Hi Dan,
Thank you Dan. This was very helpful.I installed MACS version 1.3 and now
the tool is working.
> Hi Vidya,
>
>
> One quick thing to check is that you installed MACS version 1.3 which is
> supported by the wrapper and not version 1.4 which is not yet supported.
>
>
> Thanks for using Galaxy,
>
> Dan
>
>
> On Jan 24, 2012, at 7:41 AM, Hans-Rudolf Hotz wrote:
>
>>
>>
>>
>> On 01/24/2012 06:19 AM, Vidya .H.K wrote:
>>> Hi,
>>> Actually I am not computer expert as well. I have just started to work
>>> in
>>> this area. so I am not able to figure out how to solve this problem. I
>>> request you to elaborate on what you meant in your previous mail.
>>
>> by simulating a complete command line I meant the following:
>>
>> You look how "macs_wrapper.py" is called by galaxy. This is written in
>> the "macs_wrapper.xml" and then you execute the same command line.
>>
>> But I just realize, you have re-submitted the same question in a
>> different e-mail thread again (unfortunately, again without a subject
>> line).....
>>
>>
>>>
>>> Thanks in advance
>>>
>>>
>>>
>>>
>>>
>>>> As I wrote in my previous e-mail: "Please send all follow-up with a cc
>>> to the mailing list ("reply-all")."
>>>> In order to debug you situation you need to simulate a complete
>>>> commandline, the same Galaxy is doing.
>>>> Regards, Hans
>>>> On 01/23/2012 05:35 AM, Vidya .H.K wrote:
>>>>> Hi,
>>>>> Sorry for delayed reply. When I execute "macs_wrapper.py" on command
>>>>> line,
>>>>> I get the following error.
>>>>> python macs_wrapper.py
>>>>> File "<stdin>", line 1
>>>>> python macs_wrapper.py
>>>>> Thanks in advance
>>>>>> On 01/10/2012 06:31 AM, Vidya .H.K wrote:
>>>>>>> Hi,
>>>>>>> I think macs is exceutable with galaxy user.
>>>>>> what happens if you execute "macs_wrapper.py" on the command line?
>>> Regards, Hans
>>>>>> PS: Please send all follow-up with a cc to the mailing list
>>>>>> ("reply-all").
>>>>>>>> On 01/09/2012 05:04 AM, Vidya .H.K wrote:
>>>>>>>>> Hi,
>>>>>>>>> I am new user to galaxy. I have installed galaxy on the Linux
>>>>>>>>> local
>>> server
>>>>>>>>> for ChIP-seq analysis. While running MACS, an error is flagged
>>>>>>>>> "An error occurred running this job: /bin/sh: macs: not
>>>>>>>>> found"
>>> .
>>>>>>>>> I have set the path for macs in /bin. But still the error
>>>>>>>>> persists. It
>>>>>>>>> would be great if any one help me resolve this problem.
>>>>>>>> Hi Vidya
>>>>>>>> Is macs executable for the galaxy user (ie the user the galaxy
>>> server
>>>>>>>> is
>>>>>>>> running as) ?
>>>>>>>> Regards, Hans
>>>>>>>>> Thanks in advance.
>>>>>>>>> Regards
>>>>>>>>> vidya
>>>>>>>>> ___________________________________________________________
>>>>>>>>> Please
>>> keep all replies on the list by using "reply all"
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>>>>>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>> ___________________________________________________________
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>>
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>
>
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