diff --git a/BioArchLinux/bionj/PKGBUILD b/BioArchLinux/bionj/PKGBUILD new file mode 100644 index 0000000000..b1de57920f --- /dev/null +++ b/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 +} diff --git a/BioArchLinux/bionj/bionj.install b/BioArchLinux/bionj/bionj.install new file mode 100644 index 0000000000..c1ea279836 --- /dev/null +++ b/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. " +} diff --git a/BioArchLinux/bionj/lilac.py b/BioArchLinux/bionj/lilac.py new file mode 100644 index 0000000000..95588104e1 --- /dev/null +++ b/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() diff --git a/BioArchLinux/bionj/lilac.yaml b/BioArchLinux/bionj/lilac.yaml new file mode 100644 index 0000000000..5544ea3c84 --- /dev/null +++ b/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}'