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

Tool syntax: How to get history name?
by Louise-Amélie Schmitt 18 Apr '12

18 Apr '12

Hi everyone, I as wondering if there was a way to get the history name of an input dataset within a tool (i.e. in the cheetah between the <command> tags), is there? Thanks, L-A

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Tophat output
by Xu, Jianpeng 18 Apr '12

18 Apr '12

Hi, I have installed local galaxy. I used the Tophat to do the RNA-seq alignment and got a output file: splice junction in bed format. I can not understand it clearly. What does the number 17, 14 ... in the column 5 mean ? What does the 87,93 mean ? What does the 0, 4787 mean ? Can you explain a little bit to me ? Which tool can be used to view this file ? Thanks, track name=junctions description="TopHat junctions" chr20 199821 204701 JUNC00000001 17 - 199821 204701 255,0,0 2 87,93 0,4787 chr20 204631 205520 JUNC00000002 14 - 204631 205520 255,0,0 2 96,87 0,802 chr20 205428 205775 JUNC00000003 9 - 205428 205775 255,0,0 2 92,91 0,256 chr20 205699 205958 JUNC00000004 15 - 205699 205958 255,0,0 2 87,92 0,167 chr20 205929 207067 JUNC00000005 31 - 205929 207067 255,0,0 2 95,97 0,1041 chr20 206977 207909 JUNC00000006 19 - 206977 207909 255,0,0 2 93,97 0,835 chr20 207884 212679 JUNC00000007 15 - 207884 212679 255,0,0 2 87,76 0,4719 chr20 207910 218238 JUNC00000008 1 - 207910 218238 255,0,0 2 61,39 0,10289 chr20 212628 218293 JUNC00000009 28 - 212628 218293 255,0,0 2 94,94 0,5571 ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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How to get a local file into the dataset window/browser?
by Brian Luerman 18 Apr '12

18 Apr '12

I have BAM files sitting in database/files that I want to automatically (ie: not through the Upload File tool) import/display via a tool/script/process other in the dataset pane (sorry, not sure of proper terminology, but the History/right side pane). How do I locate these files and display/load them via a tool or script? Is there a script or particular system call, a change to data_source.py or anything that will make them show up? Thanks so much, Brian

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Re: [galaxy-dev] Workflow import error
by Greg Von Kuster 17 Apr '12

17 Apr '12

Hi Robert, I've cc'd the galaxy-dev list on this reply since the workflow components are primarily supported by other Galaxy development team members and I'm not optimally suited to handle this issue. Please keep responses on the galaxy-dev mail list so others that are interested can follow the entire thread. You should receive a response on this soon. Thanks for sending your messages, Greg Von Kuster On Apr 16, 2012, at 5:53 PM, Robert Chase wrote: > Hi Greg, > > When I upload my workload ga file to galaxy, I get a screen saying that some of the tools in the workflow are not available in this instance of galaxy, specifically fastqc. I downloaded fastqc into my tools directory and restarted galaxy, but when I tried to re-upload the workflow it complained again that fastqc wasn't available. Fastqc does in fact load in the tools sidebar, but when I try to run it I get the following: > > An error occurred running this job: Fastq failed. > Error executing FastQC. /bin/sh: fastqc: command not found > > -Rob > > On Mon, Apr 16, 2012 at 10:21 AM, Greg Von Kuster <greg(a)bx.psu.edu> wrote: > Hi Rob, > > When you import a workflow into a Galaxy instance, the instance must have all tools required by the workflow available in its tool panel. I've only seen this error when the workflow requires a tool that is not available, so can you let us know if this is the case? > > Thanks, > > Greg Von Kuster > > On Apr 16, 2012, at 10:07 AM, Robert Chase wrote: > >> Hi Greg, >> >> After I modified the modules.py file that bug went away, but now I'm getting a new error: >> >> Module galaxy.web.base.controller:420 in get_stored_workflow_steps view >> << module = module_factory.from_workflow_step( trans, step ) >> #Check if tool was upgraded >> step.upgrade_messages = module.check_and_update_state() >> # Any connected input needs to have value DummyDataset (these >> # are not persisted so we need to do it every time)>> step.upgrade_messages = module.check_and_update_state() >> AttributeError: 'NoneType' object has no attribute 'check_and_update_state' >> >> -Rob >> >> On Mon, Apr 16, 2012 at 9:19 AM, Robert Chase <rerpc(a)channing.harvard.edu> wrote: >> Thanks Greg, >> >> I'll try to merge the change into my version. >> >> -Rob >> >> >> On Mon, Apr 16, 2012 at 9:18 AM, Greg Von Kuster <greg(a)bx.psu.edu> wrote: >> Hello Robert, >> >> Thanks for reporting this issue - it has been fixed in change set 7038:1fdcce63a06f, which is currently available only in our central repository. It will be available in the dist in the next update. >> >> Greg Von Kuster >> >> On Apr 13, 2012, at 5:22 PM, Robert Chase wrote: >> >>> Hello All, >>> >>> I'm pretty sure I found a bug in the main galaxy distribution. The following code diff shows the introduction of the line >>> >>> tool_version = self.__get_tool_version( trans, tool_id ) >>> >>> but if you look at the function definition containing that line, you see >>> >>> def from_workflow_step( Class, trans, step ): >>> which does not half a self in it. Then we get an error. >>> >>> https://bitbucket.org/galaxy/galaxy-dist/diff/lib/galaxy/workflow/modules.p… >>> >>> -Rob >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> >>> http://lists.bx.psu.edu/ >> >> >> > >

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Potential database corruption with local galaxy instance
by Simon Lank 17 Apr '12

17 Apr '12

Hi Dev Team. We've been running a local galaxy instance on an OS X Xserve for the past several years. You guys have been very helpful with problems we've had in the past and I'm hoping you can point us in the right direction for our current suite of server errors. We upgraded to the latest version with Hg over a week ago, and did not notice any problems, either with our custom tools or with the API scripting that we use to recursively execute workflows. However, for reasons we do not yet understand, yesterday the server started throwing errors at us, most of which seem to be related to our galaxy postgres database. After many hours of troubleshooting we were able to restore our local server to a point where we can download previously created datasets and export our workflows (which was a huge relief). My PI (Dr. David O'Connor who is cc'd here) did most of the troubleshooting to get us to that point and can provide greater details on that if needed. However, we still cannot execute tools on any datasets. We cannot upload new datasets, however we can pull them into the current history from previously created data libraries. We feel there may be duplication or corruption in the postgres database. It appears that the Galaxy can pull previous data from the database, but that sqlalchemy cannot insert properly. Is there any way you know of to cleanup our database if this is the case? I see the manage_db.py script in the server directory, but do not want to do anything that will further complicate the problem. To check if there were dependency issues (as opposed to database problems) we downloaded and installed a clean server version, which is working fine with the built-in sql-light database. We are basically looking for advice on: 1) If this is a database issue, can it be fixed using any of Galaxy's scripts or tools? 2) What other tests can we try to determine if this is not a database problem? and 3) Is it possible to migrate our existing database to a clean install if there are deeper structural problems with our local instance. I don't want to send you guys all of our errors since I am sure you are busy (unless that would be helpful and you could take the time to look at them), but I've included a representative error that occurs when trying to execute a tool below. Thanks so much for your help in the past and any advice you might have. Simon Lank Research Specialist O'Connor Lab, WNPRC 555 Science Dr. Madison WI (608) 265-3389 Error executing tool: (ProgrammingError) column "params" of relation "job" does not exist LINE 1: ...ob_runner_external_id, object_store_id, imported, params) VA... ^ 'INSERT INTO job (id, create_time, update_time, history_id, library_folder_id, tool_id, tool_version, state, info, command_line, param_filename, runner_name, stdout, stderr, traceback, session_id, user_id, job_runner_name, job_runner_external_id, object_store_id, imported, params) VALUES (%(id)s, %(create_time)s, %(update_time)s, %(history_id)s, %(library_folder_id)s, %(tool_id)s, %(tool_version)s, %(state)s, %(info)s, %(command_line)s, %(param_filename)s, %(runner_name)s, %(stdout)s, %(stderr)s, %(traceback)s, %(session_id)s, %(user_id)s, %(job_runner_name)s, %(job_runner_external_id)s, %(object_store_id)s, %(imported)s, %(params)s)' {'stdout': None, 'create_time': datetime.datetime(2012, 4, 17, 16, 11, 22, 676616), 'id': 142237L, 'runner_name': None, 'user_id': 3, 'tool_version': '1.0.0', 'command_line': None, 'state': 'new', 'params': None, 'job_runner_name': None, 'tool_id': 'Show beginning1', 'update_time': datetime.datetime(2012, 4, 17, 16, 11, 22, 676632), 'history_id': 2330, 'param_filename': None, 'imported': False, 'object_store_id': None, 'info': None, 'traceback': None, 'session_id': 3272, 'library_folder_id': None, 'stderr': None, 'job_runner_external_id': None}

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Re: [galaxy-dev] Proteomics category on main toolshed?
by Greg Von Kuster 17 Apr '12

17 Apr '12

Thanks Ira, Just so you know, the Galaxy functional test framework now supports testing installed tools if the repository tools include tests and test datasets are included in the repository in a test-data subdirectory. Here is the relevant section of the tool shed wiki describing this: http://wiki.g2.bx.psu.edu/Tool%20Shed#Using_Galaxy.27s_functional_test_fram… Greg On Mar 29, 2012, at 6:53 PM, Ira Cooke wrote: > Dear Greg, > > Thanks very much for that. I'll do a last proof-read of the tools and upload later on today. > > We're working on some better documentation ... to get it all working takes some extra setup steps on the part of the user. > > Ira > > > On 30/03/2012, at 9:49 AM, Greg Von Kuster wrote: > >> Hello Ira, >> >> I've added the category to the main tool shed. Thanks for the request and your upcoming contributions! >> >> Greg Von Kuster >> >> On Mar 29, 2012, at 5:33 PM, Ira Cooke wrote: >> >>> Dear list, >>> >>> I would like to add a suite of proteomics tools to the toolshed but there is currently no suitable category. >>> >>> Would it be possible to add a category called Proteomics? >>> >>> Thanks >>> Ira >> > >

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Create and Transfer Galaxy Page
by Todd Oakley 17 Apr '12

17 Apr '12

Hi all, [Not sure if this is better suited to galaxy-dev or -user, so I'm sending to both]. I want to document some Galaxy analyses and results for a paper I'm submitting - something like the 'Windshield Splatter' supplement: https://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter. My question is - can I create a Galaxy 'Published Page' from my local Galaxy instance/histories, and then transfer that page to the main Galaxy instance? The reason is that I cannot make my local Galaxy instance public, as I am using a campus resource to host our galaxy. If this is possible, how can I do that? If not, any other ideas? Also, are there any tutorials/pages on how to create Published Pages in Galaxy in the first place? Thanks for reading and best wishes, Todd -- *************************************** Todd Oakley, Professor Ecology Evolution and Marine Biology University of California, Santa Barbara Santa Barbara, CA 93106 USA *************************************** Lab Website <http://labs.eemb.ucsb.edu/oakley/todd/> Twitter: @UCSB_OakleyLab *Recent Papers: * * Cnidocyte discharge regulated by opsin and light BMC Biology Paper <http://tinyurl.com/7dajl2q> | Scientific American Write-up <http://blogs.scientificamerican.com/science-sushi/2012/03/05/hydra-watch-wh…> * Sponge Larvae Could be Guided by Cryptochrome J Exp Biol. Paper <http://jeb.biologists.org/content/215/8/ii> | Nature News <http://www.nature.com/nature/journal/v484/n7393/full/484145d.html>

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/bin/sh: samtools: not found
by zhengqiu cai 17 Apr '12

17 Apr '12

Hi All, I submitted a job to convert sam to bam, and the job was running forever without outputing the result. I then checked the log, and it read: Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 336, in finish_job drm_job_state.job_wrapper.finish( stdout, stderr ) File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/jobs/__init__.py", line 637, in finish dataset.set_meta( overwrite = False ) File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/model/__init__.py", line 875, in set_meta return self.datatype.set_meta( self, **kwd ) File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/datatypes/binary.py", line 179, in set_meta raise Exception, "Error Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found It means that the samtools is not in the PATH. I tried to set the PATH in a couple of methods according the Galaxy documentation: 1. put the path in the env.sh in the tool directory and symbolink default to the tool directory, e.g. default -> =/mnt/galaxyTools/tools/samtools/0.1.18 2. put -v PATH=/mnt/galaxyTools/tools/samtools/0.1.18 in ~/.sge_request 3. put -v PATH=/mnt/galaxyTools/tools/samtools/0.1.18 in /path/sge_request none of them worked, and I got the above same problem. Then I checked the job log file in the job_working_directory, and it read: Samtools Version: 0.1.18 (r982:295) SAM file converted to BAM which shows that sge knows the PATH of samtools. To double check it, I added samtools index to Galaxy, and it worked well. I am very confused why SGE knows the tool path but cannot run the job correctly. The system I am using is ubuntu on EC2. I checked out the code from galaxy-dist on bitbucket. Other tools such as bwa and bowtie worked well using the same setting method(put env.sh in the tools directory to set the tool path) Thank you very much for any help or hints. Cai

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Adapter Clipping tool
by Xianrong Wong 17 Apr '12

17 Apr '12

Dear all, I'm trying to clip adapter sequences off the ends of my sequencing reads. I tested the tool by purposefully adding parts of the adapter sequence or the full adapter sequence to the 3' end. The tools is amazing in detecting these sequences. However, I encountered some problems. On top of detecting my adapter sequence I found that unrelated sequences are sometimes trimmed off at the 3' end. For example the sequence "TATCCACGTGCTC" was trimmed off even though it does not match the adapter sequence GATCCTCGGCCGCGACC at all. Is there a way to increase the fidelity of the tool? Any comments will be appreciated! Thank you! Best Regards, Jose

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"Fetch taxonomic representation" DOESN'T WORK
by JIE CHEN 17 Apr '12

17 Apr '12

Dear all, I was trying to run the build-in function "Fetch taxonomic representation" on my local instance of Galaxy, however it doesn't work as I expect. The error message is: /bin/sh: taxBuilder: not found Anyone has seen this problem before? Please tell me what to do to solve this problem? A lot of thanks Tyler

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