[ci skip] Merge PR 29061

Merge PR #29061, commits were: 
 * Update build number
 * Add patch file
 * Fix midas patch as given here snayfach/MIDAS#113

recipes/midas/meta.yaml

@@ -1,20 +1,21 @@
-{% set name = "midas" %}
+{% set name = "MIDAS" %}
 {% set version = "1.3.2" %}
 {% set sha256 = "87621eaa5b51eb81edc87e3e6b86c7efd3e1d64f503c6abca246b1be79120859" %}
 
 package:
-  name: '{{name}}'
+  name: '{{name|lower}}'
   version: '{{version}}'
 
 source:
   url: https://github.com/snayfach/MIDAS/archive/v{{version}}.tar.gz
   sha256: '{{sha256}}'
   patches:
-    - midas.patch
+    # the working patch comes from https://github.com/snayfach/MIDAS/pull/113
+    - midas.patches
 
 build:
   noarch: python
-  number: 4
+  number: 5
   script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv
 
 requirements:
@@ -45,6 +46,10 @@ test:
 about:
   home: https://github.com/snayfach/MIDAS
   license: GPL-3.0
+  license_family: GPL
+  license_file: LICENSE
   summary: An integrated pipeline for estimating strain-level genomic variation from
     metagenomic data
-  license_family: GPL
+
+extra:
+  notes: MIDAS requires reference database that needs to be additionally downloaded and set, https://github.com/snayfach/MIDAS/blob/master/docs/ref_db.md.

recipes/midas/midas.patches

@@ -0,0 +1,76 @@
+--- setup.py	2017-11-26 11:00:47.000000000 -0600
++++ setup.py.new	2021-06-16 12:39:18.363149855 -0500
+@@ -1,5 +1,5 @@
+ try:
+-	from setuptools import setup
++	from setuptools import setup, find_packages
+ except:
+ 	from distutils.core import setup
+ import os
+@@ -12,5 +12,7 @@
+ 	author = 'Stephen Nayfach',
+ 	author_email='[email protected]',
+ 	url='https://github.com/snayfach/MIDAS',
+-	install_requires = ['biopython >= 1.62', 'numpy >= 1.7.0', 'pysam >= 0.8.1', 'pandas >= 0.17.1']
++	install_requires = ['biopython >= 1.62', 'numpy >= 1.7.0', 'pysam >= 0.8.1', 'pandas >= 0.17.1'],
++        packages = find_packages(),
++        scripts = ['scripts/build_midas_db.py', 'scripts/call_consensus.py', 'scripts/compare_genes.py', 'scripts/merge_midas.py', 'scripts/query_by_compound.py', 'scripts/run_midas.py', 'scripts/snp_diversity.py', 'scripts/strain_tracking.py']
+ )
+--- midas/utility.py	2017-11-26 11:00:47.000000000 -0600
++++ midas/utility.py.new	2021-06-16 12:37:09.019590551 -0500
+@@ -5,6 +5,7 @@
+ # Freely distributed under the GNU General Public License (GPLv3)
+
+ import io, os, stat, sys, resource, gzip, platform, bz2, Bio.SeqIO
++from distutils.spawn import find_executable
+
+ __version__ = '1.3.0'
+
+@@ -106,23 +107,23 @@
+ 		pool.join()
+ 		sys.exit("\nKeyboardInterrupt")
+
++def find_exe(exe, path):
++	""" Finding executable """
++	if find_executable(exe) is None:
++		exe = os.path.join(path, exe)
++		if not os.path.isfile(exe):
++			sys.exit("\nError: File not found: %s\n" % exe)
++		if find_executable(exe) is None:
++			sys.exit("\nError: Executable not found: %s\n" % exe)
++	return exe
++
+ def add_executables(args):
+ 	""" Identify relative file and directory paths """
+ 	src_dir = os.path.dirname(os.path.abspath(__file__))
+ 	main_dir = os.path.dirname(src_dir)
+-	args['stream_seqs'] = '/'.join([src_dir, 'run', 'stream_seqs.py'])
+-	args['hs-blastn'] = '/'.join([main_dir, 'bin', platform.system(), 'hs-blastn'])
+-	args['bowtie2-build'] = '/'.join([main_dir, 'bin', platform.system(), 'bowtie2-build'])
+-	args['bowtie2'] = '/'.join([main_dir, 'bin', platform.system(), 'bowtie2'])
+-	args['samtools'] = '/'.join([main_dir, 'bin', platform.system(), 'samtools'])
+-	
+-	for arg in ['hs-blastn', 'stream_seqs', 'bowtie2-build', 'bowtie2', 'samtools']:
+-		if not os.path.isfile(args[arg]):
+-			sys.exit("\nError: File not found: %s\n" % args[arg])
+-
+-	for arg in ['hs-blastn', 'bowtie2-build', 'bowtie2', 'samtools']:
+-		if not os.access(args[arg], os.X_OK):
+-			sys.exit("\nError: File not executable: %s\n" % args[arg])
++	args['stream_seqs'] = find_exe('stream_seqs.py', os.path.join(src_dir, 'run'))
++	for exe in ['hs-blastn',  'bowtie2-build', 'bowtie2', 'samtools']:
++		args[exe] = find_exe(exe, os.path.join(main_dir, 'bin', platform.system()))
+
+ 	import subprocess as sp
+
+--- midas/run/snps.py	2017-11-26 11:00:47.000000000 -0600
++++ midas/run/snps.py.new	2021-06-16 12:32:36.982415965 -0500
+@@ -220,6 +220,8 @@
+ 	start = time()
+ 	print("\nCounting alleles")
+ 	args['log'].write("\nCounting alleles\n")
++        args['log'].close()
++        args.pop('log', None)
+
+ 	# run pileups per species in parallel
+ 	argument_list = []