Hi all,
I might have missed something, but I found I can not launch some tools in bedops and I got the following errors:
------
$ bam2bed --help
File "/usr/local/apps/bedops/2.4.1/bam2bed", line 835
except IOError, msg:
^
SyntaxError: invalid syntax
bam2starch --help
File "/usr/local/apps/bedops/2.4.1/bam2starch", line 857
except IOError, msg:
^
SyntaxError: invalid syntax
-bash: --help: command not found
gff2bed --help
File "/usr/local/apps/bedops/2.4.1/gff2bed", line 330
except IOError, msg:
^
SyntaxError: invalid syntax
-bash: --help: command not found
gff2starch --help
File "/usr/local/apps/bedops/2.4.1/gff2starch", line 357
except IOError, msg:
^
SyntaxError: invalid syntax
-bash: --help: command not found
gtf2bed --help
File "/usr/local/apps/bedops/2.4.1/gtf2bed", line 306
except IOError, msg:
^
SyntaxError: invalid syntax
-bash: --help: command not found
gtf2starch --help
File "/usr/local/apps/bedops/2.4.1/gtf2starch", line 332
except IOError, msg:
^
SyntaxError: invalid syntax
-bash: --help: command not found
psl2bed --help
-bash: /usr/local/apps/bedops/2.4.1/psl2bed: /Usr/bin/env: bad interpreter: No such file or directory
-bash: --help: command not found
psl2starch --help
File "/usr/local/apps/bedops/2.4.1/psl2starch", line 431
except IOError, msg:
^
SyntaxError: invalid syntax
-bash: --help: command not found
sam2bed --help
File "/usr/local/apps/bedops/2.4.1/sam2bed", line 829
except IOError, msg:
^
SyntaxError: invalid syntax
-bash: --help: command not found
sam2starch --help
File "/usr/local/apps/bedops/2.4.1/sam2starch", line 853
except IOError, msg:
^
SyntaxError: invalid syntax
-bash: --help: command not found
vcf2bed --help
File "/usr/local/apps/bedops/2.4.1/vcf2bed", line 452
except IOError, msg:
^
SyntaxError: invalid syntax
-bash: --help: command not found
vcf2starch --help
File "/usr/local/apps/bedops/2.4.1/vcf2starch", line 478
except IOError, msg:
^
SyntaxError: invalid syntax
-bash: --help: command not found
---------
Your insight will be greatly appreciated.
Jack
