From fe678d1b7817c221e58888ccba98e4b52b733534 Mon Sep 17 00:00:00 2001
From: lonsbio <andrew.lonsdale@lonsbio.com.au>
Date: Tue, 7 Aug 2018 01:56:26 +1000
Subject: [PATCH] Clinker (#10244)

* Add clinker with wrapper

* Add full test

* Remove test data test as per guidelines
---
 recipes/clinker/build.sh           | 19 +++++++++
 recipes/clinker/clinker-wrapper.sh | 63 ++++++++++++++++++++++++++++++
 recipes/clinker/meta.yml           | 38 ++++++++++++++++++
 3 files changed, 120 insertions(+)
 create mode 100644 recipes/clinker/build.sh
 create mode 100644 recipes/clinker/clinker-wrapper.sh
 create mode 100644 recipes/clinker/meta.yml

diff --git a/recipes/clinker/build.sh b/recipes/clinker/build.sh
new file mode 100644
index 0000000000000..2e4fcccd9b97d
--- /dev/null
+++ b/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 $PREFIX/bin
+
+
+
diff --git a/recipes/clinker/clinker-wrapper.sh b/recipes/clinker/clinker-wrapper.sh
new file mode 100644
index 0000000000000..e5057840a5d74
--- /dev/null
+++ b/recipes/clinker/clinker-wrapper.sh
@@ -0,0 +1,63 @@
+#!/bin/bash
+CLINKERLOGO=$(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[@]}" $PACKAGE_HOME/workflow/clinker.pipe "$@"
+
diff --git a/recipes/clinker/meta.yml b/recipes/clinker/meta.yml
new file mode 100644
index 0000000000000..68a0027df414b
--- /dev/null
+++ b/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."
+