Problem using NGS: Peak Calling - MACS
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)
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 <margeemail@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:
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 <james@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 <margeemail@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:
You likely want the newest version (3) On Feb 15, 2013 9:37 AM, "greg" <margeemail@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 <james@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 <margeemail@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:
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 <james@jamestaylor.org> wrote:
You likely want the newest version (3)
On Feb 15, 2013 9:37 AM, "greg" <margeemail@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 <james@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 <margeemail@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:
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 <james@jamestaylor.org> wrote:
You likely want the newest version (3)
On Feb 15, 2013 9:37 AM, "greg" <margeemail@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 <james@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 <margeemail@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:
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:
Thanks. I'm trying to follow the instructions here to update the code: http://wiki.galaxyproject.org/Admin/Get%20Galaxy#Keep_your_code_up_to_date But I'm getting this error:
hg incoming Not trusting file /misc/local/galaxy/galaxy-dist/.hg/hgrc from untrusted user galaxy, group scicomp Not trusting file /misc/local/galaxy/galaxy-dist/.hg/hgrc from untrusted user galaxy, group scicomp abort: repository default not found!
-Greg On Fri, Feb 15, 2013 at 9:45 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
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 <james@jamestaylor.org> wrote:
You likely want the newest version (3)
On Feb 15, 2013 9:37 AM, "greg" <margeemail@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 <james@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 <margeemail@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:
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:
Ok, I created a ~/.hgrc file and add this: [trusted] users=galaxy It seems to have fixed it. -Greg On Fri, Feb 15, 2013 at 9:50 AM, greg <margeemail@gmail.com> wrote:
Thanks.
I'm trying to follow the instructions here to update the code: http://wiki.galaxyproject.org/Admin/Get%20Galaxy#Keep_your_code_up_to_date
But I'm getting this error:
hg incoming Not trusting file /misc/local/galaxy/galaxy-dist/.hg/hgrc from untrusted user galaxy, group scicomp Not trusting file /misc/local/galaxy/galaxy-dist/.hg/hgrc from untrusted user galaxy, group scicomp abort: repository default not found!
-Greg
On Fri, Feb 15, 2013 at 9:45 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
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 <james@jamestaylor.org> wrote:
You likely want the newest version (3)
On Feb 15, 2013 9:37 AM, "greg" <margeemail@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 <james@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 <margeemail@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:
participants (3)
-
greg -
Greg Von Kuster -
James Taylor