March 2013 - galaxy-dev - lists.galaxyproject.org

multiple file output
by Philipe Moncuquet 14 Mar '13

14 Mar '13

Hi, I am trying to right a tool that will generate 2 ouptuts, 1 .txt and .gz. Before the tools runs I don't know how many fasta files will be in the .gz file. I have managed to have the perl script writing files like follow : $seqio_obj = Bio::SeqIO->new(-file => $seq_library_name, -format => "fasta" ); while ($seq_obj = $seqio_obj->next_seq) { $seq_ID = $seq_obj -> display_id; $seq = $seq_obj -> seq; #print $seq_ID."\n"; #print $MID_id_ref{$seq_ID}."\n"; if (defined($combination{$seq_ID})) { open(OUT,">>/my/own/path/on/my/server/which /is/not/good/".$combination{$seq_ID}."_library.fasta")||die"Pb ouverture du fichier3"; print OUT ">".$seq_ID."\n".$seq."\n"; #open(OUT,">>".$output_name2)||die"Pb ouverture du fichier3"; #print OUT ">".$seq_ID."\n".$seq."\n"; } else { open(OUT,">>/my/own/path/on/my/server/which /is/not/good/unsorted_library.fasta")||die"Pb ouverture du fichier3"; print OUT ">".$seq_ID."\n".$seq."\n"; #open(OUT,">>".$output_name2)||die"Pb ouverture du fichier3"; #print OUT ">".$seq_ID."\n".$seq."\n"; $nb_unsorted_seq++; } $nb_total_seq++; } I then use a command line to zip as follow : system('cd $work_dir'); system('tar -zcPf '.$output_name2.' /my/own/path/on/my/server/which /is/not/good/'); If one of you have encounter the same problem or if you can point me to a tool which is doing some similar stuff. Thanks, Philippe

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Datatype dropdown only 8px wide
by Kelvin Chan 13 Mar '13

13 Mar '13

Hello, I am having a slight issue with the Datatype tab of the edit page. I am using a locally installed version of galaxy-dist obtained from bitbucket. I cannot see anything in the dropdown menu to change the datatype. According to the HTML, the box is only 8px wide. <div class="select2-container" id="s2id_autogen2" style="width: 8px> Is there any way to fix this problem without having to re-install galaxy? Thanks, Kelvin

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Tool config for accordian-like subpanels?
by Ted Goldstein 13 Mar '13

13 Mar '13

I have a single tool with several different major modes. Each mode has its own uniques group of options that can be managed separately. Rathan than make five different tools, I would like to put it together and simply have the user interface show just the options for the selected mode. People do this in web pages sometimes using Jquery "Accordian" tabs. Is there any support to have something like Jquery accordion grouping of options? see that the drill down , but it is only used for setting binary options. Thanks,Ted

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example_watch_folder.py
by Rob Leclerc 13 Mar '13

13 Mar '13

If you're having problems with example_watch_folder.py you may need to increase the delay hack on line 55 to 15-20 seconds. Without the increased delay, it would upload a zerobyte file for me. It's not clear why, but there is a delay between the creation of a file name and the setting of the file to the dataset. Cheers, Rob

1 0

Internal Server Error - Creating Workflows
by Rob Leclerc 13 Mar '13

13 Mar '13

If you create a Workflow and then try to access it through the API, https://main.g2.bx.psu.edu/api/workflows/<workflow_id> the server will emit a 500 Internal Server Error. Changing the output filename on the workflow and then saving seems to fix the issue. Cheers, Rob

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How to add images/pictures into Galaxy Published Pages?
by Huayan Gao 13 Mar '13

13 Mar '13

Hi, I am trying to create a page in Galaxy and want to add some pictures/ screenshots. So how could I do this? I clicked the image button but it needs a URL not the path from my local computer. Thanks, Huayan

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New Features
by Gary Cheung 13 Mar '13

13 Mar '13

Hi Galaxy-Team, Can you please add the AxtToFasta and AxtToConcatenatedFasta Tools, which currently exist and work on PSU Test, onto the main PSU Galaxy Server. Thank you, Gary.

1 0

example_watch_folder.py : URL did not return JSON data
by Rob Leclerc 13 Mar '13

13 Mar '13

I'm trying to get the example_watch_folder.py to work with a simple example, but I am running into an error (Caveat, python is not my native language) I call the following script, but get the subsequent error: $ ./example_watch_folder.py 8c25bc83f6f9e4001dd21eb7b64f063f http://localhost:8080/ /Users/Rob/Documents/galaxy-db/input/ /Users/Rob/Documents/galaxy-db/output/ "API Imports" 2a56795cad3c7db3 * URL did not return JSON data* The preconditions I have in place are: 1. I copied my api_key: 8c25bc83f6f9e4001dd21eb7b64f063f 2. I created a new history on http://localhost:8080 3. I downloaded the the exons from hg19/chr22 from UCSC 3. On the dataset I performed a Text Manipulation > Select first (20 lines) 4. I extracted a workflow from the history and recorded the workflow id (2a56795cad3c7db3). 5. I created directories: - /Users/Rob/Documents/galaxy-db/input/ - /Users/Rob/Documents/galaxy-db/output/ My args may be malformed. Can someone provide me an example of a theirs? Cheers, Rob

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Error during registration phase
by Ramon Tiburski 13 Mar '13

13 Mar '13

Hello, I'm trying to register me as a user in the galaxy-es. I installed galaxy-es locally and always I try to register a user I have the error message: Error during registration phase. Please contact the administrator Thanks Ramão Tiago Tiburski

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Show a cookie value in xml
by Zinonas Antoniou 13 Mar '13

13 Mar '13

Dear all, Is there a way to get a value from a cookie and show it in an xml tool file, as a checkbox? I have a value in the cookie, e.g. folderid=2841 and I want to show this value in the xml file. Thank you in advance, Zinon

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