From d124d00c9a3533be9ecab8b6e889b3a0f72d2391 Mon Sep 17 00:00:00 2001
From: Philippe Bordron <pbordron@users.noreply.github.com>
Date: Mon, 22 Oct 2018 15:52:17 +0200
Subject: [PATCH] add rnaQUAST recipe (#11470)

---
 recipes/rnaquast/build.sh  |  9 +++++++++
 recipes/rnaquast/meta.yaml | 40 ++++++++++++++++++++++++++++++++++++++
 2 files changed, 49 insertions(+)
 create mode 100644 recipes/rnaquast/build.sh
 create mode 100644 recipes/rnaquast/meta.yaml

diff --git a/recipes/rnaquast/build.sh b/recipes/rnaquast/build.sh
new file mode 100644
index 0000000000000..8736b04c39060
--- /dev/null
+++ b/recipes/rnaquast/build.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+OUTDIR=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
+mkdir -p $OUTDIR
+mkdir -p $PREFIX/bin
+chmod a+x *.py
+cp -rp * "$OUTDIR/"
+cd $PREFIX/bin
+ln -s "../${OUTDIR#$PREFIX}"/*.py .
diff --git a/recipes/rnaquast/meta.yaml b/recipes/rnaquast/meta.yaml
new file mode 100644
index 0000000000000..99b0d3acc1f4b
--- /dev/null
+++ b/recipes/rnaquast/meta.yaml
@@ -0,0 +1,40 @@
+{% set name = "rnaQUAST" %}
+{% set version = "1.5.1" %}
+{% set sha256 = "f603f847bce0346292d2d74c756d32f69c6bffad282d5fff36479d3a901d1f1e" %}
+
+package:
+  name: {{ name | lower }}
+  version: {{ version }}
+
+source:
+  url: http://cab.spbu.ru/files/{{ name | lower }}/release{{ version }}/{{ name }}-{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  number: 0
+  skip: True # [osx]
+
+requirements:
+  run:
+    - blast
+    - blat
+    - busco >=2
+    - emboss
+    - gmap
+    - python <3
+    - gffutils
+    - joblib
+    - matplotlib
+    - ucsc-pslsort
+    - star
+    - tophat
+    - samtools
+
+test:
+  commands:
+    - rnaQUAST.py --test
+
+about:
+  summary: rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software.
+  home: http://cab.spbu.ru/software/rnaquast/
+  license: GPLv2