=('Apache')
+depends=(openblas lapack)
+makedepends=(cmake)
+optdepends=()
+provides=()
+source=("http://sourceforge.net/projects/${sfname}/files/${_pkgname}-${pkgver}.tar.xz")
+
+sha256sums=('7c5d2fd4bba095733829f7fe03d4a74e732b81c75dd4d40001163487c967d5bc')
+
+build() {
+  cd "${_pkgname}-${pkgver}"
+  cmake . -DCMAKE_INSTALL_PREFIX="/usr"
+  make
+}
+
+package() {
+  cd "${_pkgname}-${pkgver}"
+  make DESTDIR=${pkgdir} install 
+  install -Dm644 LICENSE.txt "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
+}

BioArchLinux/libarmadillo/lilac.py

@@ -0,0 +1,12 @@
+#!/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/libarmadillo/lilac.yaml

@@ -0,0 +1,9 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: michaelgelliot
+    email: m.g.elliot@rug.nl
+update_on:
+  - regex: armadillo-(\d+.\d+.\d+).tar.xz
+    source: regex
+    url: https://sourceforge.net/projects/arma/files/
+

BioArchLinux/migrate-n-mpi/PKGBUILD

@@ -0,0 +1,30 @@
+# Maintainer:  Mick Elliot <m.g.elliot@rug.nl>
+# Contributor: Mick Elliot <m.g.elliot@rug.nl>
+
+pkgname=migrate-n-mpi
+_pkgname=migrate
+pkgver=4.4.4
+pkgrel=1
+pkgdesc="Bayesian estimation of effective population sizes, migration rates, and population divergences or admixture, multithreaded version"
+arch=('x86_64')
+url="https://peterbeerli.com/migrate-html5"
+license=('MIT')
+depends=(openmpi)
+makedepends=()
+optdepends=(zlib)
+provides=()
+source=("${url}/download_version4/${_pkgname}-${pkgver}.src.tar.gz")
+
+sha256sums=('e30f2e9ce8aa7ec987019eca5cad16d1e51c68f7c56711899bf61c3031115d66')
+
+build() {
+  cd "${_pkgname}-${pkgver}/src"
+  ./configure --prefix=/usr
+  make mpis
+}
+
+package() {
+  cd "${_pkgname}-${pkgver}/src"
+  install -Dm755 migrate-n-mpi "${pkgdir}/usr/bin/migrate-n-mpi"
+}
+

BioArchLinux/migrate-n-mpi/lilac.py

@@ -0,0 +1,10 @@
+#!/usr/bin/env python3
+
+from lilaclib import *
+
+def pre_build():
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+
+def post_build():
+  git_add_files('PKGBUILD')
+  git_commit()

BioArchLinux/migrate-n-mpi/lilac.yaml

@@ -0,0 +1,8 @@
+maintainers:
+  - github: michael.g.elliot
+    email: m.g.elliot@rug.nl
+build_prefix: extra-x86_64
+update_on:
+  - source: regex
+    url: "https://peterbeerli.com/migrate-html5/download_version4/"
+    regex:   migrate-(\d+.\d+.\d+).src.tar.gz

BioArchLinux/migrate-n-mt/PKGBUILD

@@ -0,0 +1,30 @@
+# Maintainer:  Mick Elliot <m.g.elliot@rug.nl>
+# Contributor: Mick Elliot <m.g.elliot@rug.nl>
+
+pkgname=migrate-n-mt
+_pkgname=migrate
+pkgver=4.4.4
+pkgrel=1
+pkgdesc="Bayesian estimation of effective population sizes, migration rates, and population divergences or admixture, multithreaded version"
+arch=('x86_64')
+url="https://peterbeerli.com/migrate-html5"
+license=('MIT')
+depends=()
+makedepends=()
+optdepends=(zlib)
+provides=(migrate-n)
+source=("${url}/download_version4/${_pkgname}-${pkgver}.src.tar.gz")
+
+sha256sums=('e30f2e9ce8aa7ec987019eca5cad16d1e51c68f7c56711899bf61c3031115d66')
+
+build() {
+  cd "${_pkgname}-${pkgver}/src"
+  ./configure --prefix=/usr
+  make thread
+}
+
+package() {
+  cd "${_pkgname}-${pkgver}/src"
+  install -Dm755 migrate-n "${pkgdir}/usr/bin/migrate-n"
+}
+

BioArchLinux/migrate-n-mt/lilac.py

@@ -0,0 +1,10 @@
+#!/usr/bin/env python3
+
+from lilaclib import *
+
+def pre_build():
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+
+def post_build():
+  git_add_files('PKGBUILD')
+  git_commit()

BioArchLinux/migrate-n-mt/lilac.yaml

@@ -0,0 +1,8 @@
+maintainers:
+  - github: michael.g.elliot
+    email: m.g.elliot@rug.nl
+build_prefix: extra-x86_64
+update_on:
+  - source: regex
+    url: "https://peterbeerli.com/migrate-html5/download_version4/"
+    regex:   migrate-(\d+.\d+.\d+).src.tar.gz

BioArchLinux/migrate-n/PKGBUILD

@@ -0,0 +1,30 @@
+# Maintainer:  Mick Elliot <m.g.elliot@rug.nl>
+# Contributor: Mick Elliot <m.g.elliot@rug.nl>
+
+pkgname=migrate-n
+_pkgname=migrate
+pkgver=4.4.4
+pkgrel=1
+pkgdesc="Bayesian estimation of effective population sizes, migration rates, and population divergences or admixture, single CPU version"
+arch=('x86_64')
+url="https://peterbeerli.com/migrate-html5"
+license=('MIT')
+depends=()
+makedepends=()
+optdepends=(zlib)
+provides=(migrate-n)
+source=("${url}/download_version4/${_pkgname}-${pkgver}.src.tar.gz")
+
+sha256sums=('e30f2e9ce8aa7ec987019eca5cad16d1e51c68f7c56711899bf61c3031115d66')
+
+build() {
+  cd "${_pkgname}-${pkgver}/src"
+  ./configure --prefix=/usr
+  make
+}
+
+package() {
+  cd "${_pkgname}-${pkgver}/src"
+  install -Dm755 migrate-n "${pkgdir}/usr/bin/migrate-n"
+}
+

BioArchLinux/migrate-n/lilac.py

@@ -0,0 +1,10 @@
+#!/usr/bin/env python3
+
+from lilaclib import *
+
+def pre_build():
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+
+def post_build():
+  git_add_files('PKGBUILD')
+  git_commit()

BioArchLinux/migrate-n/lilac.yaml

@@ -0,0 +1,8 @@
+maintainers:
+  - github: michael.g.elliot
+    email: m.g.elliot@rug.nl
+build_prefix: extra-x86_64
+update_on:
+  - source: regex
+    url: "https://peterbeerli.com/migrate-html5/download_version4/"
+    regex:   migrate-(\d+.\d+.\d+).src.tar.gz

BioArchLinux/phyx/PKGBUILD

@@ -0,0 +1,38 @@
+# Maintainer:  Mick Elliot <m.g.elliot@rug.nl>
+# Contributor: Mick Elliot <m.g.elliot@rug.nl>
+
+pkgname=phyx
+pkgver=1.3
+pkgrel=1
+pkgdesc="Command-line phylogenetic tools for unix. https://doi.org/10.1093/bioinformatics/btx063"
+arch=('x86_64')
+url="http://${sfname}.sourceforge.net/"
+license=('GPL')
+depends=(libarmadillo nlopt lapack)
+makedepends=(curl)
+optdepends=()
+provides=()
+source=("https://github.com/FePhyFoFum/${pkgname}/archive/refs/tags/v${pkgver}.tar.gz")
+
+sha256sums=('b09677f98f997838b39cd2724463be06d0627ddc90a7e659dc90d4e02db624eb')
+
+build() {
+  cd "${pkgname}-${pkgver}/src"
+  echo "Downloading config.guess and config.sub from gnu git site..."
+  curl 'https://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD' --output config.guess
+  curl 'https://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD' --output config.sub 
+  autoconf
+  ./configure
+  make
+}
+
+check() {
+  cd "${pkgname}-${pkgver}/src"
+  make check
+}
+
+package() {
+  cd "${pkgname}-${pkgver}/src"
+  make PREFIX=${pkgdir}/usr install 
+  install -Dm644 ../LICENSE "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
+}

BioArchLinux/phyx/lilac.py

@@ -0,0 +1,11 @@
+#!/usr/bin/env python3
+
+from lilaclib import *
+
+def pre_build():
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+
+def post_build():
+  git_add_files('PKGBUILD')
+  git_commit()
+

BioArchLinux/phyx/lilac.yaml

@@ -0,0 +1,9 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: michael.g.elliot
+    email: m.g.elliot@rug.nl
+update_on:
+  - source: github
+    github: FePhyFoFum/phyx
+    use_max_tag: true
+