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| author | Alex Dewar | 2018-04-12 14:41:36 +0100 |
|---|---|---|
| committer | Alex Dewar | 2018-04-12 14:41:36 +0100 |
| commit | 5de3e5ef09041f49f4abf7dfc6ab1b826ac7437b (patch) | |
| tree | 80ff12c3bf6e2bffa6290fd488166ee677682a18 | |
| download | aur-5de3e5ef09041f49f4abf7dfc6ab1b826ac7437b.tar.gz | |
initial commit: v1.81a
| -rw-r--r-- | .SRCINFO | 18 | ||||
| -rw-r--r-- | .gitignore | 4 | ||||
| -rw-r--r-- | PKGBUILD | 39 | ||||
| -rw-r--r-- | disable-logging.patch | 12 |
4 files changed, 73 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO new file mode 100644 index 000000000000..56ea596fa957 --- /dev/null +++ b/.SRCINFO @@ -0,0 +1,18 @@ +pkgbase = geneconv + pkgdesc = Statistical Tests for Detecting Gene Conversion + pkgver = 1.81a + pkgrel = 1 + url = https://www.math.wustl.edu/~sawyer/geneconv + arch = i686 + arch = x86_64 + source = geneconv-1.81a.tar.gz::https://www.math.wustl.edu/~sawyer/geneconv/unix.source.tar.gz + source = geneconv-examples-1.81a.tar.gz::https://www.math.wustl.edu/~sawyer/geneconv/unix.examples.tar.gz + source = https://www.math.wustl.edu/~sawyer/geneconv/gconvdoc.pdf + source = disable-logging.patch + sha256sums = 9423bad39fc729ac8150d0630c82ca3452d30ba0f5da862a76a7358c06d0831c + sha256sums = 58e26a065c4ddf055cad403a30c2482db500e19de6ff6a2116b2d91aaee6b7a1 + sha256sums = 14f91fe7437e115241cad83b1c0587791998498d085e58b8699186edb6735cd2 + sha256sums = d61c5ef686cd47a8f2bb6e894535ce78cb47b2b7c2a53c4a3d6ec1c6a153a068 + +pkgname = geneconv + diff --git a/.gitignore b/.gitignore new file mode 100644 index 000000000000..e2c97c02853a --- /dev/null +++ b/.gitignore @@ -0,0 +1,4 @@ +src/ +pkg/ +geneconv-* +gconvdoc.pdf diff --git a/PKGBUILD b/PKGBUILD new file mode 100644 index 000000000000..a741d3c855de --- /dev/null +++ b/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Alex Dewar <alex.dewar@gmx.co.uk> +pkgname=geneconv +pkgver=1.81a +pkgrel=1 +pkgdesc="Statistical Tests for Detecting Gene Conversion" +arch=("i686" "x86_64") +url="https://www.math.wustl.edu/~sawyer/geneconv" +source=("$pkgname-$pkgver.tar.gz::$url/unix.source.tar.gz" + "$pkgname-examples-$pkgver.tar.gz::$url/unix.examples.tar.gz" + "$url/gconvdoc.pdf" + "disable-logging.patch") +sha256sums=("9423bad39fc729ac8150d0630c82ca3452d30ba0f5da862a76a7358c06d0831c" + "58e26a065c4ddf055cad403a30c2482db500e19de6ff6a2116b2d91aaee6b7a1" + "14f91fe7437e115241cad83b1c0587791998498d085e58b8699186edb6735cd2" + "d61c5ef686cd47a8f2bb6e894535ce78cb47b2b7c2a53c4a3d6ec1c6a153a068") + +prepare() { + cd "$srcdir"/unix.source + patch -p0 -i ../disable-logging.patch + sed -i 's/getline/getline2/g' geneconv_helper.c + sed -i 's/-O3/$CFLAGS/' makgconv.csh +} + +build() { + cd "$srcdir"/unix.source + sh makgconv.csh +} + +package() { + install -Dm 644 gconvdoc.pdf "$pkgdir"/usr/share/doc/$pkgname/documentation.pdf + + cd "$srcdir"/unix.source + mkdir -p "$pkgdir"/usr/bin + install -m 755 geneconv geneconv_helper "$pkgdir"/usr/bin/ + + mkdir -p "$pkgdir"/usr/share/$pkgname/examples + cp "$srcdir"/unix.examples/* "$pkgdir"/usr/share/$pkgname/examples + chmod +x "$pkgdir"/usr/share/$pkgname/examples/dosamps.csh +} diff --git a/disable-logging.patch b/disable-logging.patch new file mode 100644 index 000000000000..f086a292437e --- /dev/null +++ b/disable-logging.patch @@ -0,0 +1,12 @@ +--- vsetopts.c.old 2018-04-12 14:26:15.347943111 +0100 ++++ vsetopts.c 2018-04-12 14:26:29.149006677 +0100 +@@ -133,7 +133,8 @@ + + /* Verbose variables */ + +-int gscale, circular, allowindelstrat, havelog=TRUE; ++int gscale, circular, allowindelstrat; ++int havelog=FALSE; + int showunal, havlabels=TRUE, use_iubnucls, phylip; + int nomacfork, no_nexus_dcomm; + int dumpfrags, dumptab, dumpdif, dumpjseqs, dumpplot; |