Merge branch 'hotfix/2.0.1'

cancerit · Feb 28, 2017 · 3ec0cc0 · 3ec0cc0
2 parents 384b335 + 618ba57
commit 3ec0cc0
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Showing 5 changed files with 10 additions and 5 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,3 +1,6 @@
+### 2.0.1
+* Test data in `examples/analysis_config.local.json` moved to a non-expiring location.
+
 ### 2.0.0
 * See [dockstore-cgp:2.0.0](https://github.com/cancerit/dockstore-cgpmap/releases/tag/2.0.0)
 * Streamlined install process to reduce build time and size of image.

diff --git a/Dockerfile b/Dockerfile
@@ -1,9 +1,9 @@
-FROM  quay.io/wtsicgp/dockstore-cgpmap:2.0.0
+FROM  quay.io/wtsicgp/dockstore-cgpmap:2.0.1
 
 MAINTAINER  keiranmraine@gmail.com
 
 LABEL uk.ac.sanger.cgp="Cancer Genome Project, Wellcome Trust Sanger Institute" \
-      version="2.0.0" \
+      version="2.0.1" \
       description="The CGP WXS pipeline for dockstore.org"
 
 USER  root

diff --git a/Dockstore.cwl b/Dockstore.cwl
@@ -19,7 +19,7 @@ dct:creator:
 
 requirements:
   - class: DockerRequirement
-    dockerPull: "quay.io/wtsicgp/dockstore-cgpwxs:2.0.0"
+    dockerPull: "quay.io/wtsicgp/dockstore-cgpwxs:2.0.1"
 
 hints:
   - class: ResourceRequirement

diff --git a/build/opt-build.sh b/build/opt-build.sh
@@ -17,6 +17,8 @@ VER_CGPPINDEL="v2.1.0"
 
 # cgpCaVEManPostProcessing
 VER_CGPCAVEPOSTPROC="1.6.8"
+# Warning bedtools 2.24.0 and 2.25.0 have a swapped usage in coverageBed
+# No upgrades until [this ticket](https://github.com/arq5x/bedtools2/issues/319) is resolved
 VER_BEDTOOLS="2.21.0"
 
 # cgpCaVEManWrapper

diff --git a/examples/analysis_config.local.json b/examples/analysis_config.local.json
@@ -12,11 +12,11 @@
     "class": "File"
   },
   "tumour": {
-    "path": "ftp://ngs.sanger.ac.uk/scratch/project/cancer/cgpwxs/testdata/COLO-829_ex.bam",
+    "path": "ftp://ngs.sanger.ac.uk/production/cancer/dockstore/cgpwxs/COLO-829_ex.bam",
     "class": "File"
   },
   "normal": {
-    "path": "ftp://ngs.sanger.ac.uk/scratch/project/cancer/cgpwxs/testdata/COLO-829-BL_ex.bam",
+    "path": "ftp://ngs.sanger.ac.uk/production/cancer/dockstore/cgpwxs/COLO-829-BL_ex.bam",
     "class": "File"
   },
   "exclude": "NC_007605,hs37d5,GL%",