On 1 May 2012 14:51, Sergei Manakov <siarheimanakov@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 <dan@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

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--
Sergei (Siarhei Manakou) Manakov

California Institute of Technology

+1 626 395 3593