I am trying to move my django project from a development server to a production server. I have ironed out almost everything with one (BIG) exception. When I run the following code in the terminal (using python manage.py shell) it works fine, however running through my apache server (with mod_wsgi) it does not run fine.
My code:
...
blastn_cline = NcbiblastnCommandline(query=filepath, db=db, evalue=0.1, outfmt=5, out=out, task="blastn-short", dust="no")
process = subprocess.Popen(str(blastn_cline),shell=True,stdout = subprocess.PIPE, stderr = subprocess.PIPE)
proc_out, proc_err = process.communicate()
err_log = open('/Users/basehunt/logs/ncbi_error_log.log', 'a+')
err_log.write("\n"+str(datetime.datetime.now())+": "+str(proc_err))
err_log.close()
...
when I look at my log file ncbi_error_log.log after I run through terminal I get (as an example):
2011-12-17 12:30:54.771292:
so no error. However, when I run through my apache server I get:
2011-12-17 12:28:59.755323: /bin/sh: blastn: command not found
I have tried to search extensively for a solution to this problem but can't find anything that gives a fix - though I hope I am missing something glaringly obvious so I can quickly sort this out.
Additional info:
OS X Snow Leopard
python version is 2.7.2
django 1.3
PATH contains the directory with blastn
If there is any additional code you want to see, let me know.
SOLVED:
by changing
process = subprocess.Popen(str(blastn_cline),shell=True,stdout = subprocess.PIPE, stderr = subprocess.PIPE)
to
process = subprocess.Popen('/Users/basehunt/BLAST/ncbi-blast-2.2.25+/bin/'+str(blastn_cline),shell=True,stdout = subprocess.PIPE, stderr = subprocess.PIPE)
in order to point absolutely to the function. Many thanks.
