New: hmftools-cobalt; Update: hmftools-purple (#11507)

- hmftools-cobalt: Add latest version of PURPLE associated read counter,
  COBALT, with support for hg38.
- hmftools-purple: PURPLE release with hg38 support.

recipes/hmftools-cobalt/COBALT.sh

@@ -0,0 +1,69 @@
+#!/bin/bash
+# hmftools COBALT executable shell script
+# https://github.com/hartwigmedical/hmftools/tree/master/count-bam-lines
+set -eu -o pipefail
+
+export LC_ALL=en_US.UTF-8
+
+# Find original directory of bash script, resolving symlinks
+# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128
+SOURCE="${BASH_SOURCE[0]}"
+while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+    DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+    SOURCE="$(readlink "$SOURCE")"
+    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+done
+DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+
+JAR_DIR=$DIR
+ENV_PREFIX="$(dirname $(dirname $DIR))"
+# Use Java installed with Anaconda to ensure correct version
+java="$ENV_PREFIX/bin/java"
+
+# if JAVA_HOME is set (non-empty), use it. Otherwise keep "java"
+if [ -n "${JAVA_HOME:=}" ]; then
+  if [ -e "$JAVA_HOME/bin/java" ]; then
+      java="$JAVA_HOME/bin/java"
+  fi
+fi
+
+# extract memory and system property Java arguments from the list of provided arguments
+# http://java.dzone.com/articles/better-java-shell-script
+default_jvm_mem_opts="-Xms512m -Xmx1g"
+jvm_mem_opts=""
+jvm_prop_opts=""
+pass_args=""
+for arg in "$@"; do
+    case $arg in
+        '-D'*)
+            jvm_prop_opts="$jvm_prop_opts $arg"
+            ;;
+        '-XX'*)
+            jvm_prop_opts="$jvm_prop_opts $arg"
+            ;;
+         '-Xm'*)
+            jvm_mem_opts="$jvm_mem_opts $arg"
+            ;;
+         *)
+	    if [[ ${pass_args} == '' ]] #needed to avoid preceeding space on first arg e.g. ' MarkDuplicates'
+            then 
+                pass_args="$arg" 
+	    else
+                pass_args="$pass_args \"$arg\"" #quotes later arguments to avoid problem with ()s in MarkDuplicates regex arg
+            fi
+            ;;
+    esac
+done
+
+if [ "$jvm_mem_opts" == "" ]; then
+    jvm_mem_opts="$default_jvm_mem_opts"
+fi
+
+pass_arr=($pass_args)
+if [[ ${pass_arr[0]:=} == org* ]]
+then
+    eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/cobalt.jar" $pass_args
+else
+    eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/cobalt.jar" $pass_args
+fi
+exit

recipes/hmftools-cobalt/build.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+
+TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM"
+[ -d "$TGT" ] || mkdir -p "$TGT"
+[ -d "${PREFIX}/bin" ] || mkdir -p "${PREFIX}/bin"
+
+cd "${SRC_DIR}"
+mv cobalt*.jar $TGT/cobalt.jar
+
+cp $RECIPE_DIR/COBALT.sh $TGT/COBALT
+ln -s $TGT/COBALT $PREFIX/bin
+chmod 0755 "${PREFIX}/bin/COBALT"

recipes/hmftools-cobalt/meta.yaml

@@ -0,0 +1,29 @@
+{% set version = "1.5" %}
+{% set sha256 = "f3faa2b0d63beab5a074f0cc9e3841c083c3ff7eb4b7d06fdff6f538148d18bb" %}
+
+package:
+  name: hmftools-cobalt
+  version: '{{ version }}'
+
+source:
+  url: https://github.com/hartwigmedical/hmftools/releases/download/cobalt-v{{ version|replace(".", "-") }}/cobalt-{{ version }}.jar
+  sha256: '{{ sha256 }}'
+
+build:
+  noarch: generic
+  number: 0
+
+requirements:
+  run:
+    - openjdk >=8
+
+test:
+  commands:
+    - 'COBALT 2>&1 | grep version'
+    - 'COBALT 2>&1 | grep usage'
+
+about:
+  home: https://github.com/hartwigmedical/hmftools/tree/master/count-bam-lines
+  license: MIT
+  license_family: MIT
+  summary: Count bam lines is designed to count the number of read starts within each 1000 base window of a tumor and reference bam.

recipes/hmftools-purple/meta.yaml

@@ -1,5 +1,5 @@
-{% set version = "2.15" %}
-{% set sha256 = "8846f6711e98c411ef4f42549d472c0b3f5c5535e2ee654f9ac19ba5ffc6faa9" %}
+{% set version = "2.16" %}
+{% set sha256 = "d6143fda59d10b9fcda6299bbe8a9180a1c1adb63e65cb1888166274f746c796" %}
 
 package:
   name: hmftools-purple