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author | Saulius Lukauskas | 2015-08-05 11:47:14 +0100 |
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committer | Saulius Lukauskas | 2015-08-05 11:47:14 +0100 |
commit | 8da3dec44dd2245b71e84b4e4af4220495fbd2f4 (patch) | |
tree | 684e79168f6cdddfa55f5b6be3383b17f9f6dcdc | |
download | aur-8da3dec44dd2245b71e84b4e4af4220495fbd2f4.tar.gz |
Initial import
-rw-r--r-- | .SRCINFO | 15 | ||||
-rw-r--r-- | PKGBUILD | 37 | ||||
-rw-r--r-- | fseq.sh | 9 |
3 files changed, 61 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO new file mode 100644 index 000000000000..e52e53033ab7 --- /dev/null +++ b/.SRCINFO @@ -0,0 +1,15 @@ +pkgbase = fseq + pkgdesc = software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser + pkgver = 1.84 + pkgrel = 1 + url = http://fureylab.web.unc.edu/software/fseq/ + arch = any + license = GPL3 + depends = java-environment + source = http://fureylab.med.unc.edu/fseq/fseq_1.84.tgz + source = fseq.sh + sha1sums = 47921ef9cce35de1304baaa529b90a41834b29fb + sha1sums = 21784aa264ed296efd630644383e2579b44af451 + +pkgname = fseq + diff --git a/PKGBUILD b/PKGBUILD new file mode 100644 index 000000000000..ced5263699e3 --- /dev/null +++ b/PKGBUILD @@ -0,0 +1,37 @@ +# Maintainer: Sauliusl <luksaulius[at]gmail[dot]com> +pkgname=fseq +pkgver=1.84 +pkgrel=1 +pkgdesc="software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser" +url="http://fureylab.web.unc.edu/software/fseq/" +arch=('any') +license=('GPL3') +depends=('java-environment') +optdepends=() +makedepends=() +conflicts=() +replaces=() +backup=() +install='' +source=("http://fureylab.med.unc.edu/fseq/${pkgname}_${pkgver}.tgz" + "fseq.sh") +sha1sums=('47921ef9cce35de1304baaa529b90a41834b29fb' + '21784aa264ed296efd630644383e2579b44af451') + +build() { + cd ${srcdir}/fseq/ +} + +package() { + cd ${srcdir}/fseq/ + + install -d ${pkgdir}/usr/share/java/${pkgname} + install -Dm0644 lib/*.jar ${pkgdir}/usr/share/java/${pkgname}/ + + install -d ${pkgdir}/usr/bin/ + + # Move our .sh script, not theirs to usr/bin + install -Dm0755 ${srcdir}/fseq.sh ${pkgdir}/usr/bin/fseq +} + +# vim:set ts=2 sw=2 et: diff --git a/fseq.sh b/fseq.sh new file mode 100644 index 000000000000..9f7e940b7a69 --- /dev/null +++ b/fseq.sh @@ -0,0 +1,9 @@ +#!/bin/sh + +#edit this to increase memory (MB) +JAVAOPTS="-Xmx8000M" + +# Setup environment variables +FSEQ_LIB="/usr/share/java/fseq/" +CLASSPATH="$FSEQ_LIB/commons-cli-1.1.jar:$FSEQ_LIB/fseq.jar" +exec /usr/bin/java -cp $CLASSPATH edu.duke.igsp.gkde.Main "$@"
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