[galaxy-dev] Database source
Hello Galaxy, We are implementing a fresh instance of Galaxy in the school server for teaching purposes. So obtaining genomic data from the UCSC servers can present a problem by overloading the connection. To make things faster, we want to obtain the data for the genomic data and have it in our servers, speeding up data retrieval. At first I was under the impression that we had to use MySQL for this, and downloaded MySQL files from the UCSC servers by using: $ rsync -avzP rsync:// hgdownload.cse.ucsc.edu/mysql . We have successfully added the data to MySQL in our server, but now do not know how to make galaxy see the data. However after searching more about the problem, I found out that I could have used the following instead: $ rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/ . Was downloading the mysql files unnecessary or can I still be able to use them? Also, would it be more efficient to use the second rsync option instead? Thank you for your help, --Ricardo Perez ___ 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] The qiuck way to upload large file
There is a tutorial on the home page of Galaxy (uploading data using FTP) that shows you step by step how to go through the uploading process. Hope this helps Giuseppe Ianiri, Ph.D. From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of James Meador [jmea...@momentapharma.com] Sent: Saturday, December 01, 2012 10:08 PM To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] The qiuck way to upload large file Hi All, Thanks for the tip, but could you specify what directory to ftp them to? I have been wondering about this myself but have not found an answer yet. Also, from my limited testing on a local setup on Mac OS X 10.6, it appears that when you upload a file (170 MB fastq file in my case), it gets placed into a directory within /usr/local/Galaxy/database/files/000/ into a file called, dataset_1.dat. This file is just a text file of the original fastq file so it might be possible to ftp to there but I am not sure that the database or Galaxy will automatically be able to read this. Can anyone comment on how to ftp files to what directory that Galaxy will be able to add to the History? Thanks in advance, Jim On Dec 1, 2012, at 8:40 AM, shamsher jagat wrote: FTP or URL On Sat, Dec 1, 2012 at 5:37 AM, 泽 蔡 caizexi...@yahoo.com.cnmailto:caizexi...@yahoo.com.cn wrote: Hi all, I'm a new guy of galaxy and bioinformatics. I read the document of galaxy, but it's so hard to find what I need. I already set up a locale instance of galaxy, it works fine. The problem is I need to analysis large data, but the upload file is so slow, is there some ways I can upload large file quickly? ___ 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/ * This email message and any attachments are confidential and may be privileged. It is intended only for the individual(s) to whom it is addressed and may not be saved, copied, printed, disclosed or otherwise used by anyone else. If you are not the intended recipient, kindly notify the sender and delete this email and any attachments immediately. Momenta Pharmaceuticals, Inc. ___ 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] pass more information on a dataset merge
Hi John, My colleague (Neil) has a bit of a problem with the multi file support: When I try and use the option Upload Directory of files I get the error below Error Traceback: View as: Interactive | Text | XML (full) ⇝ AttributeError: 'Bunch' object has no attribute 'multifiles' URL: http://140.253.78.218/library_common/upload_library_dataset Module weberror.evalexception.middleware:364 in respond view app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view environ, self.app) Module paste.wsgilib:539 in intercept_output view app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ view body = method( trans, **kwargs ) Module galaxy.web.controllers.library_common:855 in upload_library_dataset view **kwd ) Module galaxy.web.controllers.library_common:1055 in upload_dataset view json_file_path = upload_common.create_paramfile( trans, uploaded_datasets ) Module galaxy.tools.actions.upload_common:342 in create_paramfile view multifiles = uploaded_dataset.multifiles, AttributeError: 'Bunch' object has no attribute 'multifiles' Any ideas? Should we check if 'multifiles' attribute is set? Or some other call is missing which should set it to NULL if it's missing? -Alex -Original Message- From: jmchil...@gmail.com [mailto:jmchil...@gmail.com] On Behalf Of John Chilton Sent: Wednesday, 17 October 2012 3:21 AM To: Khassapov, Alex (CSIRO IMT, Clayton) Subject: Re: [galaxy-dev] pass more information on a dataset merge Wow, thanks for the rapid feedback! I have made the changes you have suggested. It seems you must be interested in this idea/implementation. Let me know if you have specific use cases/requirements in mind and/or if you would be interested in write access to the repository. -John On Mon, Oct 15, 2012 at 11:51 PM, alex.khassa...@csiro.au wrote: Hi John, I tried your galaxy-central-homogeneous-composite-datatypes implementation, works great thank you (and Jorrit). A couple of fixes: 1. Add multi_upload.xml to too_conf.xml 2. lib/galaxy/tools/parameters/grouping.py line 322 (in get_filenames( context )) - if ftp_files is not None: Remove is not None as ftp_files is empty [], but not None, then line 331 user_ftp_dir = os.path.join( trans.app.config.ftp_upload_dir, trans.user.email ) throws an exeption if ftp_upload_dir isn't set. Alex -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of John Chilton Sent: Tuesday, 16 October 2012 1:07 AM To: Jorrit Boekel Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] pass more information on a dataset merge Here is an implementation of the implicit multi-file composite datatypes piece of that idea. I think the implicit parallelism may be harder. https://bitbucket.org/galaxyp/galaxy-central-homogeneous-composite-dat atypes/compare Jorrit do you have any objection to me trying to get this included in galaxy-central (this is 95% code I stole from you)? I made the changes against a clean galaxy-central fork and included nothing proteomics specific in anticipation of trying to do that. I have talked with Jim Johnson about the idea and he believes it would be useful his mothur metagenomics tools, so the idea is valuable outside of proteomics. Galaxy team, would you be okay with including this and if so is there anything you would like to see either at a high level or at the level of the actual implementation. -John John Chilton Senior Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 Bitbucket: https://bitbucket.org/jmchilton Github: https://github.com/jmchilton Web: http://jmchilton.net On Mon, Oct 8, 2012 at 9:24 AM, John Chilton chil...@msi.umn.edu wrote: Jim Johnson and I have been discussing that approach to handling fractionated proteomics samples as well (composite datatypes, not the specifics of the interface for parallelizing). My perspective has been that Galaxy should be augmented with better native mechanisms for grouping objects in histories, operating over those groups, building workflows that involve arbitrary numbers of inputs, etc... Composite data types are kindof a kludge, I think they are more useful for grouping HTML files together when you don't care about operating on the constituent parts you just want to view pages a as a report or something. With this proteomic data we are working with, the individual pieces are really interesting right? You want to operate on the
Re: [galaxy-dev] Data/history/user export and import
I was thinking whether I could establish the same from using the DB access directly!? Or would that be too dangerous? In the past I have tried to transfer the user tables from an old instance into a fresh onebut failed due to all sorts of unpredictable errors.. We (the Galaxy team) do not recommend that you modify the database directly; there's just too much going on (keys, relationships, etc) to ensure that things go smoothly. In fact, the whole point of the API is to provide a high-level, programmer interface so that developers do not have to work at a low (e.g. database) level. If you were going to write some code, you'd be best to try extending the API to support what you want. Should you get history import/export working, we'd be happy to incorporate it in the Galaxy source. Best, J. ___ 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] Installing dependencies
Hi devs, Got the following error when trying to test the install of a dependency: URL: http://bioinf-galaxy/admin_toolshed/manage_tool_dependencies?sort=-create_ti meshow_item_checkboxes=falseasync=falsepage=1webapp=galaxyoperation=ins tallid=00f52b22f3524111 Module paste.exceptions.errormiddleware:143 in __call__ app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ body = method( trans, **kwargs ) Module galaxy.web.framework:184 in decorator return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.admin_toolshed:904 in manage_tool_dependencies self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation ) Module galaxy.web.framework:184 in decorator return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.admin_toolshed:530 in initiate_tool_dependency_installation tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', tool_shed_repository.repo_path( trans.app ) ) Module galaxy.util.shed_util:920 in get_config_from_disk for root, dirs, files in os.walk( relative_install_dir ): Module os:276 in walk names = listdir(top) TypeError: coercing to Unicode: need string or buffer, NoneType found Any ideas?? Thanks, Franco This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt. ___ 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] Reinstalling toolshed tool
Hi devs,
I get the following error when trying to reinstall a deleted repository/tool
from the toolshed:
Server Error URL:
http://bioinf-galaxy/admin_toolshed/browse_repositories?operation=activate+o
r+reinstallid=88ee2d7021e4dc1a Module paste.exceptions.errormiddleware:143
in __call__ app_iter = self.application(environ, start_response) Module
paste.debug.prints:98 in __call__ environ, self.app) Module
paste.wsgilib:539 in intercept_output app_iter = application(environ,
replacement_start_response) Module paste.recursive:80 in __call__ return
self.application(environ, start_response) Module paste.httpexceptions:632 in
__call__ return self.application(environ, start_response) Module
galaxy.web.framework.base:160 in __call__ body = method( trans, **kwargs
) Module galaxy.web.framework:184 in decorator return func( self, trans,
*args, **kwargs ) Module galaxy.web.controllers.admin_toolshed:350 in
browse_repositories return self.reselect_tool_panel_section( trans,
**kwd ) Module galaxy.web.framework:184 in decorator return func( self,
trans, *args, **kwargs ) Module galaxy.web.controllers.admin_toolshed:1352
in reselect_tool_panel_section status=status ) Module
galaxy.web.framework:746 in fill_template return
self.fill_template_mako( filename, **kwargs ) Module
galaxy.web.framework:757 in fill_template_mako return template.render(
**data ) Module mako.template:296 in render return runtime._render(self,
self.callable_, args, data) Module mako.runtime:660 in _render
**_kwargs_for_callable(callable_, data)) Module mako.runtime:692 in
_render_context _exec_template(inherit, lclcontext, args=args,
kwargs=kwargs) Module mako.runtime:718 in _exec_template
callable_(context, *args, **kwargs) Module _base_mako:42 in render_body
__M_writer(unicode(next.body())) Module
_admin_tool_shed_repository_reselect_tool_panel_section_mako:76 in
render_body __M_writer(unicode(render_tool_dependency_section(
install_tool_dependencies_check_box, [ repo_info_dict ] ))) Module
_admin_tool_shed_repository_common_mako:204 in
render_render_tool_dependency_section changeset_revision ) Module
posixpath:67 in join elif path == '' or path.endswith('/'):
AttributeError: 'NoneType' object has no attribute 'endswith'
Any ideas??
Thanks,
Franco
This email (including any attachments or links) may contain
confidential and/or legally privileged information and is
intended only to be read or used by the addressee. If you
are not the intended addressee, any use, distribution,
disclosure or copying of this email is strictly
prohibited.
Confidentiality and legal privilege attached to this email
(including any attachments) are not waived or lost by
reason of its mistaken delivery to you.
If you have received this email in error, please delete it
and notify us immediately by telephone or email. Peter
MacCallum Cancer Centre provides no guarantee that this
transmission is free of virus or that it has not been
intercepted or altered and will not be liable for any delay
in its receipt.
___
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and other Galaxy lists, please use the interface at:
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[galaxy-dev] status of deseq tool from main toolshed
Hi guys, Following the instructions in the README.md file from the successful installation of the tool, I copied deseq.R to tool-data/ I've been trying to get the deseq_and_sam2counts tool on our local galaxy-dist here: http://toolshed.g2.bx.psu.edu/repos/nikhil-joshi/deseq_and_sam2counts I note a prior message from Greg on certain requirements tags that should be added to get some things working in: http://dev.list.galaxyproject.org/environment-variables-and-paths-for-toolshed-tools-td4656231.html It's probably not relevant to the error that I am getting at the moment since we've managed to install all those packages manually through R - source(http://bioconductor.org/biocLite.R;) biocLite(DESeq) biocLite(aroma.light) The following dataset was used: dataset: 12345aba1345355777888aba24567888689 This is the error we get when running the tool. Note, it has executed the actual tool and made use of tool-data/deseq.R 29: Diagnostic Plots for DE Seq on data 27https://galaxy-qld-dev.genome.edu.au/history 0 bytes An error occurred running this job:*Error: Loading required package: Biobase Loading required package: BiocGenerics Loading required package: methods Attaching package: ‘BiocGenerics’ The following object(s) are masked from ‘package:stats’: xtabs The following object(s) are* * * * * Error: Loading required package: Biobase Loading required package: BiocGenerics Loading required package: methods Attaching package: ‘BiocGenerics’ The following object(s) are masked from ‘package:stats’: xtabs The following object(s) are masked from ‘package:base’: anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation(Biobase)', and for packages 'citation(pkgname)'. Loading required package: locfit locfit 1.5-8 2012-04-25 Loading required package: lattice Warning messages: 1: found methods to import for function ‘as.list’ but not the generic itself 2: found methods to import for function ‘eapply’ but not the generic itself Error in glm.fit(x = numeric(0), y = numeric(0), weights = NULL, start = c(0.1, : object 'fit' not found Calls: estimateDispersions ... parametricDispersionFit - glm - eval - eval - glm.fit In addition: Warning messages: 1: In is.na(rows) : is.na() applied to non-(list or vector) of type 'NULL' 2: In glm.fit(x = numeric(0), y = numeric(0), weights = NULL, start = c(0.1, : no observations informative at iteration 1 Any ideas? ___ 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] Activate or reinstall toolshed tool
Hi devs, Sorry for the bad formating, here is the error I get when trying to
reinstall a toolshed tool: Module paste.exceptions.errormiddleware:143 in
__call__ app_iter = self.application(environ, start_response) Module
paste.debug.prints:98 in __call__ environ, self.app) Module
paste.wsgilib:539 in intercept_output
app_iter = application(environ, replacement_start_response) Module
paste.recursive:80 in __call__
return self.application(environ, start_response) Module
paste.httpexceptions:632 in __call__
return self.application(environ, start_response) Module
galaxy.web.framework.base:160 in __call__
body = method( trans, **kwargs ) Module galaxy.web.framework:184 in
decorator
return func( self, trans, *args, **kwargs ) Module
galaxy.web.controllers.admin_toolshed:350 in browse_repositories
return self.reselect_tool_panel_section( trans, **kwd ) Module
galaxy.web.framework:184 in decorator
return func( self, trans, *args, **kwargs ) Module
galaxy.web.controllers.admin_toolshed:1352 in reselect_tool_panel_section
status=status ) Module galaxy.web.framework:746 in fill_template
return self.fill_template_mako( filename, **kwargs ) Module
galaxy.web.framework:757 in fill_template_mako
return template.render( **data ) Module mako.template:296 in render
return runtime._render(self, self.callable_, args, data) Module
mako.runtime:660 in _render
**_kwargs_for_callable(callable_, data)) Module mako.runtime:692 in
_render_context
_exec_template(inherit, lclcontext, args=args, kwargs=kwargs) Module
mako.runtime:718 in _exec_template
callable_(context, *args, **kwargs) Module _base_mako:42 in render_body
__M_writer(unicode(next.body())) Module
_admin_tool_shed_repository_reselect_tool_panel_section_mako:76 in render_body
__M_writer(unicode(render_tool_dependency_section(
install_tool_dependencies_check_box, [ repo_info_dict ] ))) Module
_admin_tool_shed_repository_common_mako:204 in
render_render_tool_dependency_section
changeset_revision ) Module posixpath:67 in join
elif path == '' or path.endswith('/'): AttributeError: 'NoneType' object has
no attribute 'endswith'
Any ideas would be greatly appretiated.
Also, if the galaxy devs have any (as a last resort) mysql script to delete
a tool affecting all the pertinent tables it would great.
Thanks,
Franco
This email (including any attachments or links) may contain
confidential and/or legally privileged information and is
intended only to be read or used by the addressee. If you
are not the intended addressee, any use, distribution,
disclosure or copying of this email is strictly
prohibited.
Confidentiality and legal privilege attached to this email
(including any attachments) are not waived or lost by
reason of its mistaken delivery to you.
If you have received this email in error, please delete it
and notify us immediately by telephone or email. Peter
MacCallum Cancer Centre provides no guarantee that this
transmission is free of virus or that it has not been
intercepted or altered and will not be liable for any delay
in its receipt.
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[galaxy-dev] Same error, better formatting.
URL: http://bioinf-galaxy/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a Module paste.exceptions.errormiddleware:*143* in __call__ http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# app_iter *=* self*.*application*(*environ*,* start_response*)* Module paste.debug.prints:*98* in __call__ http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# environ*,* self*.*app*)* Module paste.wsgilib:*539* in intercept_output http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# app_iter *=* application*(*environ*,* replacement_start_response*)* Module paste.recursive:*80* in __call__ http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# *return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*632* in __call__ http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# *return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*160* in __call__ http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# body *=* method*(* trans*,* kwargs *)* Module galaxy.web.framework:*184* in decorator http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# *return* func*(* self*,* trans*,* ***args*,* kwargs *)* Module galaxy.web.controllers.admin_toolshed:*350* in browse_repositories http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# *return* self*.*reselect_tool_panel_section*(* trans*,* kwd *)* Module galaxy.web.framework:*184* in decorator http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# *return* func*(* self*,* trans*,* ***args*,* kwargs *)* Module galaxy.web.controllers.admin_toolshed:*1352* in reselect_tool_panel_section http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# status*=*status *)* Module galaxy.web.framework:*746* in fill_template http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# *return* self*.*fill_template_mako*(* filename*,* kwargs *)* Module galaxy.web.framework:*757* in fill_template_mako http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# *return* template*.*render*(* data *)* Module mako.template:*296* in render http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# *return* runtime*.*_render*(*self*,* self*.*callable_*,* args*,* data*)* Module mako.runtime:*660* in _render http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# _kwargs_for_callable*(*callable_*,* data*)**)* Module mako.runtime:*692* in _render_context http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# _exec_template*(*inherit*,* lclcontext*,* args*=*args*,* kwargs*=*kwargs*)* Module mako.runtime:*718* in _exec_template http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# callable_*(*context*,* ***args*,* kwargs*)* Module _base_mako:*42* in render_body http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# __M_writer*(*unicode*(*next*.*body*(**)**)**)* Module _admin_tool_shed_repository_reselect_tool_panel_section_mako:*76* in render_body http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# __M_writer*(*unicode*(*render_tool_dependency_section*(* install_tool_dependencies_check_box*,* *[* repo_info_dict *]* *)**)**)* Module _admin_tool_shed_repository_common_mako:*204* in render_render_tool_dependency_section http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# changeset_revision *)* Module posixpath:*67* in join http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstallid=88ee2d7021e4dc1a# *elif* path *==* '' *or* path*.*endswith*(*'/'*)**:* *AttributeError: 'NoneType' object has no attribute 'endswith'* ___ 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/
