Re: [galaxy-dev] Setting the output label based on input parameters?
It looks like the Cheetah syntax only is parsed within the command
tags so I figured out a way to do it... but it seems hackish. I
basically changed the string values of truevalue and falsevalue within the
parameter to be an English sentence that would become the label for the
output. I.e., in the input section:
param name=filter_reads type=boolean truevalue=Filtered Reads Fasta
falsevalue=Unfiltered Reads Fasta label=Filter reads?/
and in the output section:
data format=fasta name=output_fasta label=$filter_reads/
This seems wrong to do, but it does work. If anyone has a better method,
please let me know!
- Nik.
On Thu, Aug 25, 2011 at 2:36 PM, Nikhil Joshi najo...@ucdavis.edu wrote:
It's actually a boolean checkbox. so I basically want the label to
change based upon whether or not the checkbox is checked. Is there any way
to do that? Again, I've tried using the Cheetah syntax to do the #if #end
inside the output tags but that didn't work.
- Nik.
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB swe...@staffmail.ed.ac.ukwrote:
I meant to say label=${input} or label=${input.value}.
If it's a select field then you can change the option values to the text
you want to add to your output label.
Shaun
Quoting Kanwei Li kan...@gmail.com on Wed, 24 Aug 2011 20:34:57 -0400:
Hi Nikhil,
The tool templates are Cheetah templates, so you can do things like:
outputs
%if param == True:
data format=txt name=blah label=Label1 /
%else
data format=txt name=blah label=Label2 /
%endif
/outputs
Thanks,
K
On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi najo...@ucdavis.edu
wrote:
Hi all,
Is there a way to set the label of the output based on the input
parameters? Perhaps by using the action tag? Basically, I want the
output label to be different if the user sets a particular parameter to
be
true.
- Nik.
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Re: [galaxy-dev] Setting the output label based on input parameters?
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB swe...@staffmail.ed.ac.uk
wrote:
I meant to say label=${input} or label=${input.value}.
Nikhil, did you try as Shaun and others have suggested? Any available
string parameter can be used in a label as far as I can tell.
This is a common idiom - ask for a string ('title') to describe the
job/output for posterity, then in an output:
data format=foo name=output1 metadata_source=input1
label=${title}.myext/
There's even a built in ${on_string} if you just want the file name
plus some history ids?
On Mon, Aug 29, 2011 at 6:54 PM, Nikhil Joshi najo...@ucdavis.edu wrote:
It looks like the Cheetah syntax only is parsed within the command
tags so I figured out a way to do it... but it seems hackish. I
basically changed the string values of truevalue and falsevalue within the
parameter to be an English sentence that would become the label for the
output. I.e., in the input section:
param name=filter_reads type=boolean truevalue=Filtered Reads Fasta
falsevalue=Unfiltered Reads Fasta label=Filter reads?/
and in the output section:
data format=fasta name=output_fasta label=$filter_reads/
This seems wrong to do, but it does work. If anyone has a better method,
please let me know!
- Nik.
On Thu, Aug 25, 2011 at 2:36 PM, Nikhil Joshi najo...@ucdavis.edu wrote:
It's actually a boolean checkbox. so I basically want the label to
change based upon whether or not the checkbox is checked. Is there any way
to do that? Again, I've tried using the Cheetah syntax to do the #if #end
inside the output tags but that didn't work.
- Nik.
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB swe...@staffmail.ed.ac.uk
wrote:
I meant to say label=${input} or label=${input.value}.
If it's a select field then you can change the option values to the text
you want to add to your output label.
Shaun
Quoting Kanwei Li kan...@gmail.com on Wed, 24 Aug 2011 20:34:57 -0400:
Hi Nikhil,
The tool templates are Cheetah templates, so you can do things like:
outputs
%if param == True:
data format=txt name=blah label=Label1 /
%else
data format=txt name=blah label=Label2 /
%endif
/outputs
Thanks,
K
On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi najo...@ucdavis.edu
wrote:
Hi all,
Is there a way to set the label of the output based on the input
parameters? Perhaps by using the action tag? Basically, I want the
output label to be different if the user sets a particular parameter to
be
true.
___
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Re: [galaxy-dev] migrate the database schema from 80 to 81
Jack Zhu wrote: Hi all, I have problems with updating my local instance of Galaxy. Specifically I can not migrate the database schema from 80 to 81: Hi Jack, Thanks for reporting this issue. It has been fixed in changeset 5951:62d51750d7df. --nate -- $$ sh manage_db.sh upgrade 80 - 81... Migration script to add a 'tool_version' column to the hda/ldda tables. Traceback (most recent call last): File ./scripts/manage_db.py, line 63, in module main( repository=repo, url=db_url ) File /home/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py, line 150, in main ret = command_func(**kwargs) File /home/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py, line 221, in upgrade return _migrate(url, repository, version, upgrade=True, err=err, **opts) File /home/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py, line 349, in _migrate schema.runchange(ver, change, changeset.step) File /home/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py, line 184, in runchange change.run(self.engine, step) File /home/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py, line 101, in run func() File lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py, line 17, in upgrade metadata.reflect() File /home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py, line 1733, in reflect Table(name, self, **reflect_opts) File /home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py, line 108, in __call__ return type.__call__(self, name, metadata, *args, **kwargs) File /home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py, line 236, in __init__ _bind_or_error(metadata).reflecttable(self, include_columns=include_columns) File /home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py, line 1265, in reflecttable self.dialect.reflecttable(conn, table, include_columns) File /home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py, line 1673, in reflecttable only=include_columns) File /home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py, line 2139, in reflect self._add_column(table, line, charset, only) File /home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py, line 2227, in _add_column type_instance = col_type(*type_args, **type_kw) File /home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py, line 569, in __init__ super(MSBigInteger, self).__init__(display_width, **kw) TypeError: super(type, obj): obj must be an instance or subtype of type -- Your help will be greatly appreciated. Jack ___ 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/
[galaxy-dev] contribute tools to galaxy?
Hi All, I'm a newbie to galaxy and enjoying it a lot these days. Thanks for the great work. I have a question regarding contribution of software to galaxy. We developed a ChIP-seq peak calling algorithm and software (R package) and hope to contribute it to galaxy. I have read the wiki and prior mailing list about the contribution system but it is still somewhat confusing to me. 1. It seems that I can contribute our software to tool shed if I prepare appropriate code definition files. Then, users can download and use it with their locally installed galaxy. However, these files committed to tool shed will not appear in galaxy main or test servers. Am I correct? 2. What is clear relationship between main/test servers tool shed? Can we contribute our software to main or test servers as well? Or only galaxy core developers can add new tools to galaxy main or test servers? If so, which software is considered to be added to servers? Are they chosen from tools contributed to tool shed? 3. If our software is a R package, then users need to download and install it first in their R system before they use our software within their galaxy system even in the case they have appropriate definition files. Am I right? Or is there any better solution for this? Thanks! Best, Dongjun ___ 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/
[galaxy-dev] contribute tools to galaxy?
Hi All, I'm a newbie to galaxy and enjoying it a lot these days. Thanks for the great work. I have a question regarding contribution of software to galaxy. We developed a ChIP-seq peak calling algorithm and software (R package) and hope to contribute it to galaxy. I have read the wiki and prior mailing list about the contribution system but it is still somewhat confusing to me. 1. It seems that I can contribute our software to tool shed if I prepare appropriate code definition files. Then, users can download and use it with their locally installed galaxy. However, these files committed to tool shed will not appear in galaxy main or test servers. Am I correct? 2. What is clear relationship between main/test servers tool shed? Can we contribute our software to main or test servers as well? Or only galaxy core developers can add new tools to galaxy main or test servers? If so, which software is considered to be added to servers? Are they chosen from tools contributed to tool shed? 3. If our software is a R package, then users need to download and install it first in their R system before they use our software within their galaxy system even in the case they have appropriate definition files. Am I right? Or is there any better solution for this? Thanks! Best, Dongjun ___ 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/
Re: [galaxy-dev] install with EPD python?
Paul Tanger wrote: Yes it works with the default python install. Any way I can get it working with EPD python? I've never worked with EPD and since it's not free it's unlikely we can do much debugging on it here. It would appear that they bundle a version of pkg_resources which changes the DistributionNotFound class, but it's hard to know exactly what's going on here. One thing that might shed a bit of light on it would be to print sys.path and pkg_resources at the top of: galaxy-dist/lib/galaxy/eggs/__init__.py After the import of pkg_resources and see which version it's using. --nate On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: Has anyone gotten galaxy installed on a mac 10.5 with EPD (enthought) python 2.6 (EPD version 6.1-1)? I get this error which I suspect is related to the fact that I have EPD python, not the generic python that was preinstalled? Any ideas? Thanks! Some eggs are out of date, attempting to fetch... Traceback (most recent call last): File ./scripts/fetch_eggs.py, line 30, in module c.resolve() # Only fetch eggs required by the config File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 345, in resolve egg.resolve() File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 184, in resolve if e.args[0].project_name != self.distribution.project_name: AttributeError: 'str' object has no attribute 'project_name' Fetch failed. Hi Paul, Can you give it a try with the system Python and see if you get the same result? All you need to do is put: /System/Library/Frameworks/Python.framework/Versions/2.6/bin At the head of your $PATH. Thanks, --nate ___ 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/
Re: [galaxy-dev] install with EPD python?
It is free for academic use. I'll try what you suggested below - thanks! On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: Yes it works with the default python install. Any way I can get it working with EPD python? I've never worked with EPD and since it's not free it's unlikely we can do much debugging on it here. It would appear that they bundle a version of pkg_resources which changes the DistributionNotFound class, but it's hard to know exactly what's going on here. One thing that might shed a bit of light on it would be to print sys.path and pkg_resources at the top of: galaxy-dist/lib/galaxy/eggs/__init__.py After the import of pkg_resources and see which version it's using. --nate On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: Has anyone gotten galaxy installed on a mac 10.5 with EPD (enthought) python 2.6 (EPD version 6.1-1)? I get this error which I suspect is related to the fact that I have EPD python, not the generic python that was preinstalled? Any ideas? Thanks! Some eggs are out of date, attempting to fetch... Traceback (most recent call last): File ./scripts/fetch_eggs.py, line 30, in module c.resolve() # Only fetch eggs required by the config File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 345, in resolve egg.resolve() File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 184, in resolve if e.args[0].project_name != self.distribution.project_name: AttributeError: 'str' object has no attribute 'project_name' Fetch failed. Hi Paul, Can you give it a try with the system Python and see if you get the same result? All you need to do is put: /System/Library/Frameworks/Python.framework/Versions/2.6/bin At the head of your $PATH. Thanks, --nate ___ 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/
Re: [galaxy-dev] install with EPD python?
sys path is: ['/Users/paultanger/galaxy-dist/scripts', '/Users/paultanger/python/scripts', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL', '/Users/paultanger/galaxy-dist/lib'] pkg_resources is: module 'pkg_resources' from '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py' On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger paul.tan...@colostate.eduwrote: It is free for academic use. I'll try what you suggested below - thanks! On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: Yes it works with the default python install. Any way I can get it working with EPD python? I've never worked with EPD and since it's not free it's unlikely we can do much debugging on it here. It would appear that they bundle a version of pkg_resources which changes the DistributionNotFound class, but it's hard to know exactly what's going on here. One thing that might shed a bit of light on it would be to print sys.path and pkg_resources at the top of: galaxy-dist/lib/galaxy/eggs/__init__.py After the import of pkg_resources and see which version it's using. --nate On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: Has anyone gotten galaxy installed on a mac 10.5 with EPD (enthought) python 2.6 (EPD version 6.1-1)? I get this error which I suspect is related to the fact that I have EPD python, not the generic python that was preinstalled? Any ideas? Thanks! Some eggs are out of date, attempting to fetch... Traceback (most recent call last): File ./scripts/fetch_eggs.py, line 30, in module c.resolve() # Only fetch eggs required by the config File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 345, in resolve egg.resolve() File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 184, in resolve if e.args[0].project_name != self.distribution.project_name: AttributeError: 'str' object has no attribute 'project_name' Fetch failed. Hi Paul, Can you give it a try with the system Python and see if you get the same result? All you need to do is put: /System/Library/Frameworks/Python.framework/Versions/2.6/bin At the head of your $PATH. Thanks, --nate ___ 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/
Re: [galaxy-dev] [API] Error message forwarding
Louise-Amélie Schmitt wrote: Hi, I ran into a little something that is a bit annoying for debug when trying to upload files through the API with library_upload_from_import_dir.py. When the specified folder is wrong, python tries to process the error tuple like a dict, so the original error is hard to find. I modified a little the code to avoid that. It might not work in all cases but at least it solved my problem. Here is the original code: lib/galaxy/web/api/contents.py l.145-end else: rval = [] for k, v in output.items(): if type( v ) == trans.app.model.LibraryDatasetDatasetAssociation: v = v.library_dataset encoded_id = trans.security.encode_id( create_type + '.' + str( v.id ) ) rval.append( dict( id = encoded_id, name = v.name, url = url_for( 'content', library_id=library_id, id=encoded_id ) ) ) return rval Here is how I modified it: else: rval = [] try: for k, v in output.items(): if type( v ) == trans.app.model.LibraryDatasetDatasetAssociation: v = v.library_dataset encoded_id = trans.security.encode_id( create_type + '.' + str( v.id ) ) rval.append( dict( id = encoded_id, name = v.name, url = url_for( 'content', library_id=library_id, id=encoded_id ) ) ) return rval except: log.debug( 'HTTP Error %s: %s' % ( output[0], output[1] ) ) return None Since it saves me some time energy I just wanted to share it, so I hope it can help. Best L-A Hi L-A, Thanks for finding this. It's been fixed in 5952:832538ba7258. --nate ___ 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/
Re: [galaxy-dev] API keys and id encryption (silly questions)
Le 29/08/2011 15:52, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Hello everyone, These questions are a bit silly but I'm really ignorant when it comes to security. Sorry about that. Why use API keys instead of user names? Is it to to prevent anyone from figuring out who is behind an URL? Or did I miss the point? Hi L-A, To provide a username password, we'd either need to implement HTTP Authentication in Galaxy for these resources, or encode it in the URL. If in the URL, the password have to be non-plaintext which would require encoding on the user's end. The key model seemed to be simplest since it doesn't require you to handle HTTP Authentication in your client-side code. Ok, I actually missed the point, thanks! :D Also, why encrypt the dataset/library/folder ids when a simple display is enough to get them? Anywhere that the IDs are visible are remnants of old code and should eventually be removed. Sorry I meant the encrypted ids. Why encrypt them? is it to prevent any direct use of the database? Thanks, L-A --nate Thanks L-A ___ 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/
[galaxy-dev] mycoplasma genomes - suggestion
Hello everybody, I would like to suggest including mycoplasma genomes (preferably all genomes in one file) as reference genomes. It would enable fast checking if cells used for deep-seq experiments were not contaminated. Best, Lukasz ___ 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/
Re: [galaxy-dev] install with EPD python?
Paul Tanger wrote: sys path is: ['/Users/paultanger/galaxy-dist/scripts', '/Users/paultanger/python/scripts', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL', '/Users/paultanger/galaxy-dist/lib'] Hi Paul, If you replace: lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), .., lib ) ) sys.path.append( lib ) With: lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), .., lib ) ) sys.path.insert( 0, lib ) In scripts/check_eggs.py and scripts/fetch_eggs.py, does this have an effect? --nate pkg_resources is: module 'pkg_resources' from '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py' On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger paul.tan...@colostate.eduwrote: It is free for academic use. I'll try what you suggested below - thanks! On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: Yes it works with the default python install. Any way I can get it working with EPD python? I've never worked with EPD and since it's not free it's unlikely we can do much debugging on it here. It would appear that they bundle a version of pkg_resources which changes the DistributionNotFound class, but it's hard to know exactly what's going on here. One thing that might shed a bit of light on it would be to print sys.path and pkg_resources at the top of: galaxy-dist/lib/galaxy/eggs/__init__.py After the import of pkg_resources and see which version it's using. --nate On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: Has anyone gotten galaxy installed on a mac 10.5 with EPD (enthought) python 2.6 (EPD version 6.1-1)? I get this error which I suspect is related to the fact that I have EPD python, not the generic python that was preinstalled? Any ideas? Thanks! Some eggs are out of date, attempting to fetch... Traceback (most recent call last): File ./scripts/fetch_eggs.py, line 30, in module c.resolve() # Only fetch eggs required by the config File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 345, in resolve egg.resolve() File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 184, in resolve if e.args[0].project_name != self.distribution.project_name: AttributeError: 'str' object has no attribute 'project_name' Fetch failed. Hi Paul, Can you give it a try with the system Python and see if you get the same result? All you need to do is put: /System/Library/Frameworks/Python.framework/Versions/2.6/bin At the head of your $PATH. Thanks, --nate ___ 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/
Re: [galaxy-dev] install with EPD python?
Getting somewhere, but it looks like it can't find numpy 1.6? error returned is: pkg_resources is: module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.py' Some eggs are out of date, attempting to fetch... pkg_resources is: module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc' Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Whoosh/Whoosh-0.3.18-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Tempita/Tempita-0.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/NoseHTML/NoseHTML-0.4.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg Traceback (most recent call last): File ./scripts/fetch_eggs.py, line 32, in module c.resolve() # Only fetch eggs required by the config File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 347, in resolve egg.resolve() File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 197, in resolve return self.version_conflict( e.args[0], e.args[1] ) File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 228, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File /Users/paultanger/galaxy-dist/lib/pkg_resources.py, line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed. On Mon, Aug 29, 2011 at 10:18 AM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: sys path is: ['/Users/paultanger/galaxy-dist/scripts', '/Users/paultanger/python/scripts', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL', '/Users/paultanger/galaxy-dist/lib'] Hi Paul, If you replace: lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), .., lib ) ) sys.path.append( lib ) With: lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), .., lib ) ) sys.path.insert( 0, lib ) In scripts/check_eggs.py and scripts/fetch_eggs.py, does this have an effect? --nate pkg_resources is: module 'pkg_resources' from '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py' On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger paul.tan...@colostate.edu wrote: It is free for academic use. I'll try what you suggested below - thanks! On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: Yes it works with the default python install. Any way I can get it working with EPD python? I've never worked with EPD and since it's not free it's unlikely we can do much debugging on it here. It would appear that they bundle a version of pkg_resources which changes the DistributionNotFound class, but it's hard to know exactly what's going on here. One thing that might shed a bit of light on it would be to print sys.path and pkg_resources at the top of: galaxy-dist/lib/galaxy/eggs/__init__.py After the import of pkg_resources and see which version it's using. --nate On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: Has anyone gotten galaxy installed on a mac 10.5 with EPD (enthought) python 2.6 (EPD version 6.1-1)? I get this error which I suspect is related to the fact that I have EPD python, not the generic python that was preinstalled? Any ideas? Thanks! Some eggs are out of date, attempting to fetch... Traceback (most recent call last): File ./scripts/fetch_eggs.py, line 30, in module c.resolve() # Only fetch eggs required by the config File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py,
Re: [galaxy-dev] install with EPD python?
Paul Tanger wrote: Getting somewhere, but it looks like it can't find numpy 1.6? error returned is: pkg_resources is: module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.py' Some eggs are out of date, attempting to fetch... pkg_resources is: module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc' Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Whoosh/Whoosh-0.3.18-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Tempita/Tempita-0.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/NoseHTML/NoseHTML-0.4.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg Traceback (most recent call last): File ./scripts/fetch_eggs.py, line 32, in module c.resolve() # Only fetch eggs required by the config File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 347, in resolve egg.resolve() File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 197, in resolve return self.version_conflict( e.args[0], e.args[1] ) File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 228, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File /Users/paultanger/galaxy-dist/lib/pkg_resources.py, line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed. It could be a conflict with the existing version, try: python -ES ./scripts/fetch_eggs.py --nate On Mon, Aug 29, 2011 at 10:18 AM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: sys path is: ['/Users/paultanger/galaxy-dist/scripts', '/Users/paultanger/python/scripts', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL', '/Users/paultanger/galaxy-dist/lib'] Hi Paul, If you replace: lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), .., lib ) ) sys.path.append( lib ) With: lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), .., lib ) ) sys.path.insert( 0, lib ) In scripts/check_eggs.py and scripts/fetch_eggs.py, does this have an effect? --nate pkg_resources is: module 'pkg_resources' from '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py' On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger paul.tan...@colostate.edu wrote: It is free for academic use. I'll try what you suggested below - thanks! On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: Yes it works with the default python install. Any way I can get it working with EPD python? I've never worked with EPD and since it's not free it's unlikely we can do much debugging on it here. It would appear that they bundle a version of pkg_resources which changes the DistributionNotFound class, but it's hard to know exactly what's going on here. One thing that might shed a bit of light on it would be to print sys.path and pkg_resources at the top of: galaxy-dist/lib/galaxy/eggs/__init__.py After the import of pkg_resources and see which version it's using. --nate On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: Has anyone gotten galaxy installed on a mac 10.5 with EPD (enthought) python 2.6 (EPD version 6.1-1)? I get this error which I suspect is related to the fact that I have EPD python, not the generic python that was preinstalled? Any ideas? Thanks! Some eggs are out of
Re: [galaxy-dev] API keys and id encryption (silly questions)
Louise-Amélie Schmitt wrote: Le 29/08/2011 15:52, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Hello everyone, These questions are a bit silly but I'm really ignorant when it comes to security. Sorry about that. Why use API keys instead of user names? Is it to to prevent anyone from figuring out who is behind an URL? Or did I miss the point? Hi L-A, To provide a username password, we'd either need to implement HTTP Authentication in Galaxy for these resources, or encode it in the URL. If in the URL, the password have to be non-plaintext which would require encoding on the user's end. The key model seemed to be simplest since it doesn't require you to handle HTTP Authentication in your client-side code. Ok, I actually missed the point, thanks! :D Also, why encrypt the dataset/library/folder ids when a simple display is enough to get them? Anywhere that the IDs are visible are remnants of old code and should eventually be removed. Sorry I meant the encrypted ids. Why encrypt them? is it to prevent any direct use of the database? There are a couple of reasons - the first is that since by default, data is public, we wanted to make it non-trivial to just run sequentially through IDs to view related data. The other is that some people may prefer that it not be obvious how many datasets/jobs/libraries/etc. there are on their server. --nate Thanks, L-A --nate Thanks L-A ___ 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/
Re: [galaxy-dev] install with EPD python?
That worked, for everything but pysam. I also tried to install it directly: pysam 0.4.2 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e pysam Some eggs are out of date, attempting to fetch... pkg_resources is: module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc' pysam 0.4.2 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e pysam Fetch failed. On Mon, Aug 29, 2011 at 10:51 AM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: Getting somewhere, but it looks like it can't find numpy 1.6? error returned is: pkg_resources is: module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.py' Some eggs are out of date, attempting to fetch... pkg_resources is: module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc' Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Whoosh/Whoosh-0.3.18-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Tempita/Tempita-0.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/NoseHTML/NoseHTML-0.4.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg Traceback (most recent call last): File ./scripts/fetch_eggs.py, line 32, in module c.resolve() # Only fetch eggs required by the config File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 347, in resolve egg.resolve() File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 197, in resolve return self.version_conflict( e.args[0], e.args[1] ) File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 228, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File /Users/paultanger/galaxy-dist/lib/pkg_resources.py, line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed. It could be a conflict with the existing version, try: python -ES ./scripts/fetch_eggs.py --nate On Mon, Aug 29, 2011 at 10:18 AM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: sys path is: ['/Users/paultanger/galaxy-dist/scripts', '/Users/paultanger/python/scripts', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL', '/Users/paultanger/galaxy-dist/lib'] Hi Paul, If you replace: lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), .., lib ) ) sys.path.append( lib ) With: lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), .., lib ) ) sys.path.insert( 0, lib ) In scripts/check_eggs.py and scripts/fetch_eggs.py, does this have an effect? --nate pkg_resources is: module 'pkg_resources' from '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py' On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger paul.tan...@colostate.edu wrote: It is free for academic use. I'll try what you suggested below - thanks! On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: Yes it works with the default python install. Any way I can get it working with EPD python? I've never worked with EPD and since it's not free it's unlikely we can do much debugging on it here. It would appear that they bundle a version of pkg_resources which changes the DistributionNotFound class, but it's hard to know exactly what's going on here. One thing that
Re: [galaxy-dev] Galaxy Test disk quota
Dear Nate, Thank you very much. Best regards, Crystal Date: Mon, 29 Aug 2011 10:04:21 -0400 From: n...@bx.psu.edu To: crysta...@live.com.my CC: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Galaxy Test disk quota Crystal Goh wrote: Dear Nate, Thanks. I used multiple account as I have several csfasta and qual files and each file is large in size. My account is gohweip...@hotmail.com. Can I get increement for disk quota for this account so that I can used only 1 account that can proceess 6 each csfasta and qual files? Sure. --nate Thanks Nate and thanks galaxy. Best regards, Crystal Date: Fri, 26 Aug 2011 14:52:51 -0400 From: n...@bx.psu.edu To: crysta...@live.com.my CC: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Galaxy Test disk quota Crystal Goh wrote: Hi, I am Crystal. As Tophat for SOLiD only available in Galaxy Test (not available in Galaxy Main), I uploaded my csfasta and qual files to Galaxy Test. As the file size very big, the disk space used up is 13.5Gb and I cannot use any tool. This means after uploading raw data, I cannot manipulate any data as the size of raw data itself already exceeds 10Gb. May I know any alternative that I can use? Thank you very much! Hi Crystal, Which account are you using on Galaxy Test? I noticed that you have multiple. I can increase your quota for this. --nate Best regards, Crystal ___ 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/ ea ___ 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/
Re: [galaxy-dev] install with EPD python?
Paul Tanger wrote: That worked, for everything but pysam. I also tried to install it directly: pysam 0.4.2 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e pysam Some eggs are out of date, attempting to fetch... pkg_resources is: module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc' pysam 0.4.2 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e pysam Fetch failed. What platform do you get from: python ./scripts/get_platforms.py ? Note that this needs to have the path changed from append to insert as in the previous scripts. Thanks, --nate On Mon, Aug 29, 2011 at 10:51 AM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: Getting somewhere, but it looks like it can't find numpy 1.6? error returned is: pkg_resources is: module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.py' Some eggs are out of date, attempting to fetch... pkg_resources is: module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc' Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Whoosh/Whoosh-0.3.18-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Tempita/Tempita-0.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/NoseHTML/NoseHTML-0.4.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg Traceback (most recent call last): File ./scripts/fetch_eggs.py, line 32, in module c.resolve() # Only fetch eggs required by the config File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 347, in resolve egg.resolve() File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 197, in resolve return self.version_conflict( e.args[0], e.args[1] ) File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 228, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File /Users/paultanger/galaxy-dist/lib/pkg_resources.py, line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed. It could be a conflict with the existing version, try: python -ES ./scripts/fetch_eggs.py --nate On Mon, Aug 29, 2011 at 10:18 AM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: sys path is: ['/Users/paultanger/galaxy-dist/scripts', '/Users/paultanger/python/scripts', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL', '/Users/paultanger/galaxy-dist/lib'] Hi Paul, If you replace: lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), .., lib ) ) sys.path.append( lib ) With: lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), .., lib ) ) sys.path.insert( 0, lib ) In scripts/check_eggs.py and scripts/fetch_eggs.py, does this have an effect? --nate pkg_resources is: module 'pkg_resources' from '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py' On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger paul.tan...@colostate.edu wrote: It is free for academic use. I'll try what you suggested below - thanks! On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: Yes it works with the default python install. Any way I can get it
Re: [galaxy-dev] install with EPD python?
I don't know if I did this correctly, but the output from python get_platforms.py is: macosx-10.5-i386-ucs2 On Mon, Aug 29, 2011 at 12:13 PM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: That worked, for everything but pysam. I also tried to install it directly: pysam 0.4.2 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e pysam Some eggs are out of date, attempting to fetch... pkg_resources is: module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc' pysam 0.4.2 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e pysam Fetch failed. What platform do you get from: python ./scripts/get_platforms.py ? Note that this needs to have the path changed from append to insert as in the previous scripts. Thanks, --nate On Mon, Aug 29, 2011 at 10:51 AM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: Getting somewhere, but it looks like it can't find numpy 1.6? error returned is: pkg_resources is: module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.py' Some eggs are out of date, attempting to fetch... pkg_resources is: module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc' Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Whoosh/Whoosh-0.3.18-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Tempita/Tempita-0.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/NoseHTML/NoseHTML-0.4.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg Traceback (most recent call last): File ./scripts/fetch_eggs.py, line 32, in module c.resolve() # Only fetch eggs required by the config File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 347, in resolve egg.resolve() File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 197, in resolve return self.version_conflict( e.args[0], e.args[1] ) File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 228, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File /Users/paultanger/galaxy-dist/lib/pkg_resources.py, line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed. It could be a conflict with the existing version, try: python -ES ./scripts/fetch_eggs.py --nate On Mon, Aug 29, 2011 at 10:18 AM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: sys path is: ['/Users/paultanger/galaxy-dist/scripts', '/Users/paultanger/python/scripts', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL', '/Users/paultanger/galaxy-dist/lib'] Hi Paul, If you replace: lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), .., lib ) ) sys.path.append( lib ) With: lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), .., lib ) ) sys.path.insert( 0, lib ) In scripts/check_eggs.py and scripts/fetch_eggs.py, does this have an effect? --nate pkg_resources is: module 'pkg_resources' from '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py' On Mon, Aug 29, 2011 at 8:17 AM, Paul
Re: [galaxy-dev] install with EPD python?
Paul Tanger wrote: I don't know if I did this correctly, but the output from python get_platforms.py is: macosx-10.5-i386-ucs2 Okay, it looks like EPD python is only compiled for one platform. To use this, you'll need to scramble your own versions of the eggs which use C code. Could you try scrambling pysam as instructed below and see what the results are? You will have to do this for each egg that can't be downloaded. --nate On Mon, Aug 29, 2011 at 12:13 PM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: That worked, for everything but pysam. I also tried to install it directly: pysam 0.4.2 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e pysam Some eggs are out of date, attempting to fetch... pkg_resources is: module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc' pysam 0.4.2 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e pysam Fetch failed. What platform do you get from: python ./scripts/get_platforms.py ? Note that this needs to have the path changed from append to insert as in the previous scripts. Thanks, --nate On Mon, Aug 29, 2011 at 10:51 AM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: Getting somewhere, but it looks like it can't find numpy 1.6? error returned is: pkg_resources is: module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.py' Some eggs are out of date, attempting to fetch... pkg_resources is: module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc' Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Whoosh/Whoosh-0.3.18-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Tempita/Tempita-0.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/NoseHTML/NoseHTML-0.4.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg Traceback (most recent call last): File ./scripts/fetch_eggs.py, line 32, in module c.resolve() # Only fetch eggs required by the config File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 347, in resolve egg.resolve() File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 197, in resolve return self.version_conflict( e.args[0], e.args[1] ) File /Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py, line 228, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File /Users/paultanger/galaxy-dist/lib/pkg_resources.py, line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed. It could be a conflict with the existing version, try: python -ES ./scripts/fetch_eggs.py --nate On Mon, Aug 29, 2011 at 10:18 AM, Nate Coraor n...@bx.psu.edu wrote: Paul Tanger wrote: sys path is: ['/Users/paultanger/galaxy-dist/scripts', '/Users/paultanger/python/scripts', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL', '/Users/paultanger/galaxy-dist/lib'] Hi Paul, If you replace: lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), .., lib ) ) sys.path.append( lib ) With:
[galaxy-dev] Galaxy is Hiring
Hello all The Galaxy Project is growing and has open positions in both the Penn State and Emory groups (http://wiki.g2.bx.psu.edu/News/Galaxy%20is%20Hiring). *Penn State: System administrators/analysts* The Nekrutenko Lab http://www.bx.psu.edu/%7Eanton/ at the Huck Institutes of Life Sciences http://www.huck.psu.edu/ at Penn State http://psu.edu/is currently recruiting system analysts/administrators with experience in building and maintaining complex performance compute environments. The areas of immediate need include: - Storage balancing and tiered storage - Virtualization - Schedulers - Deployment of Galaxy instances and dependence management - Relational databases and query optimization - User management A minimum of 5 year experience with UNIX/Linux system administration is required. Applicants should submit a CV and list of references to j...@galaxyproject.org. http://bx.mathcs.emory.edu/joining/ *Emory: Software Engineers and Post-Docs* The Taylor Lab http://bx.mathcs.emory.edu/ in the Biologyhttp://www.biology.emory.edu/and Mathematics Computer Science http://www.mathcs.emory.edu/ at Emory Universityhttp://emory.edu/is looking for software engineers http://bx.mathcs.emory.edu/joining/sw/ and postdoctoral scholarshttp://bx.mathcs.emory.edu/joining/postdocs/to work on the Galaxy project. We are seeking software engineers http://bx.mathcs.emory.edu/joining/sw/with expertise in distributed computing and systems programming, web-based visualization and visual analytics, informatics and data analysis and integration, and bioinformatics application areas such as re-sequencing, de novo assembly, metagenomics, transcriptome analysis and epigenetics. These are full time positions located in Atlanta, GA. See the official postinghttp://bx.mathcs.emory.edu/joining/sw/for full details. Postdoctoral applicants http://bx.mathcs.emory.edu/joining/postdocs/should have expertise in Bioinformatics and Computational Biology and research interests that complement but extend the lab's current interestshttp://bx.mathcs.emory.edu/research/: The Galaxy project; distributed and high-performance computing for data intensive science; vertebrate functional genomics; and genomics and epigenomic mechanisms of gene regulation, the role of transcription factors and chromatin structure in global gene expression, development, and differentiation. See the announcementhttp://bx.mathcs.emory.edu/joining/postdocs/for full details. If any of these positions describe you then please consider applying. Thanks, Dave C. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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/
Re: [galaxy-dev] Setting the output label based on input parameters?
Hi Ross,
Yes, I did try that... but what I want is string parameter that changes
based on whether or not you've checked a checkbox (or a way to change the
label of the output based on whether or not the checkbox was checked). So
my idea below did work, but it seems like a hack. Which is why I was
wondering if there was a better way.
- Nik.
On Mon, Aug 29, 2011 at 2:55 AM, Ross ross.laza...@gmail.com wrote:
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB swe...@staffmail.ed.ac.uk
wrote:
I meant to say label=${input} or label=${input.value}.
Nikhil, did you try as Shaun and others have suggested? Any available
string parameter can be used in a label as far as I can tell.
This is a common idiom - ask for a string ('title') to describe the
job/output for posterity, then in an output:
data format=foo name=output1 metadata_source=input1
label=${title}.myext/
There's even a built in ${on_string} if you just want the file name
plus some history ids?
On Mon, Aug 29, 2011 at 6:54 PM, Nikhil Joshi najo...@ucdavis.edu wrote:
It looks like the Cheetah syntax only is parsed within the command
tags so I figured out a way to do it... but it seems hackish. I
basically changed the string values of truevalue and falsevalue within
the
parameter to be an English sentence that would become the label for the
output. I.e., in the input section:
param name=filter_reads type=boolean truevalue=Filtered Reads
Fasta
falsevalue=Unfiltered Reads Fasta label=Filter reads?/
and in the output section:
data format=fasta name=output_fasta label=$filter_reads/
This seems wrong to do, but it does work. If anyone has a better method,
please let me know!
- Nik.
On Thu, Aug 25, 2011 at 2:36 PM, Nikhil Joshi najo...@ucdavis.edu
wrote:
It's actually a boolean checkbox. so I basically want the label to
change based upon whether or not the checkbox is checked. Is there any
way
to do that? Again, I've tried using the Cheetah syntax to do the #if
#end
inside the output tags but that didn't work.
- Nik.
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB swe...@staffmail.ed.ac.uk
wrote:
I meant to say label=${input} or label=${input.value}.
If it's a select field then you can change the option values to the
text
you want to add to your output label.
Shaun
Quoting Kanwei Li kan...@gmail.com on Wed, 24 Aug 2011 20:34:57
-0400:
Hi Nikhil,
The tool templates are Cheetah templates, so you can do things like:
outputs
%if param == True:
data format=txt name=blah label=Label1 /
%else
data format=txt name=blah label=Label2 /
%endif
/outputs
Thanks,
K
On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi najo...@ucdavis.edu
wrote:
Hi all,
Is there a way to set the label of the output based on the input
parameters? Perhaps by using the action tag? Basically, I want
the
output label to be different if the user sets a particular parameter
to
be
true.
___
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Re: [galaxy-dev] Setting the output label based on input parameters?
Most times I need a user supplied label substring. I'm not sure how
else to conditionally set a string to a predetermined value other than
with boolean true/false strings or select parameter values.
One even more ugly option is to use a (strictly speaking now
deprecated) post job exec hook to change the output dataset name based
on some logic - but if the boolean works, I'd recommend moving on :)
On Tue, Aug 30, 2011 at 7:56 AM, Nikhil Joshi najo...@ucdavis.edu wrote:
Hi Ross,
Yes, I did try that... but what I want is string parameter that changes
based on whether or not you've checked a checkbox (or a way to change the
label of the output based on whether or not the checkbox was checked). So
my idea below did work, but it seems like a hack. Which is why I was
wondering if there was a better way.
- Nik.
On Mon, Aug 29, 2011 at 2:55 AM, Ross ross.laza...@gmail.com wrote:
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB swe...@staffmail.ed.ac.uk
wrote:
I meant to say label=${input} or label=${input.value}.
Nikhil, did you try as Shaun and others have suggested? Any available
string parameter can be used in a label as far as I can tell.
This is a common idiom - ask for a string ('title') to describe the
job/output for posterity, then in an output:
data format=foo name=output1 metadata_source=input1
label=${title}.myext/
There's even a built in ${on_string} if you just want the file name
plus some history ids?
On Mon, Aug 29, 2011 at 6:54 PM, Nikhil Joshi najo...@ucdavis.edu wrote:
It looks like the Cheetah syntax only is parsed within the command
tags so I figured out a way to do it... but it seems hackish. I
basically changed the string values of truevalue and falsevalue within
the
parameter to be an English sentence that would become the label for the
output. I.e., in the input section:
param name=filter_reads type=boolean truevalue=Filtered Reads
Fasta
falsevalue=Unfiltered Reads Fasta label=Filter reads?/
and in the output section:
data format=fasta name=output_fasta label=$filter_reads/
This seems wrong to do, but it does work. If anyone has a better
method,
please let me know!
- Nik.
On Thu, Aug 25, 2011 at 2:36 PM, Nikhil Joshi najo...@ucdavis.edu
wrote:
It's actually a boolean checkbox. so I basically want the label to
change based upon whether or not the checkbox is checked. Is there any
way
to do that? Again, I've tried using the Cheetah syntax to do the #if
#end
inside the output tags but that didn't work.
- Nik.
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB swe...@staffmail.ed.ac.uk
wrote:
I meant to say label=${input} or label=${input.value}.
If it's a select field then you can change the option values to the
text
you want to add to your output label.
Shaun
Quoting Kanwei Li kan...@gmail.com on Wed, 24 Aug 2011 20:34:57
-0400:
Hi Nikhil,
The tool templates are Cheetah templates, so you can do things like:
outputs
%if param == True:
data format=txt name=blah label=Label1 /
%else
data format=txt name=blah label=Label2 /
%endif
/outputs
Thanks,
K
On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi najo...@ucdavis.edu
wrote:
Hi all,
Is there a way to set the label of the output based on the input
parameters? Perhaps by using the action tag? Basically, I want
the
output label to be different if the user sets a particular parameter
to
be
true.
--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
___
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Re: [galaxy-dev] migrate the database schema from 80 to 81
Hi Nate, Thanks for the fix. Everything is working great now. Jack On 29 August 2011 09:33, Nate Coraor n...@bx.psu.edu wrote: Jack Zhu wrote: Hi all, I have problems with updating my local instance of Galaxy. Specifically I can not migrate the database schema from 80 to 81: Hi Jack, Thanks for reporting this issue. It has been fixed in changeset 5951:62d51750d7df. --nate -- $$ sh manage_db.sh upgrade 80 - 81... Migration script to add a 'tool_version' column to the hda/ldda tables. Traceback (most recent call last): File ./scripts/manage_db.py, line 63, in module main( repository=repo, url=db_url ) File /home/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py, line 150, in main ret = command_func(**kwargs) File /home/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py, line 221, in upgrade return _migrate(url, repository, version, upgrade=True, err=err, **opts) File /home/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py, line 349, in _migrate schema.runchange(ver, change, changeset.step) File /home/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py, line 184, in runchange change.run(self.engine, step) File /home/zhujack/bin/galaxy/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py, line 101, in run func() File lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py, line 17, in upgrade metadata.reflect() File /home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py, line 1733, in reflect Table(name, self, **reflect_opts) File /home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py, line 108, in __call__ return type.__call__(self, name, metadata, *args, **kwargs) File /home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py, line 236, in __init__ _bind_or_error(metadata).reflecttable(self, include_columns=include_columns) File /home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py, line 1265, in reflecttable self.dialect.reflecttable(conn, table, include_columns) File /home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py, line 1673, in reflecttable only=include_columns) File /home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py, line 2139, in reflect self._add_column(table, line, charset, only) File /home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py, line 2227, in _add_column type_instance = col_type(*type_args, **type_kw) File /home/zhujack/bin/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/mysql.py, line 569, in __init__ super(MSBigInteger, self).__init__(display_width, **kw) TypeError: super(type, obj): obj must be an instance or subtype of type -- Your help will be greatly appreciated. Jack ___ 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/
