Merge branch 'master' into mick

2025-03-10 12:02:42 +00:00 · 2022-01-05 16:17:59 +01:00 · 2022-01-05 16:17:59 +01:00 · b5b2dcaf59
commit b5b2dcaf59
parent 04152894e0 7e89ade9dd
22 changed files with 79 additions and 24 deletions
--- a/BioArchLinux/bayesass/PKGBUILD
+++ b/BioArchLinux/bayesass/PKGBUILD
@ -4,7 +4,7 @@
 pkgname=bayesass
 _pkgname=BA3
 pkgver=3.0.4.2
-pkgrel=1
+pkgrel=2
 pkgdesc="Software for inferring proportions of recent migrants among populations using multilocus genotype data."
 arch=('x86_64')
 url="https://github.com/brannala/${_pkgname}"
--- a/BioArchLinux/bayesass/lilac.yaml
+++ b/BioArchLinux/bayesass/lilac.yaml
@ -3,7 +3,8 @@ maintainers:
  - github: michael.g.elliot
    email: m.g.elliot@rug.nl
 update_on:
-  - source: github
-    github: brannala/BA3
-    use_max_tag: true
+  - source: regex
+    regex: Version (\d+.\d+.\d+.\d+)
+    url: https://github.com/brannala/BA3/releases
+

--- a/BioArchLinux/gsalign/PKGBUILD
+++ b/BioArchLinux/gsalign/PKGBUILD
@ -4,7 +4,7 @@
 pkgname=gsalign
 pkgnamecaps=GSAlign
 pkgver=1.0.22
-pkgrel=1
+pkgrel=2
 pkgdesc='An ultra-fast sequence alignment algorithm for intra-species genome comparison. https://doi.org/10.1186/s12864-020-6569-1'
 arch=('x86_64')
 url="https://github.com/hsinnan75/${pkgnamecaps}"
--- a/BioArchLinux/lastz/PKGBUILD
+++ b/BioArchLinux/lastz/PKGBUILD
@ -3,7 +3,7 @@

 pkgname=lastz
 pkgver=1.04.15
-pkgrel=1
+pkgrel=2
 pkgdesc="Pairwise DNA sequence aligner"
 arch=('x86_64')
 url="https://lastz.github.io/lastz/"
--- a/BioArchLinux/lastz_backtobackgaps/PKGBUILD
+++ b/BioArchLinux/lastz_backtobackgaps/PKGBUILD
@ -4,7 +4,7 @@
 pkgname=lastz_backtobackgaps
 _pkgname=lastz
 pkgver=1.04.15
-pkgrel=1
+pkgrel=2
 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/"
--- a/BioArchLinux/libarmadillo/PKGBUILD
+++ b/BioArchLinux/libarmadillo/PKGBUILD
@ -5,7 +5,7 @@ pkgname=libarmadillo
 _pkgname=armadillo
 sfname=arma
 pkgver=10.8.0
-pkgrel=1
+pkgrel=2
 pkgdesc="C++ library for linear algebra & scientific computing"
 arch=('x86_64')
 url="http://${sfname}.sourceforge.net/"
--- a/BioArchLinux/lra/PKGBUILD
+++ b/BioArchLinux/lra/PKGBUILD
@ -3,7 +3,7 @@

 pkgname=lra
 pkgver=1.3.2
-pkgrel=1
+pkgrel=2
 pkgdesc='A long read aligner for sequences and contigs. https://doi.org/10.1371/journal.pcbi.1009078'
 arch=('x86_64')
 url="https://github.com/ChaissonLab/${pkgname^^}"
--- a/BioArchLinux/lra/lilac.yaml
+++ b/BioArchLinux/lra/lilac.yaml
@ -5,5 +5,6 @@ maintainers:
 update_on:
  - source: github
    github: ChaissonLab/LRA
-    use_max_tag: true
-
+    use_latest_release: true
+repo_depends:
+  - htslib
--- a/BioArchLinux/migrate-n-mpi/PKGBUILD
+++ b/BioArchLinux/migrate-n-mpi/PKGBUILD
@ -4,8 +4,8 @@
 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, mpi version"
+pkgrel=2
+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')
--- a/BioArchLinux/migrate-n-mpi/lilac.py
+++ b/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()
--- a/BioArchLinux/migrate-n-mpi/lilac.yaml
+++ b/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
--- a/BioArchLinux/migrate-n-mt/PKGBUILD
+++ b/BioArchLinux/migrate-n-mt/PKGBUILD
@ -4,7 +4,7 @@
 pkgname=migrate-n-mt
 _pkgname=migrate
 pkgver=4.4.4
-pkgrel=1
+pkgrel=2
 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"
--- a/BioArchLinux/migrate-n-mt/lilac.py
+++ b/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()
--- a/BioArchLinux/migrate-n-mt/lilac.yaml
+++ b/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
--- a/BioArchLinux/migrate-n/PKGBUILD
+++ b/BioArchLinux/migrate-n/PKGBUILD
@ -4,7 +4,7 @@
 pkgname=migrate-n
 _pkgname=migrate
 pkgver=4.4.4
-pkgrel=1
+pkgrel=2
 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"
--- a/BioArchLinux/migrate-n/lilac.py
+++ b/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()
--- a/BioArchLinux/migrate-n/lilac.yaml
+++ b/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
--- a/BioArchLinux/minimap2/PKGBUILD
+++ b/BioArchLinux/minimap2/PKGBUILD
@ -3,7 +3,7 @@

 pkgname=minimap2
 pkgver=2.24
-pkgrel=1
+pkgrel=2
 pkgdesc='A versatile pairwise aligner for genomic and spliced nucleotide sequences. https://doi.org/10.1093/bioinformatics/bty191'
 arch=('x86_64')
 url="https://github.com/lh3/${pkgname}"
--- a/BioArchLinux/mummer4/PKGBUILD
+++ b/BioArchLinux/mummer4/PKGBUILD
@ -3,7 +3,7 @@

 pkgname=mummer4
 pkgver=4.0.0rc1
-pkgrel=1
+pkgrel=2
 pkgdesc="A fast and versatile genome alignment system. https://doi.org/10.1371/journal.pcbi.1005944"
 arch=('x86_64')
 url="https://mummer4.github.io/"
--- a/BioArchLinux/mummer4/lilac.yaml
+++ b/BioArchLinux/mummer4/lilac.yaml
@ -3,8 +3,6 @@ maintainers:
  - github: michaelgelliot
    email: m.g.elliot@rug.nl
 update_on:
-  - source: regex
-    regex: v(\d+.\d+.\w+)
-    url: https://github.com/mummer4/mummer/releases
-
-
+  - source: github
+    github: mummer4/mummer
+    use_latest_release: true
--- a/BioArchLinux/phyx/lilac.yaml
+++ b/BioArchLinux/phyx/lilac.yaml
@ -6,4 +6,5 @@ update_on:
  - source: github
    github: FePhyFoFum/phyx
    use_max_tag: true
-
+repo_depends:
+  - libarmadillo
--- a/BioArchLinux/rasp/PKGBUILD
+++ b/BioArchLinux/rasp/PKGBUILD
@ -13,7 +13,7 @@ depends=(
 	'wine_gecko'
 	'wine-mono'
 )
-source=("http://mnh.scu.edu.cn/soft/blog/RASP/RASP_Win64_${pkgver}.zip" "rasp.desktop" "rasp.png")
+source=("https://sourceforge.net/projects/rasp2/files/RASP_Win64_${pkgver}.zip" "rasp.desktop" "rasp.png")
 md5sums=('7d39376e5a8ef44eef467ab0a511f2e0'
         '4304aead6dcffd521664dbc186997ec8'
         '5b403896e05a3da471be404bb9afe053')