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
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> >
> > http://lists.bx.psu.edu/
>
>
--
Sergei (Siarhei Manakou) Manakov
California Institute of Technology
+1 626 395 3593
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