Author Topic: bedops tools launch problem  (Read 4446 times)

zhujack

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bedops tools launch problem
« on: May 22, 2014, 11:18:52 AM »
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






AlexReynolds

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  • Posts: 72
Re: bedops tools launch problem
« Reply #1 on: May 22, 2014, 02:31:10 PM »
Can you provide some details about your setup? Specifically, what operating system and version you are running, as well as your Python setup? Thanks!
« Last Edit: May 22, 2014, 02:49:03 PM by AlexReynolds »