[galaxy-dev] Missing tool previews in tool shed, e.g. hmmer.xml
Hello all, I was looking at Edward's updated HMMER wrapper on the toolshed, http://toolshed.g2.bx.psu.edu/ There is a preview offered for the (simple) hmmpress.xml only, giving the impression that Edward's repository isn't very useful. Why isn't anything shown for the more complex hmmer.xml? If there is a problem rendering the preview, it would still be useful to list the tool in the table with its description, version and requirements. Edward - I have a query (which might be what the Tool Shed preview is unhappy about), where is the hmmer file format referenced in hmmer.xml defined? In hmmpress.xml you use hmm (as an input) and hmmpressed (as an output) which are both defined in hmmer.py, so is this an accidental inconsistency? Thanks, Peter P.S. Edward, hmmpress.xml is missing hmmpress as a requirement. ___ 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] Same error in multiple tools
Hi, I have the same error message for multiple tools (GFFtoBED, BEDtoBIGBED,BAMtoSAM,...): /from galaxy import eggs ImportError: No module named galaxy It's happening only since the last upgrade, do you know what is going wrong? Thanks, Alban / -- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84 ___ 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] Missing tool previews in tool shed, e.g. hmmer.xml
Hi Peter, Here is the error produced by attempting to load the hmmr.xml tool config into the tool shed. With regard to tool validity, the definition of a valid tool in the tool shed has always been restricted to the tool properly loading in a Galaxy instance. If a tool is not valid, it will not be returned in a search and it cannot be automatically installed (unless it belongs to a repository containing other valid tools). I'll consider ways to list invalid tools contained in repositories in the tool shed, but the preference is for tool developers to share only valid tools, or the value of the tool shed will be significantly diminished over time. Filtering out files that actually are not tools from a list of invalid tools could become a bit messy. Thanks, Greg Von Kuster Repository Actions Metadata was defined for some items in revision '66f8262e1686'. Correct the following problems if necessary and reset metadata. hmmer.xml - This file refers to a file named hmmdb.loc. Upload a file named hmmdb.loc.sample to the repository to correct this error. On Mar 19, 2012, at 6:15 AM, Peter Cock wrote: Hello all, I was looking at Edward's updated HMMER wrapper on the toolshed, http://toolshed.g2.bx.psu.edu/ There is a preview offered for the (simple) hmmpress.xml only, giving the impression that Edward's repository isn't very useful. Why isn't anything shown for the more complex hmmer.xml? If there is a problem rendering the preview, it would still be useful to list the tool in the table with its description, version and requirements. Edward - I have a query (which might be what the Tool Shed preview is unhappy about), where is the hmmer file format referenced in hmmer.xml defined? In hmmpress.xml you use hmm (as an input) and hmmpressed (as an output) which are both defined in hmmer.py, so is this an accidental inconsistency? Thanks, Peter P.S. Edward, hmmpress.xml is missing hmmpress as a requirement. ___ 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] Missing tool previews in tool shed, e.g. hmmer.xml
On Mon, Mar 19, 2012 at 1:28 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Peter, Here is the error produced by attempting to load the hmmr.xml tool config into the tool shed. With regard to tool validity, the definition of a valid tool in the tool shed has always been restricted to the tool properly loading in a Galaxy instance. If a tool is not valid, it will not be returned in a search and it cannot be automatically installed (unless it belongs to a repository containing other valid tools). I'll consider ways to list invalid tools contained in repositories in the tool shed, but the preference is for tool developers to share only valid tools, or the value of the tool shed will be significantly diminished over time. Filtering out files that actually are not tools from a list of invalid tools could become a bit messy. I see - I hope you can make some improvements for browsing the tool shed for this kind of situation. Thanks for confirming there was something the Tool Shed didn't like in hmmer.xml (missing a hmmdb.loc.sample file). For the tool uploader (in this case Edward) that kind of error is very helpful. Peter ___ 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] Hard-links and sshfs
Hello, My instance of galaxy is running on an sshfs mount. The problem comes when I set the new_file_path in the universe_wsgi.ini to be a folder within that sshfs. When I upload something, the hard link in the mkstemp_ln function fails because of apparent limitations of sshfs with hard links. It works if I replace that hard link by a file copy, but I would appreciate an alternative that would avoid me messing around the internals of the code. Thanks, Daniel ___ 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] Possible bug: Tags in a workflow gets duplicated hundreds of times
Hi,I have run into an issue with a tag being duplicated hundreds of times each time I open, edit or clone a workflow.I have tried to manually remove them, but each time the tag gets inserted somehow and duplicated each time I edit the workflow.By now there are hundreds of copies of the tags at it makes loading and running the workflow very slow.Is there a way to remove a tag from the system somehow? I am willing to dig into the database with some SQL statement but not sure where to start...ThanksThon ___ 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] Trackster cannot display INTERVAL or GATK-INTERVAL files???
It seems that trackster does not know how to display INTERVAL files?Is that true? Surely there is an easy way to support those kinds of simple files without having to convert them?Am I missing something?I also don't seem to be able to convert an interval file into a BED file?Thanks,Thon ___ 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] Trackster cannot display INTERVAL or GATK-INTERVAL files???
Oh wait..It's in the info section...Weird place for a conversion tool but it is there :)On Mar 19, 2012, at 12:02 PM, Anthonius deBoer thondeb...@me.com wrote:It seems that trackster does not know how to display INTERVAL files?Is that true? Surely there is an easy way to support those kinds of simple files without having to convert them?Am I missing something?I also don't seem to be able to convert an interval file into a BED file?Thanks,Thon___ 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] Trackster cannot display INTERVAL or GATK-INTERVAL files???
Thon, It seems that trackster does not know how to display INTERVAL files? Is that true? Yes, this is currently a limitation. However, most of the work is done that is necessary to make this happen, so it should be done soon, definitely in the next month or two. Surely there is an easy way to support those kinds of simple files without having to convert them? As you discovered, conversions can be done by clicking on the pencil icon and then performing the conversion. We're aware that isn't ideal for usability and plan to improve it in the future. 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] Help writing a tool
I'm writing some tools to integrate NCBI data resources with Galaxy. I have two questions. The first is simple. I want to write a tool for a long-running process that is handled by some other scheduler, and that produces its own job ids. Some web services, like BLAST, for example, receive a request, and take a while to complete processing. The job id can be used to fetch either job status or results from the server, depending on whether it has completed. How do you make a Galaxy tool that polls the server, and produces an output set only when the process is complete? The second question is, besides this mailing list, and the Galaxy wiki, is there are good online video or text resource that explains the Galaxy architecture and how to use it? The docs are good as far as they go, but most of what's in the command scripts in the tool files isn't documented. Thanks Mark Johnson Staff Scientist, NCBI mjohn...@ncbi.nlm.nih.gov ___ 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] Reducing costs in Cloud Galaxy
Greg, Regarding the performance of different types of instances, I came across this and thought you might potentially find it useful: http://cloudharmony.com/benchmarks Enis On Mon, Mar 19, 2012 at 7:49 PM, Greg Edwards gedwar...@gmail.com wrote: Enis, Thanks. Will try that re the storage. Greg E On Mon, Mar 19, 2012 at 4:49 PM, Enis Afgan eaf...@emory.edu wrote: Hi Greg, On Mon, Mar 19, 2012 at 11:01 AM, Greg Edwards gedwar...@gmail.comwrote: Hi, I've got an implementation of some proteomics tools going well in Galaxy on AWS EC2 under Cloudman. Thanks for the help along the way. I need to drive the costs down a bit. I'm using an m1.large AMI and it's costing about $180 - $200 / month. This is about 55% storage and 45% instance costs. That's peanuts in some senses but for now we need to get it down so that it comes out of petty cash for the department, while the case is proven for it's use. I have a few questions and would appreciate ny insights .. 1. AWS has just released an m1.medium and m1.small instance type, which are 1/2 and 1/4 the cost of m1.large. http://aws.amazon.com/ec2/instance-types/ http://aws.amazon.com/ec2/pricing/ I tried the m1.small and m1.medium with the latest Cloudman AMI * *galaxy-cloudman-2011-03-22 (ami-da58aab3) All seemed to install ok, but the Tools took up tp 30 minutes to start execution on m1.medium, and never started on m1.small. m1.medium only added about 15% to run times compared with m1.large, can't say for m1.small. t1.micro does run (and for free in my Free Tier first year) but blows execution times out by a factor of about 3 which is too much. Has anyone tried these new Instance Types ? (m1.small/medium) I have no real experience with these instance types yet either so maybe someone else can chime in on this? 2. The vast majority of the storage costs are fro the Gemome databases in the 700GB /mnt/galaxyIndices, which I don't need. Can this be reduced to the bare essentials ? You can do this manually: 1. Start a new Galaxy cluster (ie, one you can easily delete later) 2. ssh into the master instance and delete whatever genomes you don't need/want (these are all located under /mnt/galaxyIndices) 3. Create a new EBS volume of size that'll fit whatever's left on the original volume, attach it and mount it 4. Copy over the data from the original volume to the new one while keeping the directory structure the same (rsync is probably the best tool for this) 5. Unmount detach the new volume; create a snapshot from it 6. For the cluster you want to keep around (while it is terminated), edit persistent_data.yaml in it's bucket on S3 and replace the existing snap ID for the galaxyIndices with the snapshot ID you got in the previous step 7. Start that cluster and you should have a file system from the new snapshot mounted. 8. Terminate delete the cluster you created in step 1 If you don't want to have to do this the first time around on your custom cluster, you can first try it with another temporary cluster and make sure it all works as expected and then move on to the real cluster. Best, Enis Using m1.small/medium and getting rid of the 700GB would being my costs down to say $50 / month which is ok. Thanks ! Greg E -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.com ___ 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/ -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.com ___ 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] Reducing costs in Cloud Galaxy
Hi Enis, Greg, I've taken stuff from my this email, and previous conversations with Enis and put it in the wiki: http://wiki.g2.bx.psu.edu/Admin/Cloud/CapacityPlanning Please feel free to update/correct/enhance. Dave C. On Mon, Mar 19, 2012 at 2:58 PM, Enis Afgan eaf...@emory.edu wrote: Greg, Regarding the performance of different types of instances, I came across this and thought you might potentially find it useful: http://cloudharmony.com/benchmarks Enis On Mon, Mar 19, 2012 at 7:49 PM, Greg Edwards gedwar...@gmail.com wrote: Enis, Thanks. Will try that re the storage. Greg E On Mon, Mar 19, 2012 at 4:49 PM, Enis Afgan eaf...@emory.edu wrote: Hi Greg, On Mon, Mar 19, 2012 at 11:01 AM, Greg Edwards gedwar...@gmail.comwrote: Hi, I've got an implementation of some proteomics tools going well in Galaxy on AWS EC2 under Cloudman. Thanks for the help along the way. I need to drive the costs down a bit. I'm using an m1.large AMI and it's costing about $180 - $200 / month. This is about 55% storage and 45% instance costs. That's peanuts in some senses but for now we need to get it down so that it comes out of petty cash for the department, while the case is proven for it's use. I have a few questions and would appreciate ny insights .. 1. AWS has just released an m1.medium and m1.small instance type, which are 1/2 and 1/4 the cost of m1.large. http://aws.amazon.com/ec2/instance-types/ http://aws.amazon.com/ec2/pricing/ I tried the m1.small and m1.medium with the latest Cloudman AMI * *galaxy-cloudman-2011-03-22 (ami-da58aab3) All seemed to install ok, but the Tools took up tp 30 minutes to start execution on m1.medium, and never started on m1.small. m1.medium only added about 15% to run times compared with m1.large, can't say for m1.small. t1.micro does run (and for free in my Free Tier first year) but blows execution times out by a factor of about 3 which is too much. Has anyone tried these new Instance Types ? (m1.small/medium) I have no real experience with these instance types yet either so maybe someone else can chime in on this? 2. The vast majority of the storage costs are fro the Gemome databases in the 700GB /mnt/galaxyIndices, which I don't need. Can this be reduced to the bare essentials ? You can do this manually: 1. Start a new Galaxy cluster (ie, one you can easily delete later) 2. ssh into the master instance and delete whatever genomes you don't need/want (these are all located under /mnt/galaxyIndices) 3. Create a new EBS volume of size that'll fit whatever's left on the original volume, attach it and mount it 4. Copy over the data from the original volume to the new one while keeping the directory structure the same (rsync is probably the best tool for this) 5. Unmount detach the new volume; create a snapshot from it 6. For the cluster you want to keep around (while it is terminated), edit persistent_data.yaml in it's bucket on S3 and replace the existing snap ID for the galaxyIndices with the snapshot ID you got in the previous step 7. Start that cluster and you should have a file system from the new snapshot mounted. 8. Terminate delete the cluster you created in step 1 If you don't want to have to do this the first time around on your custom cluster, you can first try it with another temporary cluster and make sure it all works as expected and then move on to the real cluster. Best, Enis Using m1.small/medium and getting rid of the 700GB would being my costs down to say $50 / month which is ok. Thanks ! Greg E -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.com ___ 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/ -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.com ___ 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/ -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 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] Reducing costs in Cloud Galaxy
Just one extra thought on this-- If you leave your instance up all the time it may be worth looking into having a reserved micro instance up as the front end (cheap, or free, with your intro tier) with SGE submission disabled. Then, enable autoscaling(max 1) of m1.large/xlarge instances. -Dannon On Mar 19, 2012, at 7:20 PM, Dave Clements wrote: Hi Enis, Greg, I've taken stuff from my this email, and previous conversations with Enis and put it in the wiki: http://wiki.g2.bx.psu.edu/Admin/Cloud/CapacityPlanning Please feel free to update/correct/enhance. Dave C. On Mon, Mar 19, 2012 at 2:58 PM, Enis Afgan eaf...@emory.edu wrote: Greg, Regarding the performance of different types of instances, I came across this and thought you might potentially find it useful: http://cloudharmony.com/benchmarks Enis On Mon, Mar 19, 2012 at 7:49 PM, Greg Edwards gedwar...@gmail.com wrote: Enis, Thanks. Will try that re the storage. Greg E On Mon, Mar 19, 2012 at 4:49 PM, Enis Afgan eaf...@emory.edu wrote: Hi Greg, On Mon, Mar 19, 2012 at 11:01 AM, Greg Edwards gedwar...@gmail.com wrote: Hi, I've got an implementation of some proteomics tools going well in Galaxy on AWS EC2 under Cloudman. Thanks for the help along the way. I need to drive the costs down a bit. I'm using an m1.large AMI and it's costing about $180 - $200 / month. This is about 55% storage and 45% instance costs. That's peanuts in some senses but for now we need to get it down so that it comes out of petty cash for the department, while the case is proven for it's use. I have a few questions and would appreciate ny insights .. 1. AWS has just released an m1.medium and m1.small instance type, which are 1/2 and 1/4 the cost of m1.large. http://aws.amazon.com/ec2/instance-types/ http://aws.amazon.com/ec2/pricing/ I tried the m1.small and m1.medium with the latest Cloudman AMI galaxy-cloudman-2011-03-22 (ami-da58aab3) All seemed to install ok, but the Tools took up tp 30 minutes to start execution on m1.medium, and never started on m1.small. m1.medium only added about 15% to run times compared with m1.large, can't say for m1.small. t1.micro does run (and for free in my Free Tier first year) but blows execution times out by a factor of about 3 which is too much. Has anyone tried these new Instance Types ? (m1.small/medium) I have no real experience with these instance types yet either so maybe someone else can chime in on this? 2. The vast majority of the storage costs are fro the Gemome databases in the 700GB /mnt/galaxyIndices, which I don't need. Can this be reduced to the bare essentials ? You can do this manually: 1. Start a new Galaxy cluster (ie, one you can easily delete later) 2. ssh into the master instance and delete whatever genomes you don't need/want (these are all located under /mnt/galaxyIndices) 3. Create a new EBS volume of size that'll fit whatever's left on the original volume, attach it and mount it 4. Copy over the data from the original volume to the new one while keeping the directory structure the same (rsync is probably the best tool for this) 5. Unmount detach the new volume; create a snapshot from it 6. For the cluster you want to keep around (while it is terminated), edit persistent_data.yaml in it's bucket on S3 and replace the existing snap ID for the galaxyIndices with the snapshot ID you got in the previous step 7. Start that cluster and you should have a file system from the new snapshot mounted. 8. Terminate delete the cluster you created in step 1 If you don't want to have to do this the first time around on your custom cluster, you can first try it with another temporary cluster and make sure it all works as expected and then move on to the real cluster. Best, Enis Using m1.small/medium and getting rid of the 700GB would being my costs down to say $50 / month which is ok. Thanks ! Greg E -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.com ___ 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/ -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.com ___ 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/ -- http://galaxyproject.org/GCC2012 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
[galaxy-dev] Getting the input name of the dataset
Hi there, I am new to Galaxy and I've just recently learned how to integrate a Perl script to it. Now, my code uses the input file's name as a header for a column in the output. When I ran it in Galaxy, I did get the filename, but it's the one ending in .dat (actually, I got the entire path of the file). I was wondering if it's possible to retain the original name of the file (or retrieve the name of the input dataset) and use it in the output file. I can't think of a Perl script for this yet, for my scripting's a bit rusty (I just started learning Perl last month). I've already checked the FAQs page, the wiki and the mailing list, but I did not get any useful hints. I hope my writing made sense. Thank you for your time! - Diana ___ 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] Import error when running galaxy on Debian Lenny 64bit
Dear galaxy, I'm trying to install galaxy on a 64bit Debian (5.0) Lenny server with python2.5.2. When running %sh run.sh, the fetch_eggs completed successfully. However, I have problem with running galaxy instance. I've posted the error messages below. Traceback (most recent call last): File ./scripts/paster.py, line 34, in module command.run() File /home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/ command.py, line 84, in run invoke(command, command_name, options, args[1:]) File /home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/ command.py, line 123, in invoke exit_code = runner.run(args) File /home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/ command.py, line 218, in run result = self.command() File /home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/ serve.py, line 276, in command relative_to=base, global_conf=vars) File /home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/ serve.py, line 313, in loadapp **kw) File /home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/ loadwsgi.py, line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File /home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/ loadwsgi.py, line 225, in loadobj return context.create() File /home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/ loadwsgi.py, line 625, in create return self.object_type.invoke(self) File /home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/ loadwsgi.py, line 110, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File /home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/ util/fixtypeerror.py, line 57, in fix_call val = callable(*args, **kw) File /home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py, line 90, in app_factory add_ui_controllers( webapp, app ) File /home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py, line 39, in add_ui_controllers module = __import__( module_name ) File /home/galaxy/galaxy-dist/lib/galaxy/web/controllers/cloud.py, line 9, in module import boto ImportError: No module named boto We have another Debian (6.0) Squeeze 32 bit server with python 2.6.6, and I did the same installation of galaxy. Everything went smoothly and galaxy server instance can run successfully on it. Do you know why this importError happens on our 64bit Debian 5.0 server and how I could fix it? Many thanks. Jemma Wu Australian Proteome Analysis Facility (APAF) Level 4, Building F7B, Research Park Drive Macquarie University Sydney NSW 2109 Australia ___ 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/
