Merge pull request #3767 from bioconda/add-srst2

Added in srst2 recipes for 0.1.4.6 and 0.2.0

recipes/srst2/0.1.4.6/build.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+python setup.py install

recipes/srst2/0.1.4.6/meta.yaml

@@ -0,0 +1,38 @@
+package:
+  name: srst2
+  version: 0.1.4.6
+
+source:
+  fn: v0.1.6.tar.gz
+  url: https://github.com/katholt/srst2/archive/v0.1.6.tar.gz
+  sha256: 24cbd03933d4cc14bbfa7f8a073c9b0caafb13d55afb3bfa25f8b093fc5bc615
+  patches:
+    - use_setuptools.patch
+
+build:
+  number: 0
+  skip: True #[not py27]
+
+requirements:
+  build:
+    - python
+    - setuptools
+    - numpy >=1.7.1
+    - scipy >=0.12.0
+
+  run:
+    - python
+    - numpy >=1.7.1
+    - scipy >=0.12.0
+    - bowtie2 >=2.1.0
+    - samtools ==0.1.18
+
+test:
+  commands:
+    - srst2 -h 2>&1 | grep 'SRST2 - Short Read Sequence Typer' > /dev/null
+    - getmlst.py -h 2>&1 | grep 'usage' > /dev/null
+
+about:
+  home: https://github.com/katholt/srst2
+  license: BSD
+  summary: 'Short Read Sequence Typing for Bacterial Pathogens'

recipes/srst2/0.1.4.6/use_setuptools.patch

@@ -0,0 +1,12 @@
+diff --git a/setup.py b/setup.py
+index 37f4ca0..dbd1308 100644
+--- a/setup.py
++++ b/setup.py
+@@ -1,6 +1,6 @@
+ #!/usr/bin/env python
+
+-from distutils.core import setup
++from setuptools import setup
+
+ setup(
+     name='srst2',

recipes/srst2/build.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+python setup.py install

recipes/srst2/meta.yaml

@@ -0,0 +1,38 @@
+package:
+  name: srst2
+  version: 0.2.0
+
+source:
+  fn: v0.2.0.tar.gz
+  url: https://github.com/katholt/srst2/archive/v0.2.0.tar.gz
+  sha256: 352c59bdf00039dfa5610a4b88049a0eb114d7c2a305d4924b6e605cc6d15123
+  patches:
+    - use_setuptools.patch
+
+build:
+  number: 0
+  skip: True #[not py27]
+
+requirements:
+  build:
+    - python
+    - setuptools
+    - numpy >=1.7.1
+    - scipy >=0.12.0
+
+  run:
+    - python
+    - numpy >=1.7.1
+    - scipy >=0.12.0
+    - bowtie2 >=2.1.0
+    - samtools ==0.1.18
+
+test:
+  commands:
+    - srst2 -h 2>&1 | grep 'SRST2 - Short Read Sequence Typer' > /dev/null
+    - getmlst.py -h 2>&1 | grep 'usage' > /dev/null
+
+about:
+  home: https://github.com/katholt/srst2
+  license: BSD
+  summary: 'Short Read Sequence Typing for Bacterial Pathogens'

recipes/srst2/use_setuptools.patch

@@ -0,0 +1,12 @@
+diff --git a/setup.py b/setup.py
+index 37f4ca0..dbd1308 100644
+--- a/setup.py
++++ b/setup.py
+@@ -1,6 +1,6 @@
+ #!/usr/bin/env python
+
+-from distutils.core import setup
++from setuptools import setup
+
+ setup(
+     name='srst2',