Re: [galaxy-dev] Need help with uploading a perl script in Galaxy local instance

2011-05-31 Thread Jayant Khopale
Hi Vipin, I was successfully able to integrate the tools in my local version of Galaxy. Thanks a lot for your time and help. The issue that I could isolate was probably due to the incorrect integration of the Postgresql database. On Mon, May 30, 2011 at 2:41 AM, Vipin TS vipin...@gmail.com

[galaxy-dev] Blast2GO in Galaxy

2011-05-31 Thread Peter Cock
Hi all, As I mentioned on Twitter, at the end of last week I wrapped Blast2GO for Galaxy, using the b2g4pipe program (Blast2GO for pipelines). See http://blast2go.org/ Currently current code is on bitbucket under my tools branch, https://bitbucket.org/peterjc/galaxy-central/src/tools/

Re: [galaxy-dev] Implemented adding tools via admin console

2011-05-31 Thread Vossen, Bodo
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

[galaxy-dev] Import Library Datasets into Histories - automatically imports into current AND new history - Bug?

2011-05-31 Thread Liisa Koski
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

Re: [galaxy-dev] Blast2GO in Galaxy

2011-05-31 Thread Peter Cock
On Tue, May 31, 2011 at 11:26 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, As I mentioned on Twitter, at the end of last week I wrapped Blast2GO for Galaxy, using the b2g4pipe program (Blast2GO for pipelines). See http://blast2go.org/ Currently current code is on bitbucket under

Re: [galaxy-dev] problem with build_chrom_db.py

2011-05-31 Thread Nate Coraor
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

Re: [galaxy-dev] Import Library Datasets into Histories - automatically imports into current AND new history - Bug?

2011-05-31 Thread Greg Von Kuster
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

Re: [galaxy-dev] Implemented adding tools via admin console

2011-05-31 Thread Nate Coraor
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

Re: [galaxy-dev] database table HistoryDatasetAssociation

2011-05-31 Thread Nate Coraor
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,

Re: [galaxy-dev] Accessing Data Library Template fields in tools?

2011-05-31 Thread Nate Coraor
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}

Re: [galaxy-dev] stdout and stderr while using pbs

2011-05-31 Thread Nate Coraor
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

[galaxy-dev] MUMmer and TopHit filter

2011-05-31 Thread Bossers, Alex
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