November 2011 - galaxy-dev - lists.galaxyproject.org

downloading bowtie indexed files
by Nikhil Joshi 29 Nov '11

29 Nov '11

Hi all, Just wondering if there is a way to download the bowtie indexed files after indexing. It seems that the indexed output is simply a meta-file that points to the directory where the indexed files are kept.... but what if I want to download all of the indexed files themselves? I wrote something to do this... basically I created an html page that is the output of bowtie-build which then points to the created files... but I'm wondering if there is an easier way...? - Nik.

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Can not clean my galaxy datasets
by liram_vardi＠agilent.com 29 Nov '11

29 Nov '11

Hello, My name is Liram Vardi and I'm using local Galaxy instance. Anyway, I can't clean my deleted datasets from my own locally disk. When I am trying to delete dataset, as was explained in http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Actions, First, I used the "delete 'X' icon" near the dataset to delete the dataset, Then, when I go to "Options -> Show Deleted Datasets", I can see my "deleted dataset" on the list with the note: "This dataset has been deleted. Click _here_ to undelete it" but I don't get the also the option "or _here_ to immediately remove it from disk." . Also, when I use the option "Options -> Purge Deleted Datasets", I'm getting a message "0 datasets have been deleted permanently" and my deleted dataset still stays in the "Options -> Show Deleted Datasets" menu list. I also tried to clear the history, but when I'm doing that, the "using X Mb" tab on the upper right corner is still not reset. What is the problem? Thanks a lot for your help! Liram

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Re: [galaxy-dev] Question about from_work_dir
by Jeremy Goecks 29 Nov '11

29 Nov '11

>> Aurelien, >> >> The particular behavior that you need isn't currently supported because the value of from_work_dir isn't treated as a template. To work around this limitation, you can do the move/copy operations in your tool wrapper; see the wrappers for Bowtie and Sicer for examples on how to do this. >> >> Good luck, >> J. > > Hi Jeremy, > > Is it possible to build the required string elsewhere in the .xml file using cheetah and then pass the resulting string like from_work_dir=$result or is using a wrapper really the only way to go? I'm writing a config for a tool that names the output files using the options, so I could potentially concatenate the option values to get the required file name if I could do that. Alex, The best approach is for your tool to accept output file names; then, in the command_line tag of the tool wrapper XML, you can build the output name based on options chosen by the user. Finally, please always cc the mailing list for community and archival purposes. Thanks, J.

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Re: [galaxy-dev] only showing first lines of large output file
by Mattias de Hollander 28 Nov '11

28 Nov '11

Hello, I just noticed I get metadata errors in the paster.log file. Can someone tell me what they are and if they are related to above problem? galaxy.jobs.runners.drmaa DEBUG 2011-11-16 11:55:28,037 (840/588) state change: job finished normally galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:28,231 setting metadata externally failed for HistoryDatasetAssociation 1680: [Errno 2] No such file or directory: '../../galaxyData/tmp/metadata_in_HistoryDatasetAssociation_1680_N7JVtq' galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:28,325 setting metadata externally failed for HistoryDatasetAssociation 1679: [Errno 2] No such file or directory: '../../galaxyData/tmp/metadata_in_HistoryDatasetAssociation_1679_oTzTG_' galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:28,634 setting metadata externally failed for HistoryDatasetAssociation 1678: [Errno 2] No such file or directory: '../../galaxyData/tmp/metadata_in_HistoryDatasetAssociation_1678_MgW15e' galaxy.jobs DEBUG 2011-11-16 11:55:29,103 job 840 ended galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:29,103 Cleaning up external metadata files galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:29,152 Failed to cleanup MetadataTempFile temp files from ../../galaxyData/tmp/metadata_out_HistoryDatasetAssociation_1678_UTGZz8: [Errno 2] No such file or directory: '../../galaxyData/tmp/metadata_out_HistoryDatasetAssociation_1678_UTGZz8' galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:29,152 Failed to cleanup external metadata file (filename_in) for HistoryDatasetAssociation_1678: [Errno 2] No such file or directory: '../../galaxyData/tmp/metadata_in_HistoryDatasetAssociation_1678_MgW15e' galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:29,152 Failed to cleanup external metadata file (filename_out) for HistoryDatasetAssociation_1678: [Errno 2] No such file or directory: '../../galaxyData/tmp/metadata_out_HistoryDatasetAssociation_1678_UTGZz8' galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:29,153 Failed to cleanup external metadata file (filename_kwds) for HistoryDatasetAssociation_1678: [Errno 2] No such file or directory: '../../galaxyData/tmp/metadata_kwds_HistoryDatasetAssociation_1678_3SDMLo' And of course, how to solve it :) Any help is appreciated. Mattias -- Bioinformatician Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, the Netherlands

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Error running tool
by Toqa Manasrah 28 Nov '11

28 Nov '11

Hello everybody, I am trying to run my tool Vispa but every time i try to i got this error messages: An error occurred running this job: /home/galaxy/galaxy-dist/tools/vispa/main.bash: line 13: ./parser_v.2.sh: No such file or directory /home/galaxy/galaxy-dist/tools/vispa/main.bash: line 16: ./vispa.bash: No such file or directory although all these files are reside under the same directory and have the permission 755. how can I solve the problem? Thanks and regards, Tuqa.

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cleanup of database/pbs folder
by Mattias de Hollander 28 Nov '11

28 Nov '11

Hej Galaxy-admins, While thinking of backing up the galaxy dir I noticed the database/pbs directory on our local server contains several gigabytes of data (all *.o, *.e and galaxy_*.sh scripts). I use the cleanup scripts to remove deleted datasets, but shouldn't this directory also not be cleaned once in a while? Is this possible with the cleanup scripts? Thanks for sharing you experience or view on it! Mattias

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Running shell script
by Toqa Manasrah 28 Nov '11

28 Nov '11

Hi everybody, I am integrating my software ViSpA inside galaxy and I have two questions: 1: the main program is a shell script (.sh) which call another shell script, which call Java executables. should I include any interpreter inside the .xml <command > tag? and what that should be? 2. how to guarantee that the output files destination are on the use local host rather than the server which is running galaxy? Thanks and regards, Tuqa.

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Question about from_work_dir
by Aurélien Bernard 28 Nov '11

28 Nov '11

Hi everybody, I'm currently trying to create a wrapper for one of my program. This program generates several output file and the name of each output file is derived from the name of the main input file. _In the .xml file I try to get my output files with the following tag_: <outputs> <data from_work_dir="${input_file}.out" label="${input_file} main output" format="txt" /> ... </outputs> _The corresponding input file tag_: <param name="input_file" type="data" label="Input label" format="alr" help="Requested file type: ALR" /> The problem is that the content of the "from_work_dir" attribute is not interpreted by galaxy (Contrary to the label attribute) and therefore I get this error message: galaxy.jobs DEBUG 2011-11-28 17:44:24,431 finish(): Could not move /home/galaxy/galaxy-dist/database/job_working_directory/326/${input_file}.out to /home/galaxy/galaxy-dist/database/files/000/dataset_684.dat as directed by from_work_dir Do I made a syntax error ? Do I misunderstand the function of the from_work_dir attribute? Thank you in advance for your help. Best regards, Aurélien Bernard

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Barcode Splitter: bug
by Yunling Shi 28 Nov '11

28 Nov '11

Hi, I tried to use Barcode Splitter in Galaxy and could not get it work. In the Library to split pull down list, I could not get anything. I would expect it provides me information just like Barcodes to use pulldown list. Is this a bug? Yunling

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tool for RepeatMasker?
by Smithies, Russell 28 Nov '11

28 Nov '11

Has anyone created a tool for running RepeatMasker http://www.repeatmasker.org/ within Galaxy? It's something we'd like to do so we can create workflows where the fasta is masked before being searched with blast. Thanx, Russell Smithies New Zealand ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================

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