start_xena: startXena.py annotate

annotate startXena.py @ 3:47bb7e16dd73

Tweaked the install dependencies script

author	melissacline
date	Thu, 04 Sep 2014 15:29:38 -0700
parents	00ea1bdc1aed
children	82755b0ee5a5

rev	line source
0 0676a227dbc6 Uploaded melissacline parents: diff changeset	1 #!/usr/bin/env python
0676a227dbc6 Uploaded melissacline parents: diff changeset	2
0676a227dbc6 Uploaded melissacline parents: diff changeset	3 import argparse
0676a227dbc6 Uploaded melissacline parents: diff changeset	4 import os
0676a227dbc6 Uploaded melissacline parents: diff changeset	5 import subprocess
0676a227dbc6 Uploaded melissacline parents: diff changeset	6 import sys
0676a227dbc6 Uploaded melissacline parents: diff changeset	7
1 00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	8 def stop_err(msg, error_level=1):
0 0676a227dbc6 Uploaded melissacline parents: diff changeset	9 """Print error message to stdout and quit with given error level."""
1 00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	10 sys.stderr.write("%s\n" % msg)
00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	11 #fp.write("%s\n" % msg)
00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	12 #fp.write("error code %d\n" % error_level)
0 0676a227dbc6 Uploaded melissacline parents: diff changeset	13 sys.exit(error_level)
0676a227dbc6 Uploaded melissacline parents: diff changeset	14
0676a227dbc6 Uploaded melissacline parents: diff changeset	15
1 00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	16 def run(cmd):
0 0676a227dbc6 Uploaded melissacline parents: diff changeset	17 #Avoid using shell=True when we call subprocess to ensure if the Python
0676a227dbc6 Uploaded melissacline parents: diff changeset	18 #script is killed, so too is the child process.
0676a227dbc6 Uploaded melissacline parents: diff changeset	19 try:
0676a227dbc6 Uploaded melissacline parents: diff changeset	20 child = subprocess.Popen(cmd, stdout=subprocess.PIPE,
0676a227dbc6 Uploaded melissacline parents: diff changeset	21 stderr=subprocess.PIPE, shell=True)
0676a227dbc6 Uploaded melissacline parents: diff changeset	22 except Exception, err:
0676a227dbc6 Uploaded melissacline parents: diff changeset	23 stop_err("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
0676a227dbc6 Uploaded melissacline parents: diff changeset	24 #Use .communicate as can get deadlocks with .wait(),
0676a227dbc6 Uploaded melissacline parents: diff changeset	25 stdout, stderr = child.communicate()
0676a227dbc6 Uploaded melissacline parents: diff changeset	26 return_code = child.returncode
0676a227dbc6 Uploaded melissacline parents: diff changeset	27 if return_code:
0676a227dbc6 Uploaded melissacline parents: diff changeset	28 if stderr and stdout:
1 00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	29 stop_err("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, err, stdout, stderr))
0 0676a227dbc6 Uploaded melissacline parents: diff changeset	30 else:
1 00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	31 stop_err("Return code %i from command:\n%s\n%s" % (return_code, err, stderr))
0 0676a227dbc6 Uploaded melissacline parents: diff changeset	32
0676a227dbc6 Uploaded melissacline parents: diff changeset	33
0676a227dbc6 Uploaded melissacline parents: diff changeset	34
0676a227dbc6 Uploaded melissacline parents: diff changeset	35 def main():
1 00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	36 #parser = argparse.ArgumentParser()
00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	37 #parser.add_argument("-H", "--host", type=str)
00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	38 #parser.add_argument("-p", "--port", type=str)
00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	39 #args = parser.parse_args()
00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	40
00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	41 jarPath = os.getenv("JAVA_JAR_PATH", "~")
00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	42 xenaJarPath = os.path.join(jarPath, "xena.jar")
00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	43 xenaBaseDir = os.getenv("XENA_BASE_DIR", "~")
00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	44 #xenaBaseDir = os.getenv("__tool_data_path__", "~") + "/shared/xena"
00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	45 #xenaBaseDir = args.toolDataPath + "/shared/xena"
00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	46 cmdline = "java -jar %s -r %s/files -d %s/xena/db -t %s/tmp" % (xenaJarPath, xenaBaseDir, xenaBaseDir, xenaBaseDir)
00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	47 for ii in range(1,len(sys.argv)):
00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	48 cmdline = "%s %s" % (cmdline, sys.argv[ii])
00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	49 fp = open("/Users/melissacline/tmp/xena.out", "w")
00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	50 fp.write("jar path (not paht) %s\n" % (jarPath))
00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	51 fp.write("xena base dir %s\n" % (xenaBaseDir))
00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	52 fp.write(cmdline)
00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	53 run(cmdline)
00ea1bdc1aed Updated the repo in the test toolshed - this should work now melissacline parents: 0 diff changeset	54 fp.close()
0 0676a227dbc6 Uploaded melissacline parents: diff changeset	55
0676a227dbc6 Uploaded melissacline parents: diff changeset	56 if __name__ == '__main__':
0676a227dbc6 Uploaded melissacline parents: diff changeset	57 main( )
0676a227dbc6 Uploaded melissacline parents: diff changeset	58

Mercurial > repos > melissacline > start_xena

annotate startXena.py @ 3:47bb7e16dd73