Mercurial > repos > peterjc > mira4_assembler
changeset 34:0785a6537f3e draft
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 6405ba93fcec7ea93452bf54d559c7507ee7a57c
| author | peterjc |
|---|---|
| date | Wed, 07 Jun 2017 12:33:39 -0400 |
| parents | 1291ed21789f |
| children | 259891fce7fd |
| files | tools/mira4_0/mira4.py tools/mira4_0/mira4_bait.py tools/mira4_0/mira4_convert.py tools/mira4_0/mira4_make_bam.py tools/mira4_0/repository_dependencies.xml |
| diffstat | 5 files changed, 7 insertions(+), 5 deletions(-) [+] |
line wrap: on
line diff
--- a/tools/mira4_0/mira4.py Fri Jun 02 11:22:01 2017 -0400 +++ b/tools/mira4_0/mira4.py Wed Jun 07 12:33:39 2017 -0400 @@ -25,7 +25,7 @@ # however there is some pipe error when doing that here. cmd = [mira_binary, "-v"] try: - child = subprocess.Popen(cmd, + child = subprocess.Popen(cmd, universal_newlines=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) except Exception as err:
--- a/tools/mira4_0/mira4_bait.py Fri Jun 02 11:22:01 2017 -0400 +++ b/tools/mira4_0/mira4_bait.py Wed Jun 07 12:33:39 2017 -0400 @@ -19,7 +19,7 @@ # however there is some pipe error when doing that here. cmd = [mira_binary, "-v"] try: - child = subprocess.Popen(cmd, + child = subprocess.Popen(cmd, universal_newlines=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) except Exception as err: @@ -88,7 +88,7 @@ start_time = time.time() try: # Run MIRA - child = subprocess.Popen(cmd_list, + child = subprocess.Popen(cmd_list, universal_newlines=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) except Exception as err:
--- a/tools/mira4_0/mira4_convert.py Fri Jun 02 11:22:01 2017 -0400 +++ b/tools/mira4_0/mira4_convert.py Wed Jun 07 12:33:39 2017 -0400 @@ -29,7 +29,8 @@ # Avoid using shell=True when we call subprocess to ensure if the Python # script is killed, so too is the child process. try: - child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + child = subprocess.Popen(cmd, universal_newlines=True, + stdout=subprocess.PIPE, stderr=subprocess.PIPE) except Exception as err: sys.exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) # Use .communicate as can get deadlocks with .wait(),
--- a/tools/mira4_0/mira4_make_bam.py Fri Jun 02 11:22:01 2017 -0400 +++ b/tools/mira4_0/mira4_make_bam.py Wed Jun 07 12:33:39 2017 -0400 @@ -12,6 +12,7 @@ def run(cmd, log_handle): try: child = subprocess.Popen(cmd, shell=True, + universal_newlines=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) except Exception as err:
--- a/tools/mira4_0/repository_dependencies.xml Fri Jun 02 11:22:01 2017 -0400 +++ b/tools/mira4_0/repository_dependencies.xml Wed Jun 07 12:33:39 2017 -0400 @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="This requires the MIRA datatype definitions (e.g. the MIRA Assembly Format)."> - <repository changeset_revision="080d217544b0" name="mira_datatypes" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="3fc6ff47a3b1" name="mira_datatypes" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </repositories>