add bionj

BioArchLinux/bionj/PKGBUILD

@@ -0,0 +1,24 @@
+# guoyi
+pkgname=bionj
+pkgver=1997
+pkgrel=1
+pkgdesc="an improved version of the NJ algorithm based on a simple model of sequence data"
+arch=('x86_64')
+url="http://www.atgc-montpellier.fr/bionj/"
+license=('GPL')
+depends=('glibc')
+makedepends=('gcc')
+provides=('bionj')
+install=${pkgname}.install
+source=("http://www.atgc-montpellier.fr/download/sources/bionj/BIONJ.c")
+sha256sums=('bb98da9f361785c3c99cc8bf420c404583a42d3ba4625051c8d3d68e166e1ab9')
+build() {
+  cd $srcdir
+  gcc BIONJ.c -o $pkgname
+}
+
+package() {
+  cd "$srcdir"
+  chmod +x $pkgname
+  install -Dm755 $pkgname $pkgdir/usr/bin/$pkgname
+}

BioArchLinux/bionj/bionj.install

@@ -0,0 +1,28 @@
+post_install() {
+    echo "==>               The delta matrix is read from the input-file.                "
+    echo "==>               It is recommended to put it and the executable in            "
+    echo "==>               a special directory. The input-file and output-file          "
+    echo "==>               can be given as arguments to the executable by               "
+    echo "==>               typing them after the executable (Bionj input-file           "
+    echo "==>               output-file) or by typing them when asked by the             "
+    echo "==>               program. The input-file has to be formated according         "
+    echo "==>               the PHYLIP standard. The output file is formated             "
+    echo "==>               according to the NEWSWICK standard.                          "
+    echo "==>                                                                            "
+    echo "==>               The lower-half of the delta matrix is occupied by            "
+    echo "==>               dissimilarities. The upper-half of the matrix is             "
+    echo "==>               occupied by variances. The first column                      "
+    echo "==>               is initialized as 0 during the algorithm some                "
+    echo "==>               indices are no more used, and the corresponding              "
+    echo "==>               positions in the first column are set to 1.                  "
+    echo "==>                                                                            "
+    echo "==>               This delta matix is made symmetrical using the rule:         "
+    echo "==>               Dij = Dji <- (Dij + Dji)/2. The diagonal is set to 0         "
+    echo "==>               during the further steps of the algorithm, it is used        "
+    echo "==>               to store the sums Sx.                                        "
+    echo "==>                                                                            "
+    echo "==>               A second array, trees, is used to store taxon names.         "
+    echo "==>               During the further steps of the algoritm, some               "
+    echo "==>               positions in this array are emptied while the others         "
+    echo "==>               are used to store subtrees.                                  "
+}

BioArchLinux/bionj/lilac.py

@@ -0,0 +1,11 @@
+#!/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()
+    update_aur_repo()

BioArchLinux/bionj/lilac.yaml

@@ -0,0 +1,7 @@
+build_prefix: multilib
+maintainers:
+  - github: starsareintherose
+    email: git@malacology.net
+update_on:
+  - source: cmd
+    cmd: curl -sS http://www.atgc-montpellier.fr/download/sources/bionj/BIONJ.c | grep 'Copyright' | awk '{print$3}'