--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ctat_trinity_wrapper.py	Tue Jul 17 11:50:42 2018 -0400
@@ -0,0 +1,162 @@
+#!/usr/bin/env python
+
+'''
+trinity_runner.py
+This program is used as a wrapper for Trinity to allow an automatic rerun of failed jobs. It takes arguments for a typical Trinity run:
+~ Required args ~
+Input files - single or paired (left and right)
+File type (fasta, fastq)
+Max memory - this I need to derive somehow from the dynamic runner using Galaxy slots
+
+~ Optional args ~
+Output directory - this allows users to run the same job over in case it walltime'd out or failed for recoverable reasons.
+
+ --
+Created Tuesday, 7 March 2017.
+Carrie Ganote
+
+Licensed to Indiana University under Creative Commons 3.0
+'''
+import subprocess32
+import argparse
+import logging as log
+import sys
+import os
+import errno
+from datetime import datetime
+
+TRINITY_OUT_DIR = "trinity_out_dir"
+
+def main(*args):
+    parser = argparse.ArgumentParser(description="")
+    parser.add_argument("-o","--output", help="Name of output directory")
+    parser.add_argument("-q","--seqType", help="Type of reads; fa or fq")
+    parser.add_argument("-m","--max_memory", help="How much memory to allocate? Or maybe how many cpus?")
+    parser.add_argument("-p","--mem_per_cpu", help="Memory PER CPU, in GB, in case we want to multiply mem x cpu at runtime")
+    parser.add_argument("-s","--single", help="Single read file input")
+    parser.add_argument("-l","--left", help="Left read file from paired inputs")
+    parser.add_argument("-r","--right", help="Right read file from paired inputs")
+    parser.add_argument("-v","--verbose", help="Enable debugging messages to be displayed", action='store_true')
+    parser.add_argument("-g","--log", help="Log file")
+    parser.add_argument("-t","--timing", help="Timing file, if it exists", default=None)
+    parser.add_argument("-d","--dir", help="if supplying a rerunnable job, this is the (hopefully unique) name of the directory to run it in.")
+    parser.add_argument("-u","--user", help="Username to run job under")
+    parser.add_argument("-f","--fullpath", help="if supplying a rerunnable job, this is the full path (except the user and dir names) to run the job in.")
+    parser.add_argument("-c","--CPU", help="CPUs, either a hard coded numer or from Galaxy slots")
+#    parser.add_argument("-","--", help="")
+    args = parser.parse_args()
+
+    if args.verbose:
+        log.basicConfig(format='%(message)s',level=log.DEBUG)
+    cmd = ["Trinity"]
+
+    ### Add rerun ability ###########################################
+    # This variable tells us later whether to copy the files back to the job working directory
+    copyback = False
+    if args.dir and args.user and args.fullpath:
+        cleandir = args.dir
+        chars = "\\`*_{}[]()>#+-.!$&;| "
+        for c in chars:
+            if c in cleandir:
+                cleandir = cleandir.replace(c, "_")
+        rerunPath = "%s/%s/%s" % (args.fullpath, args.user, cleandir)
+        print "Rerunpath is ",rerunPath
+        try:
+            os.makedirs(rerunPath)
+            print "Created dir ",rerunPath
+        except OSError as exc:
+            if exc.errno == errno.EEXIST and os.path.isdir(rerunPath):
+                pass
+            else:
+                raise
+        copyback = os.getcwd()
+        outdir = copyback + "/" + TRINITY_OUT_DIR
+        try:
+            os.makedirs(outdir)
+            print "Created dir ",outdir
+        except OSError as exc:
+            if exc.errno == errno.EEXIST and os.path.isdir(outdir):
+                pass
+            else:
+                raise
+        os.chdir(rerunPath)
+
+    ### Add information for reads ###################################
+    if args.left and args.right:
+        cmd += ["--left",args.left,"--right", args.right]
+    elif args.single:
+        cmd += ["--single",args.single]
+    else:
+        raise Exception ("Need input files in order to run Trinity!")
+
+    ### Add seqtype ##################################################
+    if args.seqType:
+        cmd += ["--seqType",args.seqType]
+    else:
+        raise Exception ("Please specify a file type for your reads!")
+
+    ### Memory and CPU management ####################################
+    if args.mem_per_cpu and not args.max_memory:
+        if args.CPU:
+            memry = int(args.CPU) * int(args.mem_per_cpu)
+            memstr = "%dG" % (memry)
+            cmd += ["--max_memory",memstr]
+        else:
+            memry = 2 * int(args.mem_per_cpu)
+            memstr = "%dG" % (memry)
+            cmd += ["--max_memory",memstr]
+    elif args.max_memory and not args.mem_per_cpu:
+        cmd += ["--max_memory",args.max_memory]
+    else:
+        raise Exception ("Please pick Memory per cpu, or max mem, but not both.")
+    if args.CPU:
+        cmd += ["--CPU", args.CPU]
+    
+    ### Enough args, let's run it ####################################
+    print "About to write to %s" % args.log
+    out = open(args.log, 'w')
+    totalattempts = attempts = 2
+    ec = 1
+    finish = 1
+    out.write("Command is:\n%s\n" % (" ".join(cmd)))
+
+    ### There is definitely some value in running the job more than once, especially if it dies for stupid reasons.. ###
+    while ec != 0 and attempts > 0 and finish != 0:
+
+        dt = datetime.now()
+        dtstr = dt.strftime("%d/%m/%y %H:%M")
+        out.write("Beginning attempt %d of Trinity job at %s\n" % (totalattempts - attempts +1, dtstr) )
+        attempts -= 1
+        ec = subprocess32.call(cmd, shell=False, stdin=None, stdout=out, stderr=out, timeout=None)       
+        out.write("Trinity exited with status %d\n" % ec)
+
+        greplog = open("greplog", 'w')
+        cmds = ["grep", 'All commands completed successfully', args.log]
+        finish = subprocess32.call(cmds,shell=False,  stdin=None, stdout=greplog, stderr=greplog, timeout=None)
+        greplog.close()
+        out.write("Finished and found the success command with grep code %d\n" % finish)
+
+    if ec == 0 and args.timing is not None:
+        if copyback is not False:
+            cwd = os.getcwd()
+            dest = copyback + "/" + TRINITY_OUT_DIR + "/Trinity.fasta"
+            src = cwd + "/" + TRINITY_OUT_DIR + "/Trinity.fasta"
+            print "copying trinity outputs from %s to %s" % (src, dest)
+            os.symlink(src, dest)
+
+        #copy the timing file into the log
+        try: 
+            handle = open (args.timing, 'r')
+            for line in handle:
+                out.write(line)
+            handle.close()
+        except (OSError, IOError) as e:
+            print "Oops, no timing file found? ",e
+
+
+    out.close()
+    exit (ec)
+ 
+if __name__ == "__main__":
+    main(*sys.argv)
+