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

Where is the eye icon for datasets in error state?
by MSc. Sascha Kastens 22 Nov '12

22 Nov '12

Hey devs! It seems that many things related to history datasets has changed since I have updated my local Galaxy instance and the current version. Unfortunately it seems that one cannot "Display data in browser" (eye icon) if the dataset is in error state. Where can I get that feature back? Some of my tools write logging information to a separate logfile which will be in error state if the tool fails but contain useful information. Thanks, Sascha

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Re: [galaxy-dev] [galaxy-user] help
by Jeremy Goecks 21 Nov '12

21 Nov '12

Because your questions are about a local installation of Galaxy, your email is best suited to the galaxy-dev mailing list, so I've moved it there. > 1. FastQC not running . gives an error and doesn’t run on groomed or un-groomed FastQ file. The error message shows in the below pic. I don't see the pic, you probably need to install FastQC: (a) download the tool (b) put the fastqc script in the <galaxy_home>/tool-data/shared/jars/FastQC directory (c) make the script executable: %chmod 777 <galaxy_home>/tool-data/shared/jars/FastQC/fastqc > 2. No reference genomein the drop down list in TOPHAT for illumine tool and TOPHAt2. See the section 'Setting Up the Reference Genomes for NGS Tools' on this page for help setting up genomes/indices: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Best, J.

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Failed to run display.py
by Tom Hait 21 Nov '12

21 Nov '12

Hello, I'm new with Galaxy api. I'm following the ReadMe file in script/api. I'm trying to run: python display.py ff76834f42d18414b4aaed577466ef35 http://0.0.0.0:8080/api/libraries and it doesn't work, it says: HTTP Error 503: Service Unavailable <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" " http://www.w3.org/TR/html4/loose.dtd"> <HTML><HEAD><META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1"> <TITLE>ERROR: The requested URL could not be retrieved</TITLE> <STYLE type="text/css"></STYLE> </HEAD><BODY> <H1>ERROR</H1> <H2>The requested URL could not be retrieved</H2> <HR noshade size="1px"> <P> While trying to retrieve the URL: <A HREF=" http://0.0.0.0:8080/api/libraries?key=ff76834f42d18414b4aaed577466ef35"> http://0.0.0.0:8080/api/libraries?key=ff76834f42d18414b4aaed577466ef35</A> <P> The following error was encountered: <UL> <LI> <STRONG> Connection to 0.0.0.0 Failed </STRONG> </UL> <P> The system returned: <PRE><I> (111) Connection refused</I></PRE> <P> The remote host or network may be down. Please try the request again. <P>Your cache administrator is <A HREF="mailto:root">root</A>. <BR clear="all"> <HR noshade s so I tried to change the URL to: http://localhost:8080, http://127.0.0.1:8080 ... It also didn't work. Any Ideas about could go wrong? Thanks, Tom.

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Multiple language in one tool
by Philipe Moncuquet 20 Nov '12

20 Nov '12

Hi dev, I was wondering if the following is possible or not. What if I want to build a tool that that uses Perl and R at the same time ? If I had to do it on my local machine I would create a pipeline but wouldn't it be cool if a wrapper could use different languages. Philippe

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Direct access the fastq files stored in galaxy server local storage
by Fenglou Mao 20 Nov '12

20 Nov '12

We have a local galaxy server. I know I can get data by ftp, upload directly from browser, or by a URL. If I have some fastq files in the Galaxy server local storage, is it possible to let Galaxy use it directly? Thanks, Fenglou

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NGS assembly?
by Thyssen, Gregory - ARS 20 Nov '12

20 Nov '12

Hello I would like to assemble my Illimuna reads along with some Sanger reads. Is Velvet or ABySS hidden somewhere in the menu? Please advise. Thanks, Gregory Thyssen, PhD Molecular Biologist Cotton Fiber Bioscience USDA-ARS-Southern Regional Research Center 1100 Robert E Lee Blvd New Orleans, LA 70124 gregory.thyssen(a)ars.usda.gov 504-286-4280 This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

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Move files between histories?
by Thyssen, Gregory - ARS 20 Nov '12

20 Nov '12

Hello Is it possible to move a file from one history to another? I have generated BAM files in separate histories that now must be merged. How can I do this without downloading and then uploading the files? Thanks, Gregory Thyssen, PhD Molecular Biologist Cotton Fiber Bioscience USDA-ARS-Southern Regional Research Center 1100 Robert E Lee Blvd New Orleans, LA 70124 gregory.thyssen(a)ars.usda.gov 504-286-4280 This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

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First questions from a new developer
by Joshua Orvis 20 Nov '12

20 Nov '12

I'm building a pipeline which, initially, will use some existing tools and then I plan on adding some of my own. In running this though I've run into a few questions that might have to do with how Galaxy in general works rather than being tool-specific. I've made it up to running Realigner Target Creator (part of GATK tools) and I don't see a convention of specifying what version of GATK it expects to be installed. Then, running the tool failed with "Running with the -et NO_ET or -et STDOUT option requires a GATK Key file." It seems the -et option is hard-coded into the component without passing a key, which has to be applied for. I didn't want this at all, so I modified the following file: galaxy-dist/tools/gatk/realigner_target_creator.xml and removed the following line: -et "NO_ET" ##ET no phone home Then I added the component and tried to run again, still getting the same error. If I removed that line how is it still part of the call? Is Galaxy caching the xml tool files? Also, is there a way to see the precise commands being executed by Galaxy for any particular tool? Thanks - Joshua

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format sensitive tools not working properly after upgrade
by Langhorst, Brad 20 Nov '12

20 Nov '12

I performed an upgrade over the weekend. Since then, I've observed an odd behavior - bowtie2 will not list the new fastqsanger files in my history. It will work with files that had already been groomed before the upgrade. I also see that the groomer is not recognizing fastq files. The format does seem to be correctly set for these datasets. Is there more than one place that a dataset's format is stored (and therefore get out of sync)? Could I have messed up the data types xml file? It looks ok. Seems unlikely that this would be a global problem since nobody else has reported it… but it does seem a bit subtle (only affecting newly tweaked files) Any ideas? Brad -- Brad Langhorst langhorst(a)neb.com<mailto:langhorst@neb.com>

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Unable to run jobs in Galaxy: runners/local.py # stdout_file.close() # python2.7/tempfile.py # self.unlink(self.name) # OSError: [Errno 2] No such file or directory
by Tim te Beek 20 Nov '12

20 Nov '12

Hi all Since updating to the latest Galaxy-dist version, I'm unable to run any jobs. galaxy.jobs.handler INFO 2012-11-20 12:22:09,018 (6403) Job dispatched galaxy.objectstore CRITICAL 2012-11-20 12:22:15,362 /home/galaxy/galaxy-dist/database/job_working_directory/006/6403 delete error [Errno 2] No such file or directory: '/home/galaxy/galaxy-dist/database/job_working_directory/006/6403' CRITICAL 12:22:15 __init__.delete:322 /home/galaxy/galaxy-dist/database/job_working_directory/006/6403 delete error [Errno 2] No such file or directory: '/home/galaxy/galaxy-dist/database/job_working_directory/006/6403' galaxy.jobs.runners.local ERROR 2012-11-20 12:22:15,363 failure running job 6403 Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in run_job stdout_file.close() File "/usr/lib/python2.7/tempfile.py", line 410, in close self.unlink(self.name) OSError: [Errno 2] No such file or directory: '/home/galaxy/galaxy-dist/database/job_working_directory/006/6403/tmpKuTwAJ_stdout' ERROR 12:22:15 local.run_job:134 failure running job 6403 Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in run_job stdout_file.close() File "/usr/lib/python2.7/tempfile.py", line 410, in close self.unlink(self.name) OSError: [Errno 2] No such file or directory: '/home/galaxy/galaxy-dist/database/job_working_directory/006/6403/tmpKuTwAJ_stdout' Exception OSError: (2, 'No such file or directory', '/home/galaxy/galaxy-dist/database/job_working_directory/006/6403/tmpK7i5n4_stderr') in <bound method _TemporaryFileWrapper.__del__ of <closed file '<fdopen>', mode 'w+b' at 0x55b8f60>> ignored galaxy.objectstore CRITICAL 2012-11-20 12:22:15,723 /home/galaxy/galaxy-dist/database/job_working_directory/006/6404 delete error [Errno 2] No such file or directory: '/home/galaxy/galaxy-dist/database/job_working_directory/006/6404' CRITICAL 12:22:15 __init__.delete:322 /home/galaxy/galaxy-dist/database/job_working_directory/006/6404 delete error [Errno 2] No such file or directory: '/home/galaxy/galaxy-dist/database/job_working_directory/006/6404' I'm running the version from ~Nov 6th: 8153:5dcbbdfe1087 tip | Allow rerun to access hidden datasets. I already found this recent issue on the maillinglist which appeared similar, but my problems involve running jobs, not uploading datasets: http://dev.list.galaxyproject.org/Re-Galaxy-at-Duke-td4656946.html My setup involves 1 runner instance and 2 web instances, all inside the same VM, as per my configuration files here: https://trac.nbic.nl/brs2010p33/browser/trunk/galaxy-dist/ The folder /work/project is an sshfs mount to the server running the VM. sshfs#backup@192.168.122.1:/work/odose/ /work/project/ fuse defaults,idmap=user,allow_other,cache=no 0 0 I've setup the following paths to that mounted folder: # Dataset files are stored in this directory. file_path = /work/project/galaxy-dist/database/files # Temporary files are stored in this directory. new_file_path = /work/project/galaxy-dist/database/tmp The job_working_directory is a normal folder in the VM, but I still get the above error. Can anyone tell me what I should do to be able to run jobs in Galaxy again? Best, Tim

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