- galaxy-dev - lists.galaxyproject.org

Cloudman - is it possible to still use depreciated AMIs ?
by Ravpreet Setia 24 Jul '13

24 Jul '13

I tried launching an instance specifying "ami-da58aab3" as the AMI but I am unable to SSH or access Cloudman using the instance's URL.

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Bug report
by Jianxin Wang 24 Jul '13

24 Jul '13

Hi Galaxy dev team, I'm trying to the you galaxy server to do NGS peak calling: Tools -> NGS: Peak Calling -> MACS<https://main.g2.bx.psu.edu/tool_runner?tool_id=peakcalling_macs> Model-based Analysis of ChIP-Seq. However, the page won't allow me enter the input files: the drop-down selection box won't show anything when clicked. Same problem for the ChIP-Seq Control File selection box. Please take a look and email me back if problem is fixed. Jianxin Wang, PhD Computational Biologist jianxin.wang(a)oicr.on.ca Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Tel: 416-673-8569 www.oicr.on.ca<http://www.oicr.on.ca> This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.

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Test ToolShed repository_dependencies.xml processing
by Peter Cock 24 Jul '13

24 Jul '13

Hi Gred, I'm trying to update this repository (initially just to switch my README file to reStructuredText as the current plain text is not being rendered nicely): http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss Uploading my new tar-ball failed: Internal Server Error Galaxy was unable to sucessfully complete your request URL: http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=8067bb858e913… Module galaxy.web.framework.middleware.error:149 in __call__ >> app_iter = self.application(environ, sr_checker) Module paste.debug.prints:106 in __call__ >> environ, self.app) Module paste.wsgilib:543 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:84 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request >> body = method( trans, **kwargs ) Module galaxy.web.framework:98 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.tool_shed.controllers.upload:120 in upload >> self.upload_tar( trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ) Module galaxy.webapps.tool_shed.controllers.upload:341 in upload_tar >> altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name ) Module tool_shed.util.commit_util:243 in handle_repository_dependencies_definition >> raise Exception( exception_message ) Exception: The repository_dependencies.xml file contains an invalid <repository> tag. The tag is missing the required name attribute. The tag is missing the required owner attribute. The XML does have a name tag, it deliberately omits the ToolShed and revision as I want these fields to be auto-filled: $ more repository_dependencies.xml <?xml version="1.0"?>  <repositories description="This requires Biopython as a dependency.">  <repository owner="biopython" name="package_biopython_1_61" /> </repositories> Peter

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Disable cheetah filtering
by Joachim Jacob | VIB | 24 Jul '13

24 Jul '13

Hi all, A Cheetah question: when I enter ";" as a value in a text box of a tool (stored in $exp), Cheetah prints this as "X", and passed this string to the tool. How to disable this behaviour in Cheetah? I have tried to play with #filter directives, but to no avail. Thanks, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team

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Local Instance: BWA, Sam-to-Bam, file upload, filter Sam
by Moritz Juchler 24 Jul '13

24 Jul '13

Hello Ladies and Gentlemen, I am Moritz Juchler from University Heidelberg. For my Bachelor thesis I have to setup Galaxy to find SNP's in genomes from hcc patients. I have a 64-bit openSuse 11.3 server on which I installed Galaxy locally, since we have a) very large files (>30GB per patient) and b) the data is protection sensitive. I have to run this pipeline: > http://www.nature.com/ng/journal/v44/n6/extref/ng.2256-S1.pdf 1. Which version of BWA should I use? The current gives me the EoF error and the 0.5.9. gives me "missing argument -I" 2. Originally I had this workflow to start with https://main.g2.bx.psu.edu/u/mj--/w/ngs , but I at the sam-to-bam conversion I get the "sequences are not currently available for specified build" error when using "locally cached" and I can't figure out how to use the reference file hg19.fa without actually uploading it to Galaxy, because I do not have enough space on the filesystem where the Galaxy distribution is placed ( /home). The genedata are all on /genedata. So my question here is: How to use the hg19.fa file placed on another filesystem then the galaxydist? 3. Thus I searched the web and found this workaround: https://main.g2.bx.psu.edu/u/mj--/w/sample-workflow-whole-exome-sequencing which runs fine ONLINE at usegalaxy but produces this error in my local instance Dataset generation errors *Dataset 18: Filter SAM on data 7* Tool execution generated the following error message: Traceback (most recent call last): File "/home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py", line 148, in <module> if __name__ == "__main__": main() File "/home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py", line 137, in main flags = int( fields[flag_col] ) IndexError: list index out of range So thats my 3rd question: How to solve this error? I didnt find anything online. Best Moritz

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GATK fasta file missing ERROR
by Sridhar Srinivasan 24 Jul '13

24 Jul '13

Dear Developers, I am GATK (beta ) Unified Genotyper module to get the indels and SNP. I placed the jar file in (/galaxy-dist/tool-data/shared/jars/gatk) and i link the reference genome in .loc file (gatk_sorted_picard_index.loc). I could see the Name i mentioned in the .loc file is appearing in the galaxy page while choosing the Reference genome. Now while running GATK in galaxy , The command runs for a while and gives ERROR as i am getting ERROR as *(The fasta file you specified (/tmp/tmp-gatk-Jjg9Mi) does not exist.)* Could anybody suggest on the same.. Thanks Sridhar

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Bowtie2 error: Creates a 62 kb file.
by Perez, Ricardo 24 Jul '13

24 Jul '13

Dear all, Today we ran some problems when running bowtie2. When we run bowtie2, the run manages to complete. However, bowtie2 creates a 62kb file. The error log that we get is the following: galaxy.jobs DEBUG 2013-07-23 17:09:42,378 (1483) Persisting job destination (destination id: local:///) galaxy.jobs.handler INFO 2013-07-23 17:09:42,392 (1483) Job dispatched galaxy.tools DEBUG 2013-07-23 17:09:42,556 Building dependency shell command for dependency 'bowtie2' galaxy.tools WARNING 2013-07-23 17:09:42,556 Failed to resolve dependency on 'bowtie2', ignoring galaxy.tools DEBUG 2013-07-23 17:09:42,556 Building dependency shell command for dependency 'samtools' galaxy.tools WARNING 2013-07-23 17:09:42,556 Failed to resolve dependency on 'samtools', ignoring galaxy.jobs.runners.local DEBUG 2013-07-23 17:09:42,626 (1483) executing: bowtie2 --version &> /usr/local/galaxy/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_1483; python /usr/local/galaxy/galaxy-dist/tools/sr_mapping/bowtie2_wrapper.py --num-threads="4" --output=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1673.dat --indexes-path="/data/db/fungidb/Ncrassa_OR74A/bowtie2/Ncrassa_wt_Chr01.Chr07.+ChrM.+rDNA_v12" --single-paired=paired --input1=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1668.dat --input2=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1669.dat -I 0 -X 250 --settings=preSet galaxy.jobs DEBUG 2013-07-23 17:09:42,696 (1483) Persisting job destination (destination id: local:///) galaxy.jobs.runners.local DEBUG 2013-07-23 17:09:42,766 execution finished: bowtie2 --version &> /usr/local/galaxy/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_1483; python /usr/local/galaxy/galaxy-dist/tools/sr_mapping/bowtie2_wrapper.py --num-threads="4" --output=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1673.dat --indexes-path="/data/db/fungidb/Ncrassa_OR74A/bowtie2/Ncrassa_wt_Chr01.Chr07.+ChrM.+rDNA_v12" --single-paired=paired --input1=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1668.dat --input2=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1669.dat -I 0 -X 250 --settings=preSet galaxy.jobs.runners DEBUG 2013-07-23 17:09:42,850 executing external set_meta script for job 1483: /usr/local/galaxy/galaxy-dist/set_metadata.sh ./database/files /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483 . /usr/local/galaxy/galaxy-dist/universe_wsgi.ini /usr/local/galaxy/galaxy-dist/database/tmp/tmpUiqpPD /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/galaxy.json /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_in_HistoryDatasetAssociation_1767_wqhEmr,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_kwds_HistoryDatasetAssociation_1767_qVZjpG,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_out_HistoryDatasetAssociation_1767_vIfpRO,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_results_HistoryDatasetAssociation_1767_UNl6OR,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_override_HistoryDatasetAssociation_1767_MZilrL 165.91.11.135 - - [23/Jul/2013:17:09:43 -0500] "GET /api/histories/ca8efa3c47500414 HTTP/1.1" 200 - "http://galaxy.tamu.edu/history" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.22 (KHTML, like Gecko) Ubuntu Chromium/25.0.1364.160 Chrome/25.0.1364.160 Safari/537.22" 165.91.11.231 - - [23/Jul/2013:17:09:43 -0500] "GET /history HTTP/1.1" 200 - "http://galaxy.tamu.edu/tool_runner/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.71 Safari/537.36" 165.91.11.231 - - [23/Jul/2013:17:09:43 -0500] "GET /api/histories/1ab12f1e464820dd HTTP/1.1" 200 - "http://galaxy.tamu.edu/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.71 Safari/537.36" 165.91.11.231 - - [23/Jul/2013:17:09:43 -0500] "GET /history/get_display_application_links HTTP/1.1" 200 - "http://galaxy.tamu.edu/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.71 Safari/537.36" galaxy.jobs.runners DEBUG 2013-07-23 17:09:44,457 execution of external set_meta for job 1483 finished galaxy.datatypes.metadata DEBUG 2013-07-23 17:09:44,545 loading metadata from file for: HistoryDatasetAssociation 1767 We currently have the most recent version of bowtie2 and samtools. Anyone know how to fix this? Thank you for your time, --Ricardo Perez

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workflow: default parameters
by Keilwagen, Jens 24 Jul '13

24 Jul '13

Hi guys, when building workflows we can choose for each parameter whether to 'set at runtime' or to 'set in advance' (when creating or editing the workflow). We are looking for a possiblity to set a default value that is used (only) for the workflow, i.e., we like to specify a value that might be used by most users, but might be altered by expert users. This value might be different from the default value of the corresponding tool. So far, we did not find any possiblity. Thanks for any help. Best regards, Jens

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Cloudman master cannot connect to volume at start-up
by Ravpreet Setia 24 Jul '13

24 Jul '13

* This is what has been reported by the cluster status log: * * 20:01:14 - Master starting * 20:01:16 - Trouble getting volume reference for volume vol-91cfd1cb: EC2ResponseError: 400 Bad RequestInvalidVolume.NotFoundThe volume 'vol-91cfd1cb' does not exist.9179663c-c5ec-4e90-88ff-ecf606b5e9a6 * 20:01:16 - Attempting to connect to a non-existent volume vol-91cfd1cb * 20:01:16 - Error processing filesystems in existing cluster configuration: 'NoneType' object has no attribute '__getitem__' * 20:01:16 - ***** Manager failed to start ***** Any suggestions?

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RFC: Cheetah template in tool_dependencies.xml
by Björn Grüning 23 Jul '13

23 Jul '13

Hi, I was thinking how to tackle the build failures like the atlas library on OS-X or the ones from xlib and ease the writing of the shell_command a little bit. Dave B did some fancy shell scripting in 'package_emboss_5_0_0' and I was also sometimes forced to use some bash tricks. What about to make that more easy and powerful, and as a plus more consistent with the tool-command tag, and use cheetah for that kind of work. Something like that could work easily: #if ${os.environ}.getVar('X11_LIB_DIR', None): ./configure ... --x-includes=.... #else: ./configure #end if Also we could define some reserved variables like $__is64__ and cheetah evaluate that. $INSTALL_DIR and $REPOSITORY_DIR can also be a cheetah variable and we do not need to replace it later manually. What do you think any comments? If no one has any objections I can try to implement an <action type="cheetah_command">. Thanks, Björn

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