diff utils.py @ 11:2c2ad8af0a4e draft default tip

planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/phylogenetics/plant_tribes/assembly_post_processor commit 5b19bd262023af92bc9aaa65f75b5ec81814e90f-dirty

--- a/utils.py	Wed Jun 09 20:26:55 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-import os
-import shutil
-import subprocess
-import sys
-
-FSTDERR = 'stderr.txt'
-FSTDOUT = 'stdout.txt'
-
-
-def check_execution_errors(rc, fstderr, fstdout):
-    if rc != 0:
-        fh = open(fstdout, 'rb')
-        out_msg = fh.read()
-        fh.close()
-        fh = open(fstderr, 'rb')
-        err_msg = fh.read()
-        fh.close()
-        msg = '%s\n%s\n' % (str(out_msg), str(err_msg))
-        stop_err(msg)
-
-
-def get_response_buffers():
-    fstderr = os.path.join(os.getcwd(), FSTDERR)
-    fherr = open(fstderr, 'wb')
-    fstdout = os.path.join(os.getcwd(), FSTDOUT)
-    fhout = open(fstdout, 'wb')
-    return fstderr, fherr, fstdout, fhout
-
-
-def move_directory_files(source_dir, destination_dir, copy=False, remove_source_dir=False):
-    source_directory = os.path.abspath(source_dir)
-    destination_directory = os.path.abspath(destination_dir)
-    if not os.path.isdir(destination_directory):
-        os.makedirs(destination_directory)
-    for dir_entry in os.listdir(source_directory):
-        source_entry = os.path.join(source_directory, dir_entry)
-        if copy:
-            shutil.copy(source_entry, destination_directory)
-        else:
-            shutil.move(source_entry, destination_directory)
-    if remove_source_dir:
-        os.rmdir(source_directory)
-
-
-def run_command(cmd):
-    fstderr, fherr, fstdout, fhout = get_response_buffers()
-    proc = subprocess.Popen(args=cmd, stderr=fherr, stdout=fhout, shell=True)
-    rc = proc.wait()
-    # Check results.
-    fherr.close()
-    fhout.close()
-    check_execution_errors(rc, fstderr, fstdout)
-
-
-def stop_err(msg):
-    sys.exit(msg)