April 2012 - galaxy-dev - lists.galaxyproject.org

CloudMan/Galaxy wiki suggestion
by Assaf Gordon 15 Apr '12

15 Apr '12

Hello, Great work with the Galaxy on the Cloud - it's the first time I've used it and it looks very impressive (and I'm not a big cloud fan :) ). Once I got it working it was very nice, but before it worked I encountered two issues (not sure if those were voodoo or not) that could be perhaps documented in the Wiki (under "troubleshooting"?): 1. the "User Data" is sensitive to trailing white-space, or senstive to copy&paste in the edit box. I accidentally had: access_key: XXXXXXXXXXXXXX<space><space> and it seems it completely prevent the Cloudman from starting. when the stared, I couldn't connect to it with a web-browser. I logged on using SSH, and saw that there was nothing running/listening on port 80 (no nginx, no python). Not sure exactly why it happened, but it did. removing white-space (and also saving the user-data to a file instead of pasting it directly in the editbox) solved the problem. 2. If the "user-data" password is all numeric, there's no way to login to the cloudman. I suspect the reason is that an all numeric password is treated as a number, not a string. Then, the log shows: $ cat /opt/galaxy/pkg/ec2autorun.py.log [...] [DEBUG] ec2autorun:337 2012-04-13 20:22:50,983: Composed user data: {'access_key': 'XXXXXXXXXXXXXXXXXX', 'cloudman_home': '/mnt/cm', 'cluster_name': 'galaxy-TGAC-workshop', 'bucket_default': 'cloudman', 'role': 'master', 'bucket_cluster': 'cm-169ca4be88c386ce8ec3078d69a6dc3a', 'boot_script_path': '/tmp/cm', 'boot_script_name': 'cm_boot.py', 'secret_key': 'XXXXXXXXXXXXX', 'password': 12345678} [...] you'll notice that the password key is a numeric value, not a string - and login wasn't possible (perhaps it was voodoo and I'm wrong in my guess, but once I changed it to alphanumeric password, with the same user data settings, it workd). -gordon

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Problem with cleaning up galaxy datasets
by Klaus Metzeler 14 Apr '12

14 Apr '12

Dear all, I have a problem with the cleanup scripts on my local galaxy instance. I am using the updated cleanup_datasets.py, as per Nate's earlier reply here http://gmod.827538.n3.nabble.com/Problem-running-purge-datasets-sh-cleanup-…. <http://gmod.827538.n3.nabble.com/Problem-running-purge-datasets-sh-cleanup-…> This is the output I get when running cleanup_datasets.py: ~/ngs-bin/galaxy-dist $ scripts/cleanup_datasets/cleanup_datasets.py -d 2 -6 -r Traceback (most recent call last): File "scripts/cleanup_datasets/cleanup_datasets.py", line 524, in <module> if __name__ == "__main__": main() File "scripts/cleanup_datasets/cleanup_datasets.py", line 82, in main ini_file = args[0] IndexError: list index out of range ... and this if I call it via the shell script cleanup_datasets.sh ~/ngs-bin/galaxy-dist $ scripts/cleanup_datasets/delete_datasets.sh Traceback (most recent call last): File "./scripts/cleanup_datasets/cleanup_datasets.py", line 524, in <module> if __name__ == "__main__": main() File "./scripts/cleanup_datasets/cleanup_datasets.py", line 101, in main app = CleanupDatasetsApplication( config ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 512, in __init__ self.model = galaxy.model.mapping.init( config.file_path, config.database_connection, engine_options={}, create_tables=False, object_store=self.object_store ) File "/home/klausmetzeler/ngs-bin/galaxy-dist/lib/galaxy/model/mapping.py", line 1818, in init load_egg_for_url( url ) File "/home/klausmetzeler/ngs-bin/galaxy-dist/lib/galaxy/model/mapping.py", line 1798, in load_egg_for_url dialect = guess_dialect_for_url( url ) File "/home/klausmetzeler/ngs-bin/galaxy-dist/lib/galaxy/model/mapping.py", line 1794, in guess_dialect_for_url return (url.split(':', 1))[0] AttributeError: 'bool' object has no attribute 'split' Any idea what might be wrong? Thanks a lot for your support, Klaus

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Creating a workflow of workflows
by Aaron Gallagher 13 Apr '12

13 Apr '12

Hi again, I'm trying to set up a workflow for Galaxy (6799:40f1816d6857), but I can't seem to find a way to make a workflow that invokes another workflow. It seems like this wouldn't be unreasonable, since workflows have defined inputs and outputs. There might be another way to accomplish what I'm trying to ultimately do, though. We have a set of analyses and conversions, and want to assemble a workflow that goes through a long series of steps. The workflow can roughly be organized into three parts. Once the workflow is finished, we might want to rerun the third or second and third parts after modifiying some of the intermediate files. It seems like this might also be accomplished by somehow marking that some input files should be substituted instead of using the outputs of some of the steps in the workflow. Anyway, I've been unable to find a simple way of doing this.. I could make each part of the workflow a tool, but if I also wanted to expose the tools used in each part, I would be duplicating those invocations and increasing the maintenance burden. I could also make separate workflows for parts 1+2+3, 2+3, and 3, but that would also be duplicating work and increasing the maintenance burden. I could also make this three completely separate workflows, but that would mean that the user would have to remember to run each of these separately. Each part can take a very long time, so it would be useful to have this set up so that a user can start from the first part on a Friday and have the output from the third part available on Monday. Thanks in advance for any help, ~Aaron

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Nested conditionals
by Joachim Jacob 13 Apr '12

13 Apr '12

Hello, I am building a tool config, and I am looking for a way to have nested conditionals being automatically selected based on a previous conditional. Schematically it looks like this: Choose: option 1 or option 2 if option 1: no extra parameters if option 2: extra parameters to set Choose: additional option A or B if additional option A: no extra parameters if additional option B: set extra parameter Choose: option 1 or option 2 (<--------------) if option 1: one extra parameter to set if option 2: two other extra parameters to set Nested options are possible (indicated by <----------------). However, instead of again choosing the same option as in the first conditional, the outcome of the nested conditional should be the same already known. It is no option to reverse conditional A/B with conditional 1/2. In Galaxy syntax it looks like: (note that the last, nested, conditional is the same as the first conditional) <conditional name='*condition12*'> <param name="condition" type="select"> <option value="1" selected="True">1</option> <option value="2" >2</option> </param> <when value='1'/> <when value='2'> <param name='extra1' .../> <param name='extra2' .../> </when> </conditional> <conditional name="conditionAB"> <param name="condition" type="select"> <option value="A" selected="True">A</option> <option value="B">B</option> </param> <when value="A"/> <when value="B"> <param name="extra4" .../> <conditional name='*condition12*'> <param name="condition" type="select"> <option value="1" selected="True">1</option> <option value="2" >2</option> </param> <when value='1'> <param name='extra5' .../> </when> <when value='2'> <param name='extra6' .../> <param name='extra7' .../> </when> </conditional> </conditional> The goal is to get automatically the nested conditional right (condition12), based on the selection the user makes in the first conditional. Any hint on how to get this right? Regards, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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Installation issue...
by Gregory Miles 12 Apr '12

12 Apr '12

Hello, I am trying to install Galaxy on Linux. I ran the "sh run.sh" command and was greeted with the following error: File "/install_folder/galaxy-dist/lib/galaxy/datatypes/registry.py", line 146 finally: ^ SyntaxError: invalid syntax I am using Python version 2.7.1 and was hoping that anyone who has seen this before might be able to assist me. Thank you very much in advance for your help. Greg -- Dr. Gregory Miles Bioinformatics Specialist Cancer Institute of New Jersey @ UMDNJ Office: (732) 235 8817

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param type=select and multiple=true
by Yuri D'Elia 12 Apr '12

12 Apr '12

Hi everyone. I'm trying to use a <param type="select" display="checkboxes" multiple="true"> in a tool, but galaxy doesn't seem to work correctly if I "unselect all". This is what I have: <param name="test" type="select" display="checkboxes" multiple="true" label="A test"> <option value="a" selected="true">A</option> <option value="b" selected="true">B</option> <option value="c">C</option> </param> If I "unselect all", execute the tool, and then try to re-run the tool by examining the output dataset, parameter A and B are selected, but they shouldn't! When the history is converted to a workflow this breaks the intent of the user! Second problem: how do I test for single values in the <command> template? Right now I'm (wrongly?) doing: #if 'a' in $test.value: ... #end if but it breaks badly when all values are unselected ("$test.value" does not exist, and thus cheetah fails to compile the template). My solution would be: #set $foo = str($test).split(',') #if 'a' in $foo: #end if but this is _incredibly_ ugly. When I use a multi-select, I often want to see if there's some single parameter in it. Any suggestions?

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GATK tools
by Robert Chase 12 Apr '12

12 Apr '12

Hello, One of our users has been using the GATK (beta) tools on the main instance of galaxy and would like to have them locally accessible. I have looked at the main toolshed but I couldn't find them there. Is there a place I can download the GATK files and xml files? -Rob

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Error on local galaxy using SAM-to-BAM tool on a cluster
by Carlos Borroto 12 Apr '12

12 Apr '12

Hi, I'm running into this error: "Error sorting alignments from (/tmp/5800600.1.all.q/tmpXOc5mD/tmpAZCzt_), " When using SAM-to-BAM tool on a locally install Galaxy using a SGE cluster. I'm using the last version of galaxy-dist. I'm guessing I have a problem with the configuration for the tmp folder. I have this on "universe_wsgi.ini": # Temporary files are stored in this directory. new_file_path = /home/cborroto/galaxy_dist/database/tmp But I don't see this directory being used and from the error looks like /tmp in the node is used. I wonder if this is the problem, as I don't know if there is enough space in the local /tmp directory at the nodes? I ran the same tool in a subset of the same SAM file and it ran fine. Also, I see this in the description of the tool: "This tool uses the SAMTools toolkit to produce an indexed BAM file based on a sorted input SAM file." But what I actually need is to sort a SAM file output from bwa, I haven't found any other way than to converting it to BAM. Looking at "sam_to_bam.py" I see the BAM file will also be sorted. Would it be wrong to feed an unsorted SAM file into this tool? Finally, just to be sure there is nothing wrong with the initial SAM file, I ran "samtools view ..." and "samtools sort ..." on this file manually outside of Galaxy and it ran fine. Thanks in advance, Carlos

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Local display application questions
by Lukasse, Pieter 12 Apr '12

12 Apr '12

Hi Greg, I made a tool for Galaxy which produces a normal XML output file and next to that it also produces a HTML report with some quick summarized details for the user. I could solve this by using 2 output files, but I don't want to keep the history as concise as possible. To I found the option to use "display application". I defined my as below: <display id="sedmatreport" version="1.0.0" name="Show "> <link id="sedmatreport" name="SedMat_report"> <url target_frame="galaxy_main">${BASE_URL}/static/prims/reports/${dataset.id}/sedmat_report.html</url> </link> </display> So in my tool config xml I have the following respective configuration: <command interpreter=" java -jar "> Mytool.jar ...some parameters.... -outReport /galaxy-dist/static/prims/reports/$outputData.dataset.id/sedmat_report.html #end if </command> è This works fine, but I would like to avoid using the static directory. Do you know if there is an alternative web directory configured by default in the Galaxy web-server? è è I also want to avoid the /galaxy-dist/ part in the tool configuration since the Galaxy home directory can vary. Is there a variable which I can use for this? Thanks and regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

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galaxy-dev@lists.bx.psu.edu
by khanjan gandhi 12 Apr '12

12 Apr '12

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