Version updates to support mismatchQc and fragment based analysis in …

…downstream tools

CHANGES.md

@@ -1,5 +1,16 @@
 # CHANGES
 
+## 3.1.0
+
+* Update to dockstore-cgpbigwig:2.1.0 for base image
+* Update dependencies:
+  * gt1/biobambam2 - 2.0.87
+  * HTSLib - 1.9
+  * Samtools -1.9
+  * Bio::DB::HTS - 2.10
+  * PCAP-core - 4.3.1
+* Drop `expected` tree, will be revising how verification of container is achieved.
+
 ## 3.0.4
 
 * Update to dockstore-cgpbigwig:2.0.1 for base image

Dockerfile

@@ -1,4 +1,4 @@
-FROM  quay.io/wtsicgp/dockstore-cgpbigwig:2.0.1 as builder
+FROM  quay.io/wtsicgp/dockstore-cgpbigwig:2.1.0 as builder
 
 USER  root
 
@@ -22,7 +22,9 @@ RUN apt-get install -yq --no-install-recommends\
   nettle-dev\
   libp11-kit-dev\
   libtasn1-dev\
-  libgnutls-dev
+  libgnutls-dev\
+  libgd-dev\
+  libdb-dev
 
 RUN locale-gen en_US.UTF-8
 RUN update-locale LANG=en_US.UTF-8
@@ -45,7 +47,7 @@ MAINTAINER  [email protected]
 
 LABEL vendor="Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute"
 LABEL uk.ac.sanger.cgp.description="PCAP-core for dockstore.org"
-LABEL uk.ac.sanger.cgp.version="3.0.4"
+LABEL uk.ac.sanger.cgp.version="3.1.0"
 
 RUN apt-get -yq update
 RUN apt-get install -yq --no-install-recommends\

README.md

@@ -11,20 +11,16 @@ packaged specifically for use with the [Dockstore.org](https://dockstore.org/) f
 | --------------------------------------------- | ----------------------------------------------- |
 | [![Master Badge][travis-master]][travis-base] | [![Develop Badge][travis-develop]][travis-base] |
 
-<!-- TOC depthFrom:2 depthTo:6 withLinks:1 updateOnSave:1 orderedList:0 -->
-
-- [Supported input formats](#supported-input-formats)
-- [Options for customisation:](#options-for-customisation)
-- [Usable Cores](#usable-cores)
-- [Other uses](#other-uses)
-	- [Native docker](#native-docker)
-	- [Singularity](#singularity)
-- [Verifying your deployment](#verifying-your-deployment)
-- [Development environment](#development-environment)
-- [Release process](#release-process)
-- [LICENCE](#licence)
-
-<!-- /TOC -->
+* [Supported input formats](#supported-input-formats)
+* [Options for customisation:](#options-for-customisation)
+* [Usable Cores](#usable-cores)
+* [Other uses](#other-uses)
+	* [Native docker](#native-docker)
+	* [Singularity](#singularity)
+* [Verifying your deployment](#verifying-your-deployment)
+* [Development environment](#development-environment)
+* [Release process](#release-process)
+* [LICENCE](#licence)
 
 ## Supported input formats
 
@@ -101,8 +97,6 @@ via the options of `ds-cgpmap.pl`
 The `examples/` tree contains test json files populated with data that can be used to verify the
 tool.  More details can be found [here](examples/README.md).
 
-The `expected/` tree contains the expected output for each tool.  More details can be found [here](expected/README.md).
-
 ## Development environment
 
 This project uses git pre-commit hooks.  Please enable them to prevent inappropriate large files
@@ -120,12 +114,12 @@ git config core.hooksPath git-hooks
 This project is maintained using HubFlow.
 
 1. Make appropriate changes
-1. Bump version in `Dockerfile` and `cwls/mixins/requirements.yml`
-1. Push changes
-1. Check state on Travis
-1. Generate the release (add notes to GitHub)
-1. Confirm that image has been built on [quay.io][quay-builds]
-1. Update the [dockstore][dockstore-cgpmap] entry, see [their docs][dockstore-get-started].
+2. Bump version in `Dockerfile` and `cwls/mixins/requirements.yml`
+3. Push changes
+4. Check state on Travis
+5. Generate the release (add notes to GitHub)
+6. Confirm that image has been built on [quay.io][quay-builds]
+7. Update the [dockstore][dockstore-cgpmap] entry, see [their docs][dockstore-get-started].
 
 ## LICENCE
 

build/opt-build.sh

@@ -9,12 +9,12 @@ fi
 set -u
 
 # for PCAP
-VER_BBB2="2.0.86-release-20180228171821"
+VER_BBB2="2.0.87-release-20180301132713"
 VER_BIODBHTS="2.10"
 VER_BWA="v0.7.17"
-VER_HTSLIB="1.7"
-VER_SAMTOOLS="1.7"
-VER_PCAP="4.2.2"
+VER_HTSLIB="1.9"
+VER_SAMTOOLS="1.9"
+VER_PCAP="4.3.1"
 
 if [ "$#" -lt "1" ] ; then
   echo "Please provide an installation path such as /opt/ICGC"

cwls/mixins/requirements.yml

@@ -1,2 +1,2 @@
 class: DockerRequirement
-dockerPull: "quay.io/wtsicgp/dockstore-cgpmap:3.0.4"
+dockerPull: "quay.io/wtsicgp/dockstore-cgpmap:3.1.0"

examples/README.md

@@ -4,13 +4,3 @@ An example tree exists for each of the possible output types (see cwls tree)
 
 Within the folder for output type there are example of different input type and in some cases
 other parameters we would test as routine.
-
-For each `examples/cgpmap/<output>/<params>.json` file there is a corresponding folder named
-`expected/cgpmap/<output>/<params>/` containing the expected file listing for the result archive.
-
-e.g.
-
-* JSON: `examples/cgpmap/bamBaiOut/bam_in.json` generates a set of files: `bam_in.bam*`
-* These are stored in: `expected/cgpmap/bamBaiOut/bam_in/`
-
-See [`expected/README.md`](../expected/README.md) for content of that area.