Clinker (#10244)

* Add clinker with wrapper

* Add full test

* Remove test data test as per guidelines

recipes/clinker/build.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+# Setup path variables
+BINARY_HOME=$PREFIX/bin
+PACKAGE_HOME=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
+
+# Create destination directories
+mkdir -p $PACKAGE_HOME
+
+# Copy files over into $PACKAGE_HOME
+cp -aR * $PACKAGE_HOME
+
+DEST_FILE=$PACKAGE_HOME/clinker
+cp $RECIPE_DIR/clinker-wrapper.sh $DEST_FILE
+chmod +x $DEST_FILE
+ln -s $DEST_FILE $PREFIX/bin
+
+
+

recipes/clinker/clinker-wrapper.sh

@@ -0,0 +1,63 @@
+#!/bin/bash
+CLINKERLOGO=$(cat <<END
+      ___         ___             ___         ___         ___         ___     
+     /\  \       /\__\  ___      /\__\       /\__\       /\  \       /\  \    
+    /::\  \     /:/  / /\  \    /::|  |     /:/  /      /::\  \     /::\  \   
+   /:/\:\  \   /:/  /  \:\  \  /:|:|  |    /:/__/      /:/\:\  \   /:/\:\  \  
+  /:/  \:\  \ /:/  /   /::\__\/:/|:|  |__ /::\__\____ /::\~\:\  \ /::\~\:\  \ 
+ /:/__/ \:\__/:/__/ __/:/\/__/:/ |:| /\__/:/\:::::\__/:/\:\ \:\__/:/\:\ \:\__\ 
+ \:\  \  \/__\:\  \/\/:/  /  \/__|:|/:/  \/_|:|~~|~  \:\~\:\ \/__\/_|::\/:/  / 
+  \:\  \      \:\  \::/__/       |:/:/  /   |:|  |    \:\ \:\__\    |:|::/  / 
+   \:\  \      \:\  \:\__\       |::/  /    |:|  |     \:\ \/__/    |:|\/__/  
+    \:\__\      \:\__\/__/       /:/  /     |:|  |      \:\__\      |:|  |    
+     \/__/       \/__/           \/__/       \|__|       \/__/       \|__|    
+END
+)
+# Clinker wrapper - invoke bpipe
+
+#bpipe -p option1="something" -p option2="something_else" [...] $CLINKERDIR/workflow/clinker.pipe /path/to/*.fastq.gz
+# parse and accept parameters in bpipe style, then pass on to fixed clinker.pipe location
+CLINKERFILES=()
+CLINKEROPTIONS=()
+ECHO="echo usage: call clinker -h for more detailed information or clinker -w to run:"
+while [[ $# -gt 0 ]]
+do
+arg="$1"
+
+case $arg in
+    -h)
+    echo "$CLINKERLOGO"
+    echo ""
+    echo "Clinker Wrapper Script"
+    echo ""
+    echo "The command clinker will invoke the Clinker bpipe pipeline with simple options. Use the direct pipeline method to use any advanced bpipe features."
+    echo "See https://github.com/Oshlack/Clinker/wiki/ for further information onusing Clinker."
+    echo ""
+    echo -e "\nusage (info): clinker [-h] "
+    echo -e "\nusage (wrapper): clinker -w [-p option1=\"values\" -p option2=\"values\" ...]\" *.fastq.gz "
+    echo -e "\nusage (direct):\n export \$CLINKERDIR=$PACKAGE_HOME;\n bpipe run  [-p option1=\"values\" -p option2=\"values\" ...] [ <other bpipe options >] \n\t \$CLINKERDIR/workflow/clinker.pipe *.fastq.gz"
+    echo ""
+    exit 0
+    shift
+    ;;
+    -w)
+    ECHO=""
+    shift
+    ;;
+    -p)
+    OPTIONNAME="${2%=*}"
+    OPTIONVAL="${2#*=}"
+    CLINKEROPTIONS+=("-p  $OPTIONNAME=\"$OPTIONVAL\"") 
+    shift 
+    shift 
+    ;;
+    *)    # files
+    CLINKERFILES+=("$1") 
+    shift 
+    ;;
+esac
+done
+
+set -- "${CLINKERFILES[@]}" 
+$ECHO bpipe run "${CLINKEROPTIONS[@]}" $PACKAGE_HOME/workflow/clinker.pipe "$@"
+

recipes/clinker/meta.yml

@@ -0,0 +1,38 @@
+{% set name = "clinker" %}
+{% set version = "1.32" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  fn: "v{{ version }}.tar.gz"
+  url: https://github.com/Oshlack/Clinker/archive/v{{ version }}.tar.gz
+  sha256: "5dbb97da27f29f53a8282e456ba0093bbdde292eb9e76405434117da4d1a76be"
+
+build:
+  number: 0
+  skip: True  # [not py27]
+
+requirements:
+  run:
+    - samtools
+    - bpipe
+    - star >= 2.5.3a
+    - bioconductor-gviz
+    - bioconductor-biomart
+    - python
+
+test:
+  commands:
+    - clinker -h
+    - bpipe --help
+
+about:
+  home: https://github.com/Oshlack/Clinker
+  summary: "Clinker is a bioinformatics pipeline that generates a superTranscriptome from popular fusion finder outputs (JAFFA, tophatFusion, SOAP, deFUSE, Pizzly, etc), that can be then be either viewed in genome viewers such as IGV or through the included plotting feature developed with GViz."
+  license: MIT
+
+extra:
+  notes: "Wrapper script provided to indicate clinker is a bpipe pipeline, provide example command from wiki, and also a passthrough option."
+