- galaxy-dev - lists.galaxyproject.org

database table HistoryDatasetAssociation
by Harendra chawla 31 May '11

31 May '11

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. Regards Harendra

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Implemented adding tools via admin console
by Vossen, Bodo 31 May '11

31 May '11

Hi all, I've implemented functionality for adding tools via the admin menu. Let me just briefly explain what I did. You can upload a binary/script file to a specific folder (choosable). Then this file is analyzed. The analysis is at the moment only done for Perl/Python script, as those are mostly used in our institute. First, it is checked in what language the script is written in (if it is not a binary), then a syntax check is performed (for python pyflakes must be installed), and then it is checked how many arguments are in the script. Once you uploaded a file, you can add the XML file for this script. The XML file is analyzed as well, in the following matter. First it is checked that the XML is well formed. Then it is checked if the mandatory tags are in the XML ( I choosed for mandatory tags: root = tool, command, input, help ) Then it is checked if script and XML are "compatible" by checking if they have the same number of arguments. I also wrote unit tests for the main methods. They can be executed by "python lib/galaxy/util/test_tool_analysis.py" The main files I changed are lib/galaxy/web/base/controller.py lib/galaxy/util/tool_analysis.py lib/galaxy/util/helper.py lib/galaxy/util/tool_conf_helper.py and the templates for the admin in templates/admin The "update tools" is only done for one web process, there is no hup signal sent at the moment. If you have any questions or something is not working for you, please let me know, I probably have some time to check it. There are still some things that can be / should be implemented later on but I think this can be a good start for you guys. I forked galaxy-central, so you can check it out by cloning https://bitbucket.org/Bodolski/galaxy-central-adding-tools hg clone https://Bodolski@bitbucket.org/Bodolski/galaxy-central-adding-tools If you have any comments or question please do not hesitate to contact me, I'm open for every kind of critics. Best wishes from Germany, Bodo Vossen

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Import Library Datasets into Histories - automatically imports into current AND new history - Bug?
by Liisa Koski 31 May '11

31 May '11

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

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Re: [galaxy-dev] Need help with uploading a perl script in Galaxy local instance
by Jayant Khopale 31 May '11

31 May '11

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.ts(a)gmail.com> wrote: > > >> >> >>> The log file comes out to be clean. However I have 2 questions - >>> >> >> When you start your instance I am sure apache log will say something for >> ex: clicking on the page, selecting tool etc. I am sure about that. >> >> >>> >>> 1. Which version are you using to run your test instance? >>> >> >> The recent one, but it is quite sure that the tool integration in quite >> stable from past couple of months. >> >> >>> 2. Did you make any changes to your Python execution environment for >>> Galaxy? >>> >>> >> From the error it seems that it is not problem with Python environment >> set-up. >> >> >>> Please let me know. >>> >>> >> >> > How is going with your Galaxy tool integration, I was away for the last > couple of days. > Hope things are worked at your end. > > -- JAYANT KHOPALE

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Is dynamic associated information per dataset possible?
by Duddy, John 30 May '11

30 May '11

We'd like to be able to associate fixed things (project, Sample, sequencer used) with user's FASTQ files, and we'd also like to allow users to associate dynamic, site-specific stuff with the sequencing run. Currently, users track their runs using a CSV sample sheet, and often they add columns to that sample sheet for their own information. Is it possible to associate that information with the FASTQ file when it is placed in Galaxy? I know about metadata, but the supported fields look like they are fixed in the code. I was hoping for a solution where the users do not need to modify the Galaxy code to pull this off. John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jduddy(a)illumina.com<mailto:jduddy@illumina.com>

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thanks for the conference; presentations availbale?
by Martin Senger 30 May '11

30 May '11

I really enjoyed the recent conference. Many thanks for the splendid logistics and, of course, the content. I wonder if the slides presented there will be available for downloading perhaps? Cheers, Martin -- Martin Senger email: martin.senger@gmail.com,martin.senger@kaust.edu.sa skype: martinsenger

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semi-colons converted to X in config file?
by Jon Sorenson 29 May '11

29 May '11

I suspect I've run into a rare XML entity/Cheetah conversion bug. I have a parameter definition like <param name="schedule" type="text" value="6,3,75;6,3,75;5,3,75;5,3,75;6,2,75;6,2,75;5,2,75;5,2,75" label="Parameter Schedule" size="60"/> I also am creating a configfile using <configfile name="iniFile"> ... paramSchedule=${schedule} ... </configfile> The file that gets created has ... paramSchedule=6,3,75X6,3,75X5,3,75X5,3,75X6,2,75X6,2,75X5,2,75X5,2,75 ... i.e. the ';' character gets converted to X. I suspect that this is an XML parsing issue (trying to interpret ';' as marking an entity resolution?) but the default value get displayed correctly in the Galaxy UI so it might not be so simple as this. I can't see how Cheetah is converting ';' to 'X' but maybe that's it. I'm planning on hacking around this, but wanted to post to the list to see if anyone else has seen this or has quick recommendations. Jon

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Filter data and cut column bugs
by Peter Cock 27 May '11

27 May '11

Hi all, I filled the following bugs 2 weeks ago, with patches: https://bitbucket.org/galaxy/galaxy-central/issue/537/ Filter data on any column tool casts unused columns https://bitbucket.org/galaxy/galaxy-central/issue/536/ Filter data on any column tools shows nonsense % vs total on stdout https://bitbucket.org/galaxy/galaxy-central/issue/535/ Filter data on any column tool complains about hash comment lines https://bitbucket.org/galaxy/galaxy-central/issue/534/ Cut column tool messes up # header lines I'm sure the team has been busier than usual with the run up to the Galaxy Community Conference (hopefully I'll see you all tomorrow night - fingers crossed the ash from the Grimsvotn volcano doesn't cause too much trouble)... However, for future reference would it help if I emailed the list in parallel with filing bugs? None of these issues individually are overly complicated, and the sooner they get looked at the more likely it is my patches will still apply cleanly. Thanks, Peter

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Workflows and unknown number of output datasets
by Louise-Amélie Schmitt 27 May '11

27 May '11

Hi everyone First let me thank all the Team Galaxy, the conference was really great. Kanwei asked me to send the tool I told him about. It's one of these tools for which you can't know the exact number of output datasets before tool run. Here are the files. It's really simple actually, but it would be nice if I could integrate it in workflows without it having to be the final step. Would it even be possible? And please ignore the idiotic comments in the files, I was really tired that day. Cheers, L-A

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Re: [galaxy-dev] stdout and stderr
by Peter Cock 27 May '11

27 May '11

On Fri, May 27, 2011 at 3:27 AM, shashi shekhar <meshashi29(a)gmail.com> wrote: > if i am using pbs . in this i am getting stderror and stdout . then how can > i handle such type of problem How does the tool you are wrapping signal an error? Does it write to stderr and/or does it give a non-zero return code? The BLAST+ wrapper script looks for a non-zero return code, since BLAST+ will write harmless warnings to stderr which should not be treated as an error. Note the changes suggested on issue 325 have have not been made yet (in part because supporting PBS nicely would be hard). Peter

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