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-rw-r--r--.SRCINFO15
-rw-r--r--PKGBUILD37
-rw-r--r--fseq.sh9
3 files changed, 61 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 00000000000..e52e53033ab
--- /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 00000000000..ced5263699e
--- /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 ${pkgdir}/usr/bin/fseq
+}
+
+# vim:set ts=2 sw=2 et:
diff --git a/fseq.sh b/fseq.sh
new file mode 100644
index 00000000000..9f7e940b7a6
--- /dev/null
+++ b/fseq.sh
@@ -0,0 +1,9 @@
+#!/bin/sh
+
+#edit this to increase memory (MB)
+JAVAOPTS="-Xmx8000M"
+
+# Setup environment variables
+FSEQ_LIB="/usr/share/java/fseq/"
+CLASSPATH="$FSEQ_LIB/commons-cli-1.1.jar:$FSEQ_LIB/fseq.jar"
+exec /usr/bin/java -cp $CLASSPATH edu.duke.igsp.gkde.Main "$@" \ No newline at end of file