[galaxy-dev] Import Library Datasets into Histories - automatically imports into current AND new history - Bug?
Hello, I noticed a change in the newest version. When importing Library Datasets into Histories...if you enter a New History name for the destination Galaxy will import into the new AND current history. So it is getting imported into two histories. Is this a bug? It would really be nice to only import a dataset into a new history like before. Thanks, Liisa ___ 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] problem with build_chrom_db.py
Curt Palm wrote: I've been configuring my local instance of galaxy to use trackster according to the instructions on https://bitbucket.org/galaxy/galaxy-central/wiki/Visualization when I run the script: python ./cron/build_chrom_db.py ./tool-data/shared/ucsc/chrom/ I get files that begin with: META http-equiv=Content-Script-Type content=text/javascript chr1247249719 chr1_random 166326 ... this causes an error in the browser: Could not load chroms for this dbkey: if i delete the first line META http-equiv=Content-Script-Type content=text/javascript from the .len file, then trackster works fine. I'm thinking there is a new line the input to build_chrom_db.py that is not getting stripped by this script Hi Curt, This appears to be a problem with the query that is being used for some of the builds. I'm looking in to it now and will let you know what I find out. --nate thanks, Curt Palm *** Curtis J. Palm cp...@stanford.edu Stanford Genome Technology Center MC: 8307 office: 650-812-1994cell: 408 858-7849 *** ___ 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] Import Library Datasets into Histories - automatically imports into current AND new history - Bug?
Lisa, Thanks very much for reporting this bug. It has been fixed in our development repo in change set 5608, which should be available in the distribution within the next few weeks. Greg Von Kuster On May 31, 2011, at 8:39 AM, Liisa Koski wrote: Hello, I noticed a change in the newest version. When importing Library Datasets into Histories...if you enter a New History name for the destination Galaxy will import into the new AND current history. So it is getting imported into two histories. Is this a bug? It would really be nice to only import a dataset into a new history like before. Thanks, Liisa ___ 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 Von Kuster Galaxy Development Team g...@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] Implemented adding tools via admin console
Vossen, Bodo wrote: Hi Peter, thanks a lot for your comments. I think it is more comfortable to be able to upload tools and xml via the webbrowser than to open a terminal and copy them, that was the idea behind my work. Especially for our institute this is very useful. You're right about the check_argument methods. I wasn't sure to add this kind of functionality in the first place, because it can become very tricky. What I did should just be the very first step for someone who wants to continue the work (if this makes sense). That's why I added a checkbox that disable this check, so that you still can upload your tool/xml even the argument test would fail. Do you have some comments about the other parts ? Is this something you would be interested in using ? Hi Bodo, My thoughts on the argument checking are similar to those of Peter's, although I like that you can essentially use these as a sort of sanity check warning. We will soon be working on simplifying tool management and when that work gets started we can have a look at your code to see how much overlap it has with the work we're doing. Thanks for your contribution! --nate Best wishes, Bodo Vossen -Original Message- From: Peter Cock [mailto:p.j.a.c...@googlemail.com] Sent: Sat 5/28/2011 10:19 PM To: Vossen, Bodo Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Implemented adding tools via admin console On Fri, May 27, 2011 at 11:21 AM, Vossen, Bodo bodo.vos...@mpi-bn.mpg.de wrote: Hi all, I've implemented functionality for adding tools via the admin menu. That sounds very useful in principle, although perhaps the less flexible alternative of reloading tool_conf.xml would achieve the same aim? ... Then it is checked if script and XML are compatible by checking if they have the same number of arguments. This seems very fragile, and having looked at the code for detecting the number of arguments in a Python script it looks like it will get it wrong in many situations. Even for something quite simple like this: #sys.argv[0] is the script file itself assert len(sys,argv)==4, Expect 3 arguments arg1, arg2, arg3 = sys.argv[1:] Also, what about conditional code like this? assert len(sys.argv)==4, Expect 3 arguments if sys.argv[1] == db: database = sys.argv[2] filename = None else: database = None filename = sys.argv[2] out_filename = sys.argv[3] If I have read your get_parameter_number code right, it would claim there are four arguments since there are four lines of the basic form variable = sys.argv[i] Also, it cannot possibly work when there are a varying number of arguments, for example a repeat argument. If you want a test case, my Venn Diagram tool on the Tool Shed should be relevant (its a python script). If you have any comments or question please do not hesitate to contact me, I'm open for every kind of critics. I would remove the attempt to check the number of arguments. It is practically impossible to get this right in all cases, so I don't think it is worth doing. Having valid script/xml combinations rejected would be quite annoying. 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/ ___ 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] database table HistoryDatasetAssociation
Harendra chawla wrote: Hi, I am trying to modify the history_datset_association table in the database by adding one column, as per my requirement. I have changed the schema of the table but not able to add data for that column. Can anyone suggest how and where it can be done. Hi Harendra, You'd need to modify the table definition and mapping in lib/galaxy/model/mapping.py. Our official database changes are propogated in lib/galaxy/model/migrate/versions, but if you were to write a migrate script, you'd have version conflicts with our own versions, so unfortunately the best solution is probably to change mapping.py and then add the column to your database manually. --nate Regards Harendra ___ 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] Accessing Data Library Template fields in tools?
Duddy, John wrote:
I have my data in a data library and have a form template defined so I can
enter the sample information.
So, I import a data file into a history and want to run a tool on it. Can I
pass the values of those form templates to my tool? Sort of line
${input.form_field_id} ?
Hi John,
It's not available directly on the history item, but you can go
backwards to the library item to get it:
${input.copied_from_library_dataset_dataset_association.info_association...}
--nate
Thanks!
John Duddy
Sr. Staff Software Engineer
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Tel: 858-736-3584
E-mail: jdu...@illumina.commailto:jdu...@illumina.com
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Re: [galaxy-dev] stdout and stderr while using pbs
shashi shekhar wrote: Hi All, if i am using pbs . in this i am getting stderror and stdout . then how can i handle such type of problem. can i check the standard error before displaying anything on browser. Hi Shashi, There's no difference when running via PBS or locally in this regard. If you need to capture stderr to prevent it from causing a failure, please see this page: https://bitbucket.org/galaxy/galaxy-central/wiki/Job_failure_when_stderr --nate Reagrds shashi shekhar ___ 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] MUMmer and TopHit filter
Our first tools arrived at the toolshed; The MUMmer genome comparison suite and a TopHit filter. Enjoy and we appreciate any feedback for improvement: http://community.g2.bx.psu.edu/tool/browse_tools?operation=tools_by_categoryid=062d90505b2e763dwebapp=community Alex ___ 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/
