add bioperl

BioArchLinux/perl-bioperl/PKGBUILD

@@ -0,0 +1,49 @@
+# Contributor: Ordoban <dirk.langer@vvovgonik.de>
+# Generator  : CPANPLUS::Dist::Arch 1.32
+
+pkgname='perl-bioperl'
+pkgver='1.7.8'
+pkgrel='1'
+pkgdesc="Perl modules for biology"
+arch=('any')
+license=('PerlArtistic' 'GPL')
+options=('!emptydirs')
+depends=('perl-data-stag>=0' 'perl-error>=0' 'perl-graph>=0' 'perl-http-message>=0' 'perl-io-string>=0' 'perl-io-stringy>=0' 'perl-ipc-run>=0' 'perl-list-moreutils>=0' 'perl-module-build>=0' 'perl-set-scalar>=0' 'perl-uri>=0' 'perl-xml-dom>=0' 'perl-xml-libxml>=0' 'perl-xml-sax>=0' 'perl-xml-sax-base>=0' 'perl-xml-sax-writer>=0' 'perl-xml-twig>=0' 'perl-xml-writer>=0' 'perl-yaml>=0' 'perl-libwww>=0' 'libxml-perl>=0' 'perl>=5.006')
+makedepends=()
+checkdepends=('perl-test-memory-cycle>=0' 'perl-test-most>=0' 'perl-test-requiresinternet>=0' 'perl-test-weaken>=0')
+url='https://metacpan.org/dik/BioPerl'
+source=("https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-$pkgver.tar.gz")
+md5sums=('8164ac52f37bc6355ec1b69633ac795f')
+sha512sums=('0fa4ca0691409dd2d0ad431f47be41544c3a627098d17a09b6796b3a4cb0d7d1502bed5118b6e2139d299e72780f60e5d97570e945d03d63f38e8326f49e3ba9')
+_distdir="BioPerl-$pkgver"
+
+build() {
+  export PERL_MM_USE_DEFAULT=1 PERL5LIB=""                      \
+         PERL_AUTOINSTALL=--skipdeps                            \
+         PERL_MM_OPT="INSTALLDIRS=vendor DESTDIR='$pkgdir'"     \
+         PERL_MB_OPT="--installdirs vendor --destdir '$pkgdir'" \
+         MODULEBUILDRC=/dev/null
+
+  cd "$srcdir/$_distdir"
+  /usr/bin/perl Makefile.PL
+  make
+}
+
+check() {
+  cd "$srcdir/$_distdir"
+  export PERL_MM_USE_DEFAULT=1 PERL5LIB="."
+  make test
+}
+
+package() {
+  cd "$srcdir/$_distdir"
+  make install
+
+  find "$pkgdir" \( -name .packlist -o -name perllocal.pod \) -delete
+}
+
+# Local Variables:
+# mode: shell-script
+# sh-basic-offset: 2
+# End:
+# vim:set ts=2 sw=2 et:

BioArchLinux/perl-bioperl/lilac.py

@@ -0,0 +1,10 @@
+#!/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/perl-bioperl/lilac.yaml

@@ -0,0 +1,8 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: starsareintherose
+    email: kuoi@bioarchlinux.org
+update_on:
+  - regex: BioPerl-(\d+.\d+.\d+)
+    source: regex
+    url: https://metacpan.org/dist/BioPerl

BioArchLinux/perl-data-stag/PKGBUILD

@@ -0,0 +1,50 @@
+# Contributor: John D Jones III <jnbek1972 -_AT_- g m a i l -_Dot_- com>
+# Generator  : CPANPLUS::Dist::Arch 1.27
+
+pkgname='perl-data-stag'
+pkgver='0.14'
+pkgrel='1'
+pkgdesc="Structured Tags datastructures"
+arch=('any')
+license=('PerlArtistic' 'GPL')
+options=('!emptydirs')
+depends=('perl-io-string')
+makedepends=()
+url='http://search.mcpan.org/dist/Data-Stag'
+source=('http://search.cpan.org/CPAN/authors/id/C/CM/CMUNGALL/Data-Stag-0.14.tar.gz')
+md5sums=('f803acf74f1bfccc118aeac5483ee871')
+sha512sums=('72b0b5995795d593a844356e1955bd15e5c1cfc31934e55b748badcc21a29b7862475e7304bd56bd22086fcd31657a37f83acd8aee9343767c31dbfe8aba8e99')
+_distdir="Data-Stag-0.14"
+
+build() {
+  ( export PERL_MM_USE_DEFAULT=1 PERL5LIB=""                 \
+      PERL_AUTOINSTALL=--skipdeps                            \
+      PERL_MM_OPT="INSTALLDIRS=vendor DESTDIR='$pkgdir'"     \
+      PERL_MB_OPT="--installdirs vendor --destdir '$pkgdir'" \
+      MODULEBUILDRC=/dev/null
+
+    cd "$srcdir/$_distdir"
+    /usr/bin/perl Makefile.PL
+    make
+  )
+}
+
+check() {
+  cd "$srcdir/$_distdir"
+  ( export PERL_MM_USE_DEFAULT=1 PERL5LIB=""
+    make test
+  )
+}
+
+package() {
+  cd "$srcdir/$_distdir"
+  make install
+
+  find "$pkgdir" -name .packlist -o -name perllocal.pod -delete
+}
+
+# Local Variables:
+# mode: shell-script
+# sh-basic-offset: 2
+# End:
+# vim:set ts=2 sw=2 et:

BioArchLinux/perl-data-stag/lilac.py

@@ -0,0 +1,10 @@
+#!/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/perl-data-stag/lilac.yaml

@@ -0,0 +1,8 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: starsareintherose
+    email: kuoi@bioarchlinux.org
+update_on:
+  - regex: Data-Stag-(\d+.\d+)
+    source: regex
+    url: https://metacpan.org/dist/Data-Stag

BioArchLinux/perl-graph/PKGBUILD

@@ -0,0 +1,54 @@
+#!/bin/bash
+
+# Maintainer: PumpkinCheshire <me at pumpkincheshire dot com>
+# Contributor: John D Jones III AKA jnbek <jnbek1972 -_AT_- g m a i l -_Dot_- com>
+
+pkgname='perl-graph'
+_dist='Graph'
+pkgver='0.9725'
+pkgrel='1'
+pkgdesc='graph data structures and algorithms'
+url='https://metacpan.org/disk/Graph'
+arch=('any')
+license=('PerlArtistic' 'GPL')
+options=('!emptydirs')
+depends=(
+  'perl'
+  'perl-heap'
+  'perl-set-object'
+)
+
+source=("http://search.cpan.org/CPAN/authors/id/E/ET/ETJ/$_dist-$pkgver.tar.gz")
+b2sums=('ab63a75653848ed6297f687cf8431f9e871f9b0473448008ad10d0f8e9d122bddc469069d4eefff1d0d03ba38facca5cc41048afea5f654b155812786e21d86c')
+
+build() {
+  cd "$srcdir/$_dist-$pkgver" || exit
+
+  unset PERL5LIB PERL_MM_OPT PERL_LOCAL_LIB_ROOT
+
+  export PERL_MM_USE_DEFAULT=1 \
+    PERL_AUTOINSTALL=--skipdeps \
+    MODULEBUILDRC=/dev/null
+
+  /usr/bin/perl Makefile.PL
+  make
+}
+
+check() {
+  cd "$srcdir/$_dist-$pkgver" || exit
+
+  unset PERL5LIB PERL_MM_OPT PERL_LOCAL_LIB_ROOT
+  export PERL_MM_USE_DEFAULT=1
+
+  make test
+}
+
+package() {
+  cd "$srcdir/$_dist-$pkgver" || exit
+
+  unset PERL5LIB PERL_MM_OPT PERL_LOCAL_LIB_ROOT
+
+  make install INSTALLDIRS=vendor DESTDIR="$pkgdir"
+
+  find "$pkgdir" -name .packlist -o -name perllocal.pod -delete
+}

BioArchLinux/perl-graph/lilac.py

@@ -0,0 +1,10 @@
+#!/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/perl-graph/lilac.yaml

@@ -0,0 +1,11 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: starsareintherose
+    email: kuoi@bioarchlinux.org
+update_on:
+  - regex: Graph-(\d+.\d+)
+    source: regex
+    url: https://metacpan.org/dist/Graph
+repo_depends:
+  - perl-heap
+  - perl-set-object

BioArchLinux/perl-heap/PKGBUILD

@@ -0,0 +1,50 @@
+# Contributor: John D Jones III <j[nospace]n[nospace]b[nospace]e[nospace]k[nospace]1972 -_AT_- the domain name google offers a mail service at ending in dot com>
+# Generator  : CPANPLUS::Dist::Arch 1.25
+
+pkgname='perl-heap'
+pkgver='0.80'
+pkgrel='1'
+pkgdesc="Perl extensions for keeping data partially sorted"
+arch=('any')
+license=('PerlArtistic' 'GPL')
+options=('!emptydirs')
+depends=('perl')
+makedepends=()
+url='http://search.cpan.org/dist/Heap'
+source=('http://search.cpan.org/CPAN/authors/id/J/JM/JMM/Heap-0.80.tar.gz')
+md5sums=('05fed19a7552dadee11c780cd68c0116')
+sha512sums=('133e2668a90de8cea13302464188415fa30e4a0a85fb51af7409ff2e3466e33a6daf172b2466f046c5275db6ab19bb573e8b2d14acf616b110bdd60869865690')
+_distdir="Heap-0.80"
+
+build() {
+  ( export PERL_MM_USE_DEFAULT=1 PERL5LIB=""                 \
+      PERL_AUTOINSTALL=--skipdeps                            \
+      PERL_MM_OPT="INSTALLDIRS=vendor DESTDIR='$pkgdir'"     \
+      PERL_MB_OPT="--installdirs vendor --destdir '$pkgdir'" \
+      MODULEBUILDRC=/dev/null
+
+    cd "$srcdir/$_distdir"
+    /usr/bin/perl Makefile.PL
+    make
+  )
+}
+
+check() {
+  cd "$srcdir/$_distdir"
+  ( export PERL_MM_USE_DEFAULT=1 PERL5LIB=""
+    make test
+  )
+}
+
+package() {
+  cd "$srcdir/$_distdir"
+  make install
+
+  find "$pkgdir" -name .packlist -o -name perllocal.pod -delete
+}
+
+# Local Variables:
+# mode: shell-script
+# sh-basic-offset: 2
+# End:
+# vim:set ts=2 sw=2 et:

BioArchLinux/perl-heap/lilac.py

@@ -0,0 +1,10 @@
+#!/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/perl-heap/lilac.yaml

@@ -0,0 +1,8 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: starsareintherose
+    email: kuoi@bioarchlinux.org
+update_on:
+  - regex: Heap-(\d+.\d+)
+    source: regex
+    url: https://metacpan.org/dist/Heap

BioArchLinux/perl-set-object/PKGBUILD

@@ -0,0 +1,27 @@
+# This PKGBUILD was generated by cpan4pacman via CPANPLUS::Dist::Pacman
+# Maintainer: Jozef Riha <jose1711@gmail.com>
+
+pkgname=perl-set-object
+pkgver=1.42
+pkgrel=1
+pkgdesc="Set of Objects (smalltalkish: IdentitySet)"
+arch=('i686' 'x86_64')
+url="https://metacpan.org/dist/Set-Object"
+license=('GPL' 'PerlArtistic')
+depends=('perl')
+options=('!emptydirs')
+source=(http://www.cpan.org/authors/id/R/RU/RURBAN/Set-Object-$pkgver.tar.gz) 
+md5sums=('31875a6d0e0abaf08fbba47f0936bfaf')
+
+build() {
+  cd  $srcdir/Set-Object-$pkgver
+  PERL_MM_USE_DEFAULT=1 perl Makefile.PL INSTALLDIRS=vendor
+  make
+}
+
+package() {
+  cd  $srcdir/Set-Object-$pkgver
+  make install DESTDIR=$pkgdir
+  find $pkgdir -name '.packlist' -delete
+  find $pkgdir -name '*.pod' -delete
+}

BioArchLinux/perl-set-object/lilac.py

@@ -0,0 +1,10 @@
+#!/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/perl-set-object/lilac.yaml

@@ -0,0 +1,8 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: starsareintherose
+    email: kuoi@bioarchlinux.org
+update_on:
+  - regex: Set-Object-(\d+.\d+)
+    source: regex
+    url: https://metacpan.org/dist/Set-Object

BioArchLinux/perl-set-scalar/PKGBUILD

@@ -0,0 +1,51 @@
+# CPAN Name  : Set-Scalar
+# Contributor: Anonymous
+# Generator  : CPANPLUS::Dist::Arch 1.29
+
+pkgname='perl-set-scalar'
+pkgver='1.29'
+pkgrel='2'
+pkgdesc="basic set operations"
+arch=('any')
+license=('PerlArtistic' 'GPL')
+options=('!emptydirs')
+depends=('perl>=0')
+makedepends=()
+url='https://metacpan.org/dist/Set-Scalar'
+source=('https://search.cpan.org/CPAN/authors/id/D/DA/DAVIDO/Set-Scalar-1.29.tar.gz')
+md5sums=('4af73c0d6f562d1eddd4ebf6014ac67f')
+sha512sums=('ee77f72a237ed7d3f0467395009b00163c33e095fe5e8bdc971c8cd0eee8dbc825c83ab486e6f54ed6c1aedf1539cde9d9b1a54b8be703d5dc01ee48017ce45c')
+_distdir="Set-Scalar-1.29"
+
+build() {
+  ( export PERL_MM_USE_DEFAULT=1 PERL5LIB=""                 \
+      PERL_AUTOINSTALL=--skipdeps                            \
+      PERL_MM_OPT="INSTALLDIRS=vendor DESTDIR='$pkgdir'"     \
+      PERL_MB_OPT="--installdirs vendor --destdir '$pkgdir'" \
+      MODULEBUILDRC=/dev/null
+
+    cd "$srcdir/$_distdir"
+    /usr/bin/perl Makefile.PL
+    make
+  )
+}
+
+check() {
+  cd "$srcdir/$_distdir"
+  ( export PERL_MM_USE_DEFAULT=1 PERL5LIB=""
+    make test
+  )
+}
+
+package() {
+  cd "$srcdir/$_distdir"
+  make install
+
+  find "$pkgdir" -name .packlist -o -name perllocal.pod -delete
+}
+
+# Local Variables:
+# mode: shell-script
+# sh-basic-offset: 2
+# End:
+# vim:set ts=2 sw=2 et:

BioArchLinux/perl-set-scalar/lilac.py

@@ -0,0 +1,10 @@
+#!/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/perl-set-scalar/lilac.yaml

@@ -0,0 +1,8 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: starsareintherose
+    email: kuoi@bioarchlinux.org
+update_on:
+  - regex: Set-Scalar-(\d+.\d+)
+    source: regex
+    url: https://metacpan.org/dist/Set-Scalar

BioArchLinux/perl-test-weaken/PKGBUILD

@@ -0,0 +1,50 @@
+# Contributor: John D Jones III <j[nospace]n[nospace]b[nospace]e[nospace]k[nospace]1972 -_AT_- the domain name google offers a mail service at ending in dot com>
+# Generator  : CPANPLUS::Dist::Arch 1.25
+
+pkgname='perl-test-weaken'
+pkgver='3.022000'
+pkgrel='1'
+pkgdesc="Test that freed memory objects were, indeed, freed"
+arch=('any')
+license=('PerlArtistic' 'GPL')
+options=('!emptydirs')
+depends=('perl>=5.006')
+makedepends=()
+url='http://search.cpan.org/dist/Test-Weaken'
+source=('http://search.cpan.org/CPAN/authors/id/K/KR/KRYDE/Test-Weaken-3.022000.tar.gz')
+md5sums=('67aa37a1de788bf40abf7dd07c787f6a')
+sha512sums=('07ed16a29c3de052cb0f5884fc06715e10e6214e46b4ed7f7d8524931da293a903ae283e2935c109ea1be9336aeb5d092403249d60730624c590e9e54b38ff1b')
+_distdir="Test-Weaken-3.022000"
+
+build() {
+  ( export PERL_MM_USE_DEFAULT=1 PERL5LIB=""                 \
+      PERL_AUTOINSTALL=--skipdeps                            \
+      PERL_MM_OPT="INSTALLDIRS=vendor DESTDIR='$pkgdir'"     \
+      PERL_MB_OPT="--installdirs vendor --destdir '$pkgdir'" \
+      MODULEBUILDRC=/dev/null
+
+    cd "$srcdir/$_distdir"
+    /usr/bin/perl Makefile.PL
+    make
+  )
+}
+
+check() {
+  cd "$srcdir/$_distdir"
+  ( export PERL_MM_USE_DEFAULT=1 PERL5LIB=""
+    make test
+  )
+}
+
+package() {
+  cd "$srcdir/$_distdir"
+  make install
+
+  find "$pkgdir" -name .packlist -o -name perllocal.pod -delete
+}
+
+# Local Variables:
+# mode: shell-script
+# sh-basic-offset: 2
+# End:
+# vim:set ts=2 sw=2 et:

BioArchLinux/perl-test-weaken/lilac.py

@@ -0,0 +1,10 @@
+#!/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/perl-test-weaken/lilac.yaml

@@ -0,0 +1,8 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: starsareintherose
+    email: kuoi@bioarchlinux.org
+update_on:
+  - regex: Test-Weaken-(\d+.\d+)
+    source: regex
+    url: https://metacpan.org/dist/Test-Weaken

BioArchLinux/perl-xml-dom/PKGBUILD

@@ -0,0 +1,29 @@
+# Maintainer: Brian Bidulock <bidulock@openss7.org>
+# Contributor: kfgz <kfgz at interia pl>
+# Contributor: François Charette <firmicus at gmx dot net>
+
+pkgname=perl-xml-dom
+pkgver=1.46
+pkgrel=1
+pkgdesc="Implements Level 1 of W3's DOM"
+arch=('any')
+url="http://search.cpan.org/dist/XML-DOM"
+license=('GPL' 'PerlArtistic')
+#'perlxml>=2.30'
+depends=('perl-xml-regexp' 'libxml-perl>=0.07' 'perl-libwww')
+options=('!emptydirs')
+source=(http://www.cpan.org/authors/id/T/TJ/TJMATHER/XML-DOM-${pkgver}.tar.gz) 
+md5sums=('91ec808de616a2af54a5118619f8f9cc')
+
+build() {
+  cd ${srcdir}/XML-DOM-${pkgver}
+  PERL_MM_USE_DEFAULT=1 perl Makefile.PL INSTALLDIRS=vendor 
+  make
+}
+
+package() {
+  cd ${srcdir}/XML-DOM-${pkgver}
+  make install DESTDIR=${pkgdir}
+  find ${pkgdir} -name '.packlist' -delete
+  find ${pkgdir} -name '*.pod' -delete
+}

BioArchLinux/perl-xml-dom/lilac.py

@@ -0,0 +1,10 @@
+#!/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/perl-xml-dom/lilac.yaml

@@ -0,0 +1,8 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: starsareintherose
+    email: kuoi@bioarchlinux.org
+update_on:
+  - regex: XML-DOM-(\d+.\d+)
+    source: regex
+    url: https://metacpan.org/dist/XML-DOM