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 <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 ___________________________________________________________ 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:
-- Sergei (Siarhei Manakou) Manakov
California Institute of Technology
+1 626 395 3593
-- Sergei (Siarhei Manakou) Manakov California Institute of Technology +1 626 395 3593