From 324b6806572061516dd6f54c7a2ddee5ba358858 Mon Sep 17 00:00:00 2001
From: Hui Yiqun <huiyiqun@gmail.com>
Date: Sun, 20 Aug 2017 12:00:19 +0800
Subject: [PATCH] script to sync bioconductor

---
 bioconductor.sh | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100755 bioconductor.sh

diff --git a/bioconductor.sh b/bioconductor.sh
new file mode 100755
index 0000000..34793ba
--- /dev/null
+++ b/bioconductor.sh
@@ -0,0 +1,30 @@
+#!/bin/bash
+# requires: wget, rsync
+#
+
+set -e
+set -o pipefail
+
+UPSTREAM=${TUNASYNC_UPSTREAM_URL:-"rsync://master.bioconductor.org"}
+VERSIONS=("3.5")
+RELEASE_VERSION="3.5"
+
+RSYNC_OPTS="-aHvh --no-o --no-g --stats --exclude .~tmp~/ --delete --delete-after --delay-updates --safe-links --timeout=120 --contimeout=120"
+
+USE_IPV6=${USE_IPV6:-"0"}
+if [[ $USE_IPV6 == "1" ]]; then
+	RSYNC_OPTS="-6 ${RSYNC_OPTS}"
+fi
+
+mkdir -p ${TUNASYNC_WORKING_DIR}/packages
+
+for version in ${VERSIONS[@]}; do
+	upstream=${UPSTREAM}:${version}
+	dest=${TUNASYNC_WORKING_DIR}/packages/${version}
+
+	[ ! -d "$dest" ] && mkdir -p "$dest"
+	
+	rsync ${RSYNC_OPTS} "$upstream" "$dest"
+done
+
+ln -sfT ${TUNASYNC_WORKING_DIR}/packages/${RELEASE_VERSION} ${TUNASYNC_WORKING_DIR}/packages/release