Hello Greg, What version of Galaxy are you running - it is likely older than the December 20, 2012 Galaxy release. You'll have to upgrade to at least that release to use the main Galaxy tool shed.
Greg Von Kuster On Feb 15, 2013, at 9:43 AM, greg wrote: > Hi guys, > > I'm getting an error when trying to install this from the toolshed? > Let me know what I should do? > > Thanks, > > Greg > > Error - <type 'exceptions.ValueError'>: too many values to unpack > URL: > http://galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=67abe7fe2882a54c&changeset_revisions=cdd9791c0afa > File > '/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', > line 143 in __call__ > app_iter = self.application(environ, start_response) > File > '/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', > line 80 in __call__ > return self.application(environ, start_response) > File > '/misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', > line 91 in __call__ > return self.app( environ, start_response ) > File > '/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', > line 632 in __call__ > return self.application(environ, start_response) > File '/misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', > line 160 in __call__ > body = method( trans, **kwargs ) > File '/misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', > line 206 in decorator > return func( self, trans, *args, **kwargs ) > File > '/misc/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', > line 1201 in prepare_for_install > description, repository_clone_url, changeset_revision, ctx_rev, > repository_owner, tool_dependencies = repo_info_tuple > ValueError: too many values to unpack > > > > On Fri, Feb 15, 2013 at 9:39 AM, James Taylor <ja...@jamestaylor.org> wrote: >> You likely want the newest version (3) >> >> On Feb 15, 2013 9:37 AM, "greg" <margeem...@gmail.com> wrote: >>> >>> Thanks! So one question, when I go to install it from the toolshed I >>> see two choices for a revision to select: >>> >>> 3:cdd9791c0afa >>> 0:c1eeccec29d1 >>> >>> Which would I choose and why? >>> >>> Thanks, >>> >>> Greg >>> >>> On Fri, Feb 15, 2013 at 9:30 AM, James Taylor <ja...@jamestaylor.org> >>> wrote: >>>> The wrapper you are using is for MACS 1.3, there is a wrapper that is >>>> compatible with 1.4 in the toolshed. >>>> >>>> -- >>>> James Taylor, Assistant Professor, Biology/CS, Emory University >>>> >>>> >>>> On Fri, Feb 15, 2013 at 9:26 AM, greg <margeem...@gmail.com> wrote: >>>>> Hi guys, >>>>> >>>>> I'm trying to run MACS in my local galaxy install (see screenshot: >>>>> http://snag.gy/5QGUH.jpg) >>>>> >>>>> And I'm getting this error: >>>>> >>>>> Usage: macs <-t tfile> [-n name] [-g genomesize] [options] >>>>> >>>>> Example: macs -t ChIP.bam -c Control.bam -f BAM -g h -n test -w >>>>> --call-subpeaks >>>>> >>>>> macs: error: no such option: --lambdaset >>>>> >>>>> Thanks in advance for any help. >>>>> >>>>> -Greg >>>>> >>>>> Here's how I installed Macs (I guess it doesn't come built in?) >>>>> >>>>>> cd /usr/local/galaxy/downloads/ >>>>>> wget https://github.com/downloads/taoliu/MACS/MACS-1.4.2-1.tar.gz >>>>>> tar -xzvf MACS-1.4.2-1.tar.gz >>>>>> cd MACS-1.4.2 >>>>>> source /usr/local/galaxy/job_environment_setup_file >>>>>> python setup.py install >>>>>> deactivate >>>>>> cd /misc/local/galaxy/galaxy_python/bin >>>>>> ln -s macs14 macs >>>>> >>>>> (and made sure /misc/local/galaxy/galaxy_python/bin is on the galaxy >>>>> user's path) >>>>> ___________________________________________________________ >>>>> 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/ > ___________________________________________________________ > 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/ ___________________________________________________________ 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/
