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?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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