July 2014 - galaxy-dev - lists.galaxyproject.org

ImportError: No module named galaxy_utils.sequence.fastq
by julie dubois 07 Jul '14

07 Jul '14

Hi, I've this error message when I run groomer. My local instance of galaxy runs on a python virtualenv (python 2.7) and I have make the latest update with : hg pull -u. I've verified and this library is present in my galaxy-dist/lib/galaxy_utils/sequence directory. I've found no other idea than the update on this forum to run groomer correctly, any other idea ? Thanks. Julie

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Question: Problems on Running Functional Tests on an External Instance of Galaxy
by speillet＠jouy.inra.fr 07 Jul '14

07 Jul '14

Hi, I try to apply functional tests of tools against my instance of Galaxy. When I launch run_functional_tests.sh with the default behavior on the local machine for running the tests it works. But when I try to run tests against an external instance deployed on http://138.102.22.90:8080 and configuring environment variables as: GALAXY_TEST_EXTERNAL=1, GALAXY_TEST_HOST=138.102.22.90 and GALAXY_TEST_PORT=8080 and then launch run_functional_tests.sh, I have for answer the error: $ export GALAXY_TEST_EXTERNAL=1 && export GALAXY_TEST_HOST=138.102.22.90 && export GALAXY_TEST_PORT=8080 $ ./run_functional_tests.sh No handlers could be found for logger "functional_tests.py" I use the Galaxy Distribution of June 2, 2014, and my python version is "Python 2.7.5". May I need to do another configurations in my instance fortesting tools on an external instance? Thanks a lot, Stéphane INRA - Unité MIG (Mathématique, Informatique et Génome) F-78352 Jouy-en-Josas stephane.peillet(a)jouy.inra.fr

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Escaped text from input fields
by Renato Alves 05 Jul '14

05 Jul '14

Hi everyone, I'm writing a wrapper that includes one text field. I'm then passing the contents of this field to the underlying tool with a simple: command $textfield However when a user inputs something like Test#1 the command ends up as: command Test__pd__1 I did a quick search on the web and it seems to be the name of some escaping function in galaxy. Is there any way I can get the text field content across untouched? Thanks, Renato

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Re: [galaxy-dev] Job execution order mixed-up
by Jean-Francois Payotte 04 Jul '14

04 Jul '14

Hi John, Thank you for your answer and for trying to help. This is greatly appreciated! I didn't really made any progress in tracking down this error, and hopefully this weird behaviour will not happen anymore with the November 4th, distribution. But here are my answers to your questions, in case it would ring a bell: Has this behaviour been reported with any other workflow? It has been reported with 2 different workflows as of now. These 2 workflows doesn't have anything in common, except that they are huge (one of them has 37 steps, producing a total of about 110 datasets). Are you running Galaxy as a single process or multiple processes? If multiple processes, how many web, handler and manager processes do you have and are they all on the same machine? We are running Galaxy in multiple processes with 5 web servers, 3 job handlers and no manager (I believe the manager was rendered obsolete in one of the latest Galaxy distributions). All these processes are run on the same machine. Have you made any modifications to Galaxy that could result in this behaviour? No. What is the value of track_jobs_in_database in your universe_wsgi.ini configuration file? We never touched this part of the configuration file and the line still reads: "#track_jobs_in_database = None". After reading your answer, I've decided to modify this line to: "track_jobs_in_database = True" Unfortunately, running one of the faulty workflows several times (5x), I noticed that one of them was still showing this strange behaviour where some jobs were executed before their inputs were ready. Do you think this issue could be related to the fact that we are using Galaxy with the multiple processes configuration? We implemented this configuration some time ago because some of our users were complaining about the slow responsiveness of the web interface. Would you recommend using Galaxy without the multiple processes configuration? (Lets say if updating to November 4th distribution doesn't fix this issue) I guess you are probably using the multiple processes configuration as well on Galaxy main? Thanks again for your help! Jean-François ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Posted by John Chilton on Nov 09, 2013; 2:50pm Hello Jean-François, Have you made any progress tracking down this error? This appears very serious, but to tell you the truth I have no clue what could cause it. The distribution you are using is pretty old at this point I feel like if it was a bug the exhibited under relatively standard parameter combinations someone else would have reported it by now. Can you tell me some things: has this been reported with any other workflows? Is there anything special about this workflow? Can you rebuild the workflow and see if the error occurs again? Additional questions if the problem is not restricted to the workflow: are you running Galaxy as a single process or multiple processes? If multiple processes, how many web, handler, and manager processes do you have? Are they all on the same machine? Have you made any modifications to Galaxy that could result in this behavior? What is the value of track_jobs_in_database in your universe_wsgi.ini configuration file? -John On Thu, Nov 7, 2013 at 10:34 AM, Jean-Francois Payotte <[hidden email]> wrote: Dear Galaxy mailing-list, Once again I come seeking for your help. I hope someone already had this issue or will have an idea on where to look to solve it. :) One of our users reported having workflows failing because some steps were executed before all their inputs where ready. You can find a screenshot attached, where we can see that step (42) "Sort on data 39" has been executed while step (39) is still waiting to run (gray box). This behaviour has been reproduced with at least two different Galaxy tools (one custom, and the sort tool which comes standard with Galaxy). This behaviour seems to be a little bit random, as running two times a workflow where this issue occurs, only one time did some steps were executed in the wrong order. I could be wrong, but I don't think this issue is grid-related as, from my understanding, Galaxy is not using SGE job dependencies functionality. I believe all jobs stays in some internal queues (within Galaxy) until all input files are ready, and only then the job is submitted to the cluster. Any help or any hint on what to look at to solve this issue would be greatly appreciated. We have updated our Galaxy instance to August 12th distribution on October 1st, and I believe we never experienced this issue before the update. Many thanks for your help, Jean-François

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Run a tool's workflow one by one ?
by Pat-74100 04 Jul '14

04 Jul '14

Hi ! I have a big workflow and sometime when I launched it, I got an error message for some of my tools : unable to finish job. I think it's maybe Galaxy ran multiple job so I get this error message. I'm looking to run my workflow "step by step". For example this workflow: http://hcsvlab.org.au/wp-content/uploads/2014/02/PsySoundTest1.png I'm looking to run Hilbert THEN FFT THEN SLM and no Hilbert, FFT and SLM at the same time. Is it possible to make a workflow which wait to finish a job before run an another job ? Thanks

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Re: [galaxy-dev] repeat tag enhancement?
by Keilwagen, Jens 04 Jul '14

04 Jul '14

Hi guys, this threads has been inactive for quite a long while. However, I'd like to restart the discussion. There are two alternatives for improving the usability of the repeat tag. 1) If the repeat tag arguments could be populated using white pages and a filter similar to the possibility for workflow, the user would be able to add several inputs at once. 2) If workflows would allow for using multiple (but not fixed number of) inputs obtained via white pages as input of a repeat tag argument of a tool, the user could use the functionality of multiple inputs (white pages) in workflows. I would vote for the second proposal as it allows for building workflows with variable number of inputs (e.g. read mapping and combined SNP calling for a variable number of samples). Workflows with variable number of inputs have been brought up from time to time at several posts or meetings. Hence, solving this could be hitting 2 birds with one stone. However, proposal 2 has the drawback that using repeat tag arguments outside of workflows is still a lot of manual work. This could be circumvented by tiny workflows consisting only of the tool of interest (containing the repeat tag argument). best regards, Jens

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Galaxy/ODoSE - Output accessory orthologous genes ERROR
by Sérgio Miguel Marcelino dos Santos 03 Jul '14

03 Jul '14

Dear Galaxy team, I am having a problem running Galaxy/ODoSE. In the step "Extract & categorize orthologs", I selected the option "Output accessory orthologous genes" but it didn't work and didn't output any file. The stdout contains multiple warnings: ... WARNING 15:18:06 select_taxa.select_genomes_by_ids:33 Could not find genome with BioProject ID 11 in complete genomes table WARNING 15:18:06 select_taxa.select_genomes_by_ids:33 Could not find genome with BioProject ID 10 in complete genomes table WARNING 15:18:06 select_taxa.select_genomes_by_ids:33 Could not find genome with BioProject ID 14 in complete genomes table WARNING 15:18:08 __init__.get_most_recent_gene_name:186 Could not retrieve gene name annotation based on date; returning first gene name annotation instead WARNING 15:18:08 __init__.get_most_recent_gene_name:186 Could not retrieve gene name annotation based on date; returning first gene name annotation instead WARNING 15:18:08 __init__.get_most_recent_gene_name:186 Could not retrieve gene name annotation based on date; returning first gene name annotation instead ... How can I solve this problem? Thank you in advance! Best Regards, Sérgio

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Sort error while running Cuffdiff
by TD 01 Jul '14

01 Jul '14

Hi All -- I'm a novice when it comes to all things programming, but I recently installed my own instance of Galaxy because I'm working with very large datasets. Everything seems to be running OK, but when I attempt to run Cuffdiff (w/ ref. annotation and bias correction from UCSC genome) on output from Tophat2, I get the following error: "*Error: sort order of reads in BAMs must be the same*." I'm perplexed, because I downloaded this output from Tophat2 that I ran on the public server, before putting it through Cuffdiff on my local instance. When I tried running the same files (prior to download) in Cuffdiff on the public server, they ran just fine. So, why do the files run properly when I run them publicly, but not locally? Am I missing some metadata? Is my install not complete? Does the ordering of bam files change when you download them? I've had a hard time finding solutions, so any tips are greatly appreciated. Cheers!

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Tophat for illumina reference genome
by Findlay Bewicke-Copley 01 Jul '14

01 Jul '14

Hello, I've recently set up a local instance of galaxy in our office. I've downloaded the data mangers for Bowtie and Bowtie 2 and have been able to use these to index the reference genomes for both these tools. However our tophat for illumina and tophat 2 installations do not show any reference genomes. I was under the impression that these tools used the same genomes as Bowtie and Bowtie 2 respectively and thought that the data managers would also index the genomes for these tools. Is this correct or will I need to set the indexes up manually using the .loc files? Thanks, Findlay.

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