Fixes related to problems with samtools & bowtie2

-see issues #73, #72, #69, #68
-added new samtools and bowtie2 binaries which should work on more systems
-added checks for samtools and bowtie2 binaries; if binaries don't work instructions for replacing them are provided

midas/utility.py

@@ -4,7 +4,7 @@
 # Copyright (C) 2015 Stephen Nayfach
 # Freely distributed under the GNU General Public License (GPLv3)
 
-import io, os, stat, sys, resource, gzip, platform, subprocess, bz2, Bio.SeqIO
+import io, os, stat, sys, resource, gzip, platform, bz2, Bio.SeqIO
 
 __version__ = '1.3.0'
 
@@ -119,10 +119,36 @@ def add_executables(args):
 	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])
 
+	import subprocess as sp
+
+	process = sp.Popen("%s view" % args['samtools'], shell=True, stdout=sp.PIPE, stderr=sp.PIPE)
+	process.wait()
+	if process.returncode != 0:
+		err = "\nError: could not execute samtools binary: %s\n" % args['samtools']
+		err += "(exited with error code %s)\n" % process.returncode
+		err += "To solve this issue, follow these steps:\n"
+		err += "  1) Download samtools v1.4: https://github.com/samtools/samtools/releases/download/1.4/samtools-1.4.tar.bz2\n"
+		err += "  2) Unpack and compile the software on your system\n"
+		err += "  3) Copy the new samtools binary to: %s\n" % os.path.dirname(args['samtools'])
+		sys.exit(err)
+
+	process = sp.Popen("%s -h" % args['bowtie2'], shell=True, stdout=sp.PIPE, stderr=sp.PIPE)
+	process.wait()
+	if process.returncode != 0:
+		err = "\nError: could not execute bowtie2 binary: %s\n" % args['bowtie2']
+		err += "(exited with error code %s)\n" % process.returncode
+		err += "To solve this issue, follow these steps:\n"
+		err += "  1) Go to https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.2\n"
+		err += "  2) Download bowtie2-2.3.2-linux-x86_64.zip\n"
+		err += "  3) Unpack the software on your system\n"
+		err += "  4) Copy the new bowtie2 binaries to: %s\n" % os.path.dirname(args['bowtie2'])
+		sys.exit(err)
+
 def auto_detect_file_type(inpath):
 	""" Detect file type [fasta or fastq] of <p_reads> """
 	infile = iopen(inpath)
@@ -207,8 +233,9 @@ def check_exit_code(process, command):
 
 def check_bamfile(args, bampath):
 	""" Use samtools to check bamfile integrity """
+	import subprocess as sp
 	command = '%s view %s > /dev/null' % (args['samtools'], bampath)
-	process = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+	process = sp.Popen(command, shell=True, stdout=sp.PIPE, stderr=sp.PIPE)
 	out, err = process.communicate()
 	if err.decode('ascii') != '': # need to use decode to convert to characters for python3
 		err_message = "\nWarning, bamfile may be corrupt: %s\nSamtools reported this error: %s\n" % (bampath, err.rstrip())