sorry, I meant "is NOW trying to call the correct executable", but I still
get the error.

thanks,
S.

On 1 May 2012 14:51, Sergei Manakov <siarheimana...@gmail.com> wrote:

> hi Dan,
>
> Thanks for your replay. I have now installed MACS 1.3.7.1, so the script
> macs_wrapper.py is not trying to call the correct executable.
>
> When I try to run MACS from galaxy, I do however get what an error:
>
> Messages from MACS:
>
> INFO  @ Tue, 01 May 2012 14:47:42:
> # ARGUMENTS LIST:
> # name = MACS_in_Galaxy
> # format = SAM
> # ChIP-seq file = 
> /usr/local/galaxy/galaxy-dist/database/files/002/dataset_2345.dat
> # control file = None
> # effective genome size = 2.70e+09
> # tag size = 25
> # band width = 300
> # model fold = 32
> # pvalue cutoff = 1.00e-05
> # Ranges for calculating regional lambda are : peak_region,1000,5000,10000
> INFO  @ Tue, 01 May 2012 14:47:42: #1 read tag files...
> INFO  @ Tue, 01 May 2012 14:47:42: #1 read treatment tags...
> Traceback (most recent call last):
>   File "/usr/local/bin/macs", line 273, in
>     main()
>   File "/usr/local/bin/macs", line 57, in main
>     (treat, control) = load_tag_files_options (options)
>   File "/usr/local/bin/macs", line 252, in load_tag_files_options
>     treat = options.build(open2(options.tfile, gzip_flag=options.gzip_flag))
>   File "/usr/local/lib/python2.6/dist-packages/MACS/IO/__init__.py", line 
> 1480, in build_fwtrack
>     (chromosome,fpos,strand) = self.__fw_parse_line(thisline)
>   File "/usr/local/lib/python2.6/dist-packages/MACS/IO/__init__.py", line 
> 1524, in __fw_parse_line
>     thisstart = int(thisfields[3]) - 1        
> ValueError: invalid literal for int() with base 10: '*'
>
> how should I look at it?
>
>
> thanks,
> Sergei
>
>
>
>
>
> On 9 April 2012 18:13, Daniel Blankenberg <d...@bx.psu.edu> wrote:
>
>> Hi Sergei,
>>
>> The current MACS tool that comes with Galaxy uses MACS 1.3.7.1 from
>> http://liulab.dfci.harvard.edu/MACS/Download.html.
>>
>>
>> Thanks for using Galaxy,
>>
>> Dan
>>
>>
>> On Mar 28, 2012, at 6:38 PM, Sergei Manakov wrote:
>>
>> > Hello,
>> >
>> > I am trying to set up MACS tool on local Galaxy. Galaxy comes with
>> > it's macs-wrapper.py and macs-wrapper.xml, but it wants to use "macs"
>> > not "macs14" executable.
>> >
>> > I tried to to editing macs-wrapper.py to make it use "macs14" instead,
>> > but some options are not the same between the two, and the tool
>> > crashes.
>> >
>> > I would appreciate if someone could give me an advice on where I can
>> > get "macs" executable for 64-bit Linux.
>> >
>> > thanks,
>> > Sergei
>> >
>> > --
>> > Sergei (Siarhei Manakou) Manakov
>> >
>> > California Institute of Technology
>> >
>> > +1 626 395 3593
>> > ___________________________________________________________
>> > Please keep all replies on the list by using "reply all"
>> > in your mail client.  To manage your subscriptions to this
>> > and other Galaxy lists, please use the interface at:
>> >
>> >  http://lists.bx.psu.edu/
>>
>>
>
>
> --
> Sergei (Siarhei Manakou) Manakov
>
> California Institute of Technology
>
> +1 626 395 3593
>
>


-- 
Sergei (Siarhei Manakou) Manakov

California Institute of Technology

+1 626 395 3593
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