initial commit

2 files changed, 88 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..47e2d7ec224b
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,18 @@
+pkgbase = mummer
+	pkgdesc = MUMmer is a program for rapidly aligning large genomes
+	pkgver = 3.23
+	pkgrel = 2
+	url = http://mummer.sourceforge.net
+	arch = i686
+	arch = x86_64
+	license = PerlArtistic
+	depends = perl
+	optdepends = gnuplot: for alignment visualization
+	optdepends = xfig: for alignment visualization
+	optdepends = transsfig: for alignment visualization
+	optdepends = tcsh: for running some optional scripts
+	source = http://downloads.sourceforge.net/project/mummer/mummer/3.23/MUMmer3.23.tar.gz
+	md5sums = f2422b3d2638dba4baedb71b1acdffa2
+
+pkgname = mummer
+
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..302857d3550b
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,70 @@
+# Maintainer:  Eric Biggers <ebiggers3 at gmail dot com>
+
+
+# Note: this software is difficult to install.
+
+pkgname=mummer
+pkgver=3.23
+pkgrel=2
+pkgdesc="MUMmer is a program for rapidly aligning large genomes"
+arch=('i686' 'x86_64')
+url="http://mummer.sourceforge.net"
+license=('PerlArtistic')
+depends=('perl')
+optdepends=('gnuplot: for alignment visualization'
+                'xfig: for alignment visualization'
+                'transsfig: for alignment visualization'
+		'tcsh: for running some optional scripts')
+
+source=("http://downloads.sourceforge.net/project/mummer/mummer/${pkgver}/MUMmer${pkgver}.tar.gz")
+
+build() {
+  cd MUMmer${pkgver}
+  make CPPFLAGS="-O3 -DSIXTYFOURBITS"
+
+  # patch defined(%hash) out
+  # https://github.com/bioconda/bioconda-recipes/issues/1254
+  perl -i -pe 's/defined \(%/\(%/' mummerplot
+
+  #Fix escaping symbol @ included in the path to the library (mainly for conda virtual env with galaxy)
+  for i in exact-tandems dnadiff mapview mummerplot nucmer promer run-mummer1 run-mummer3; do
+    perl -i -pe 's/(envs\/\_\_.*)(\K\@)/\\@/' $i
+  done
+}
+
+package() {
+  cd MUMmer${pkgver}
+
+  mkdir -p ${pkgdir}/usr/share/doc/mummer \
+           ${pkgdir}/usr/bin \
+           ${pkgdir}/usr/lib/mummer/{aux_bin,scripts} \
+           ${pkgdir}/usr/share/man/man1
+
+  install -m755 annotate combineMUMs delta-filter dnadiff exact-tandems \
+                gaps mapview mgaps mummer mummerplot nucmer nucmer2xfig \
+                promer repeat-match run-mummer1 run-mummer3 show-aligns \
+                show-coords show-diff show-snps show-tiling \
+                ${pkgdir}/usr/bin
+
+  install -m755 aux_bin/{prenuc,postnuc,prepro,postpro} \
+                ${pkgdir}/usr/lib/mummer/aux_bin
+
+  install -m755 scripts/*.{pl,awk,csh} ${pkgdir}/usr/lib/mummer/scripts
+
+  # The software hard-codes the build directory into some scripts.  Fix this...
+  cp -r README ACKNOWLEDGEMENTS docs/*{.README,.pdf} docs/web \
+                ${pkgdir}/usr/share/doc/mummer
+  install -Dm644 scripts/Foundation.pm ${pkgdir}/usr/lib/perl5/site_perl/Foundation.pm
+  #first replace scripts and aux_bin
+  find ${pkgdir} -type f -exec sed -i -e "s@$PWD/scripts@/usr/lib/mummer/scripts@g" {} \;
+  find ${pkgdir} -type f -exec sed -i -e "s@$PWD/aux_bin@/usr/lib/mummer/aux_bin@g" {} \;
+  # now replace all that's left with /usr/bin
+  find ${pkgdir} -type f -exec sed -i -e "s@$PWD@/usr/bin@g" {} \;
+
+  # Fix conflict with `gd' package
+  mv ${pkgdir}/usr/bin/{,mummer-}annotate
+  sed -i -e 's@\$bindir/annotate@\$bindir/mummer-annotate@' \
+  			${pkgdir}/usr/bin/run-mummer1 \
+			${pkgdir}/usr/lib/mummer/scripts/run-mummer1.csh
+}
+md5sums=('f2422b3d2638dba4baedb71b1acdffa2')