July 2013 - galaxy-dev - lists.galaxyproject.org

Scripts interacting with the database
by Lee Katz 05 Jul '13

05 Jul '13

Sorry for being really verbose on this list recently, but we are making a huge push for Galaxy right now. Hopefully you all aren't annoyed by me yet...! One thing we want to do after a MiSeq run is to run all assemblies and then report certain statistics such as N50. These metrics would then be reported in an exportable spreadsheet for our molecular biologists. I have the scripts ready to calculate these metrics. My questions here are: 1) Is there any kind of existing functionality that is close to what I want? 2) If not, 2a) Is there a way to trigger some scripts for assembly and metrics (and maybe more) once a MiSeq dumps all the data into Galaxy? 2b) Is there a certain convention on interaction with the database? And documentation on that? 2c) Is there an existing convention on reading the Galaxy database, so that I can produce the spreadsheet? Documentation? 2d) Our lab would call this functionality Rover, since it will roam Galaxy looking for and retrieving data (not really a question, but I thought they came up with a good name!) -- Lee Katz, Ph.D.

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Startup problem after upgrade
by Bertrand PITOLLAT 04 Jul '13

04 Jul '13

Hi, I have just upgraded my galaxy instance. When trying to access my galaxy instance home page, I get the following error : 195.221.174.40 - - [02/Jul/2013:15:34:23 +0200] "GET / HTTP/1.1" 500 - "-" "Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/27.0.1453.116 Safari/537.36" Error - <class 'mako.exceptions.TopLevelLookupException'>: Cant locate template for uri 'root/index.mako' URL: http://marmadais.cirad.fr:7090/ File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/web/framework/middleware/ error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/r ecursive.py', line 84 in __call__ return self.application(environ, start_response) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/h ttpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/webapps/galaxy/controller s/root.py', line 39 in index params=kwd ) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/web/framework/__init__.py ', line 957 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/lib/galaxy/web/framework/__init__.py ', line 964 in fill_template_mako template = self.webapp.mako_template_lookup.get_template( filename ) File '/SATA/bioinfo/galaxy_dev/galaxy_dist/eggs/Mako-0.4.1-py2.6.egg/mako/looku p.py', line 221 in get_template "Cant locate template for uri %r" % uri) TopLevelLookupException: Cant locate template for uri 'root/index.mako' Any help welcome. Bertrand.

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Empty & 'no peek' Returned Instead of HTML Output?
by Amanda Zuzolo 04 Jul '13

04 Jul '13

I recently updated my local testing Galaxy install to the latest stable version. When I went to test the working of HTML output in some scripts that worked in previous installs of Galaxy, the latest stable version gave me an empty return with a message of 'no peek' rather than outputting the HTML file with the embedded Javascript functionality. Additionally, the HTML output from previous runs of the same tool no longer shows the Javascript file/functionality when opened from the eye button in Galaxy, but still works fine from the HTML file opened out of the file directory. Any assistance on this issue would be greatly appreciated. -- Amanda Zuzolo Bioengineering Major, George Mason University Metabiome Informatics Group, Environmental Biocomplexity

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sqlite to postgresql conversion
by Lee Katz 03 Jul '13

03 Jul '13

Hi, I am realizing, hopefully not to late, that I need to convert my database to postgresql so that I can have concurrent sessions and all the other goodness that it brings to the table. Is there an easy way to convert? I am trying to do it on the command line, but it isn't working so well. I am kind of new to postgres and even sqlite I tried this dump/import command, but it does not work. It didn't seem to like "PRAGMA" so I removed it (sqlite3 universe.sqlite .dump|grep -v 'PRAGMA'|psql chapman galaxy) 2>&1|less BEGIN NOTICE: CREATE TABLE / PRIMARY KEY will create implicit index "migrate_version_pkey" for table "migrate_version" CREATE TABLE INSERT 0 1 NOTICE: CREATE TABLE / PRIMARY KEY will create implicit index "dataset_pkey" for table "dataset" CREATE TABLE ERROR: column "deleted" is of type boolean but expression is of type integer LINE 1: ...5:50:25.714594','2013-06-28 15:51:00.760008','ok',0,0,0,'/me... ^ HINT: You will need to rewrite or cast the expression. ERROR: current transaction is aborted, commands ignored until end of transaction block ERROR: current transaction is aborted, commands ignored until end of transaction block ERROR: current transaction is aborted, commands ignored until end of transaction block

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samtools BAM to SAM tmp directory
by Matt Shirley 03 Jul '13

03 Jul '13

Is there a reason that the samtools BAM to SAM does not respect the new_file_path set in the config file? The tmp directory handling by different tool wrappers seems to be an issue right now on systems with small system tmp directories. -- Matt Shirley Ph.D Candidate - BCMB Pevsner Lab <http://pevsnerlab.kennedykrieger.org/> Johns Hopkins Medicine

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nglims/removing multiplexing
by Lee Katz 03 Jul '13

03 Jul '13

Hi, I would like to remove the "multiplexed" menu from the nglims sample information form. How would I do that? In our lab, we don't want submitters making their own libraries since they might accidentally use the same barcodes or somehow mess up others' libraries. We want to remove that option altogether. Actually along the same lines, we would like to remove all "services needed" check boxes too and simply have all of the data entry on one page. Thank you for your help. -- Lee Katz, Ph.D.

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Galaxy + google analytics?
by Steve.Mcmahon＠csiro.au 03 Jul '13

03 Jul '13

Has anyone hooked Galaxy up to Google analytics? We get great reporting from the Galaxy reports interface but we don't get number of connections and some other things that Google analytics would give us. :) Sent from my iPad

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Debugging the execution errors of the Python tools
by Hyungro Lee 02 Jul '13

02 Jul '13

Hi, I am new here and trying to use the Galaxy toolkit for my project on the Windows Azure cloud environment. The thing is I got errors when I tested the 101 example on my local machine, so I looked 'stderr' via View details and it only showed 'Killed' which is not much information to do debugging. I looked web logs and found out the execution is : 'python /home/.../galaxy-dist/tools/new_operations/gops_join.py /home/.../galaxy-dist/database/files/000/dataset_1.dat /home/.../galaxy-dist/database/files/000/dataset_2.dat /home/.../galaxy-dist/database/files/000/dataset_3.dat -1 1,2,3,6 -2 1,2,3,6 -m 1 -f none' which is about joining two datasets. I believe the input data sets and the parameters are okay since I tested it on the galaxy public server. To get more debugging information, I tried to run the job on shell but got same results, Killed. I was wondering is there a way that I can get more information about the execution of the tool other than looking into the source code line by line? That might be helpful to figure out what I am doing wrong for this test. Thanks, Hyungro

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error while writing to pdf in python
by vijayalakshmi 02 Jul '13

02 Jul '13

Hi, I am writing a python script that will take in two parameters (an input file and an ouput file name) , plot a graph and output it to the filename specified. PYTHON SCRIPT #!/usr/bin/python import sys import numpy as np import matplotlib.pyplot as plt input_file = sys.argv[1] output_file = sys.argv[2] mydata = np.loadtxt(input_file) plt.figure(1) plt.plot(mydata[:,0],mydata[:,1],label = "Feature"); plt.plot(mydata[:,0],mydata[:,2], label = "Variance"); plt.xlabel('Distance from feature(bp)'); plt.ylabel('Score'); plt.title(sys.argv[1]); plt.legend(loc="best") plt.savefig(output_file) SAMPLE COMMAND : <command interpreter="python"> plot.py $ref_filename $out_file1 </command> <inputs> <param name="ref_filename" type="data" format="gen,txt,gtf,bed" label="Reference/Coordination file" help="Choose a reference file"/> </inputs> <outputs> <data name="out_file1" format="pdf" /> </outputs> When I run this, I am getting the following error. File "/panfs/panfs.ccr.buffalo.edu/projects/mjbuck/galaxy/CistromeAP/tools/ArchTex/plot.py", line 22, in <module> plt.savefig(output_file) File "/data/apps/python/lib/python2.6/site-packages/matplotlib/pyplot.py", line 345, in savefig return fig.savefig(*args, **kwargs) File "/data/apps/python/lib/python2.6/site-packages/matplotlib/figure.py", line 990, in savefig self.canvas.print_figure(*args, **kwargs) File "/data/apps/python/lib/python2.6/site-packages/matplotlib/backend_bases.py", line 1399, in print_figure '%s.' % (format, ', '.join(formats))) ValueError: Format "dat" is not supported. Supported formats: emf, eps, pdf, png, ps, raw, rgba, svg, svgz. I don't know how to make the script extract ".pdf" from the ".dat" Thanks, VJ.

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Re: [galaxy-dev] [Galaxy-gcc2013] Strange behaviour with galaxy history
by Ambrose Andongabo (RRes-Roth) 02 Jul '13

02 Jul '13

Dear Carl, The javascript console displayed no errors. Below is the output of hg summary [root@vnc galaxy-dist]# hg summary not trusting file /home/data/galaxy-python/galaxy-dist/.hg/hgrc from untrusted user andongab, group csys not trusting file /home/data/galaxy-python/galaxy-dist/.hg/hgrc from untrusted user andongab, group csys parent: 10002:9d42f1e32efb For user impersonation, fully log the admin out prior to assuming user persona to avoid any history/session corruption. branch: stable commit: 241 unknown (clean) update: (current) As for the galaxy log, there is no error 149.155.13.62 - - [02/Jul/2013:15:40:33 +0100] "GET /api/histories/2d89e36a8c9b5508 HTTP/1.1" 200 - "http://vnc:8080/history" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:22.0) Gecko/20100101 Firefox/22.0" 149.155.13.62 - - [02/Jul/2013:15:40:37 +0100] "GET /api/histories/2d89e36a8c9b5508 HTTP/1.1" 200 - "http://vnc:8080/history" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:22.0) Gecko/20100101 Firefox/22.0" 149.155.13.62 - - [02/Jul/2013:15:40:42 +0100] "GET /api/histories/2d89e36a8c9b5508 HTTP/1.1" 200 - "http://vnc:8080/history" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:22.0) Gecko/20100101 Firefox/22.0" I hope this helps Thanks Ambrose From: Carl Eberhard [mailto:carlfeberhard@gmail.com] Sent: 02 July 2013 15:33 To: Ambrose Andongabo (RRes-Roth) Cc: galaxy-dev(a)lists.bx.psu.edu Subject: Re: [Galaxy-gcc2013] Strange behaviour with galaxy history Hi, Ambrose A couple of places to start: Did the javascript console (in Firefox: Tools->Web Developer->Web Console) display any errors when you reloaded the failing saved history page? What does is the output of 'hg summary' when run in a terminal from your Galaxy root directory? I believe you mentioned there were no 'ERROR' messages in the Galaxy log; is this correct? Thanks for the report. (I'm moving this to the galaxy-dev mailing list). Carl On Tue, Jul 2, 2013 at 3:50 PM, Ambrose Andongabo (RRes-Roth) <Ambrose.Andongabo(a)rothamsted.ac.uk<mailto:Ambrose.Andongabo@rothamsted.ac.uk>> wrote: Dear All, I updated my local galaxy instance yesterday and all my users cannot access their saved histories. When they click on saved histories all they get is an empty page. Checking the database, all the histories are there. I cleared the browser cache as many suggested but no luck yet. Any ideas of what can be done?? Thanks Ambrose -- This message has been scanned for viruses and dangerous content by MailScanner, and we believe but do not warrant that this e-mail and any attachments thereto do not contain any viruses. However, you are fully responsible for performing any virus scanning. _______________________________________________ Galaxy-gcc2013 mailing list Galaxy-gcc2013(a)lists.bx.psu.edu<mailto:Galaxy-gcc2013@lists.bx.psu.edu> http://lists.bx.psu.edu/listinfo/galaxy-gcc2013 -- This message has been scanned for viruses and dangerous content by MailScanner<http://www.mailscanner.info/>, and we believe but do not warrant that this e-mail and any attachments thereto do not contain any viruses. However, you are fully responsible for performing any virus scanning. -- This message has been scanned for viruses and dangerous content by MailScanner, and we believe but do not warrant that this e-mail and any attachments thereto do not contain any viruses. However, you are fully responsible for performing any virus scanning.

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