From 2f60950b4221c81943d28703222825d60e347d95 Mon Sep 17 00:00:00 2001 From: Christopher Tomkins-Tinch Date: Wed, 10 Jul 2019 14:31:29 -0400 Subject: [PATCH 1/2] update DNAnexus object referenced for the spike-ins DB the old object had spaces in the sequence of ERCC-00003 from the original source, and these spaces may be interpreted differently by various programs. This changes the reference to one where the spaces have been removed. --- pipes/WDL/dx-defaults-demux_plus.json | 2 +- pipes/WDL/dx-defaults-spikein.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pipes/WDL/dx-defaults-demux_plus.json b/pipes/WDL/dx-defaults-demux_plus.json index b5009a36e..168d485f2 100644 --- a/pipes/WDL/dx-defaults-demux_plus.json +++ b/pipes/WDL/dx-defaults-demux_plus.json @@ -1,6 +1,6 @@ { "demux_plus.spikein_db": - "dx://file-FYvfqyQ0xf5g4Q350gzFP0yz", + "dx://file-FZY2v7Q0xf5VBy5FFY3z5fz7", "demux_plus.bwaDbs": [ "dx://file-F9k7Bx00Z3ybJjvY3ZVj7Z9P" diff --git a/pipes/WDL/dx-defaults-spikein.json b/pipes/WDL/dx-defaults-spikein.json index c042217b5..8f02b7109 100644 --- a/pipes/WDL/dx-defaults-spikein.json +++ b/pipes/WDL/dx-defaults-spikein.json @@ -1,4 +1,4 @@ { "spikein.spikein_report.spikein_db": - "dx://file-FYvfqyQ0xf5g4Q350gzFP0yz" + "dx://file-FZY2v7Q0xf5VBy5FFY3z5fz7" } From 1e2aed74be9c35bdb2d76aa8e8753328c3990dff Mon Sep 17 00:00:00 2001 From: Christopher Tomkins-Tinch Date: Wed, 10 Jul 2019 14:43:27 -0400 Subject: [PATCH 2/2] update dx toolkit source since they've retired the wiki --- travis/install-wdl.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/travis/install-wdl.sh b/travis/install-wdl.sh index 84efc626b..577efdfc8 100755 --- a/travis/install-wdl.sh +++ b/travis/install-wdl.sh @@ -21,10 +21,10 @@ cached_fetch_jar_from_github broadinstitute cromwell womtool 33.1 cached_fetch_jar_from_github broadinstitute cromwell cromwell 33.1 cached_fetch_jar_from_github dnanexus dxWDL dxWDL 0.72 -TGZ=dx-toolkit-v0.255.0-ubuntu-14.04-amd64.tar.gz +TGZ=dx-toolkit-v0.285.0-ubuntu-16.04-amd64.tar.gz if [ ! -f $CACHE_DIR/$TGZ ]; then echo "Fetching $TGZ" - wget --quiet https://wiki.dnanexus.com/images/files/$TGZ + wget --quiet https://dnanexus-sdk.s3.amazonaws.com/$TGZ mv $TGZ $CACHE_DIR else echo "Using cached $TGZ"