Mercurial > repos > peterjc > mira_assembler
comparison tools/mira3/mira.py @ 24:ad14a345f1b0 draft
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira3/ commit 6405ba93fcec7ea93452bf54d559c7507ee7a57c
| author | peterjc |
|---|---|
| date | Wed, 07 Jun 2017 12:33:07 -0400 |
| parents | 83a94a5038a7 |
| children | 85b86f31327c |
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| 23:83a94a5038a7 | 24:ad14a345f1b0 |
|---|---|
| 17 """Run MIRA to find its version number""" | 17 """Run MIRA to find its version number""" |
| 18 # At the commend line I would use: mira -v | head -n 1 | 18 # At the commend line I would use: mira -v | head -n 1 |
| 19 # however there is some pipe error when doing that here. | 19 # however there is some pipe error when doing that here. |
| 20 cmd = ["mira", "-v"] | 20 cmd = ["mira", "-v"] |
| 21 try: | 21 try: |
| 22 child = subprocess.Popen(cmd, | 22 child = subprocess.Popen(cmd, universal_newlines=True, |
| 23 stdout=subprocess.PIPE, | 23 stdout=subprocess.PIPE, |
| 24 stderr=subprocess.STDOUT) | 24 stderr=subprocess.STDOUT) |
| 25 except Exception as err: | 25 except Exception as err: |
| 26 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) | 26 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) |
| 27 sys.exit(1) | 27 sys.exit(1) |
| 89 # print(cmd) | 89 # print(cmd) |
| 90 | 90 |
| 91 handle = open(out_log, "w") | 91 handle = open(out_log, "w") |
| 92 try: | 92 try: |
| 93 # Run MIRA | 93 # Run MIRA |
| 94 child = subprocess.Popen(cmd_list, | 94 child = subprocess.Popen(cmd_list, universal_newlines=True, |
| 95 stdout=handle, | 95 stdout=handle, |
| 96 stderr=subprocess.STDOUT) | 96 stderr=subprocess.STDOUT) |
| 97 except Exception as err: | 97 except Exception as err: |
| 98 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err)) | 98 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err)) |
| 99 # TODO - call clean up? | 99 # TODO - call clean up? |