March 2011 - galaxy-dev - lists.galaxyproject.org

new_file_path vs $TMP
by Louise-Amélie Schmitt 29 Mar '11

29 Mar '11

Hello We managed to install Galaxy according to the unified method, with the runner and the web application running on separate machines sharing by NFS the same storage space where the Galaxy files are. The thing is, the data must be saved in another NFS storage space so we had to define the file paths accordingly, including modifying (and exporting) the TMP environment variables for both machines, so that the temporary directory is in the shared NFS volume meant to host the data. My question is: What exactly is the new_file_path configuration value for since it doesn't seem to have any effect if the TMP environment variable doesn't do the job? Wouldn't there be a solution for using the new_file_path value instead of having to rely on the shell variables for temporary files? Best regards L-A

2 1

Cufflinks v0.9.3 integration
by Ryan Golhar 28 Mar '11

28 Mar '11

Hi all - I'm running Cufflinks 0.9.3 locally in my galaxy instance but it keeps failing because of information cufflinks writes to stderr. cufflinks provides the parameter "-q" to suppress this output. This needs to be included in the cufflinks_wrapper.py file. I've made the following change at about line 90: # Base. cmd = "cufflinks" + + cmd += " -q" + # Add options. Ryan -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information.

2 1

Re: [galaxy-dev] Running a workflow programatically
by Darren Brown 28 Mar '11

28 Mar '11

Hi Dannon, Thanks very much for answering these questions. I think this all I need to get it going. I'll report back soon. Darren On Mar 15, 2011 6:06 PM, "Dannon Baker" <dannonbaker(a)me.com> wrote:

3 7

Restricted user builds
by Dan MacLean (TSL) 28 Mar '11

28 Mar '11

Dear Galaxy, We have an internal installation of Galaxy running very nicely with a fair number of internally generated builds and plenty of data libraries, recently a user asked if it was possible to add a build and restrict to just a few users. Is this possible? I couldn't find any specific documentation on the subject. Thanks for any help Dan

2 1

Galaxy and PBS Pro
by Susan J. Miller 24 Mar '11

24 Mar '11

I've seen posts that some people have been able to use Galaxy with PBS Pro. Our group is trying to do that, but first I tried to run the drmaa-python tutorial scripts. Running script #3 results in a pbs_submit "hook error." We have drmaa version 1.0.6 and PBS Pro 10.2. To those who have galaxy running with PBS Pro, did you first run the drmaa tutorial scripts before integrating galaxy? Can anyone suggest things to try to get around the PBS hook error? Thanks for any help with this. -- Regards, -susan Susan J. Miller Manager, Scientific Data Analysis Biotechnology Computing Facility Arizona Research Laboratories (520) 626-2597

1 0

Re: [galaxy-dev] Balloon tooltips
by Assaf Gordon 24 Mar '11

24 Mar '11

Revisiting the tooltip issue, I'm still looking for the best way to disable them. IMHO a seasoned galaxy user doesn't really need them, and they still misbehave with Firefox 3.5.6 on Linux (and possibly on other browsers) - ghost tooltips (especially the "show-param" window) linger on and never disappear. With the current very short delay, moving the mouse cursor quickly over the history pane, it flashes with tooltips, I find it distracting. Simply removing "static/jquery.tipsy.js" helps, after that the tooltips are managed by the browser (or so I assume), so they are ugly yellow, but at least appear only after a long delay, and are always properly removed. Any ideas ? Thanks, -gordon James Taylor wrote, On 03/17/2010 03:51 PM: > Lighter background creates contrast problems. Delay is easy using > hoverintent although I personally prefer no delay. > > On Mar 17, 2010, at 3:49 PM, Kanwei Li wrote: > >> I think a delay would be good and maybe a lighter background >> >> On Wed, Mar 17, 2010 at 3:35 PM, Assaf Gordon <gordon(a)cshl.edu> wrote: >>> Hi, >>> >>> I was wondering if there's an easy way to disable the pop-up >>> balloon tooltips (on the save, rerun, view, delete icons) ? >>> >>> The new beautiful icons (or the old text-label) are informative >>> enough - and the constantly appearing/disappearing black tooltip >>> balloons (when you move the mouse over datasets) is a bit annoying. >>> Alternatively, is it possible to add a short delay before showing >>> the tooltip (like in all regular GUI client-side applications) ? >>> >>> Thanks, >>> -gordon >>> _______________________________________________ >>> galaxy-dev mailing list >>> galaxy-dev(a)lists.bx.psu.edu >>> http://lists.bx.psu.edu/listinfo/galaxy-dev >>> >> >> _______________________________________________ >> galaxy-dev mailing list >> galaxy-dev(a)lists.bx.psu.edu >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >

1 0

Re: [galaxy-dev] [galaxy-bugs] TF binding site database
by Anton Nekrutenko 24 Mar '11

24 Mar '11

Jose: Thank you for sharing your tool! We have a new mechanism for making tools like your available to the community: Galaxy Tool Shed (http://usegalaxy.org/community) We would ask you to contribute the pricat to the Tool Shed. Thanks! anton On Mar 24, 2011, at 10:46 AM, Muino, Jose wrote: > Dear, > > Congratulations for your fantastic tool GALAXY!. > We were developing a web-tool (http://www.ab.wur.nl/pricat/) for the analysis and storage of plant ChIP-seq data, and we made it compatible with GALAXY. Installing this tool (http://www.ab.wur.nl/pricat/quickload/PRICAT4GALAXY.rar) in a GALAXY instance, it will allow users to have access to all the binding events storage in our web-tool > > I am wondering if you will be interested to add this tool to your public GALAXY instance, > > Thanks a lot for your time, > Jose > > > Dr. Jose M Muino > Plant Research International B.V. > Droevendaalsesteeg 1 > P.O. Box 16, 6700 AA Wageningen, The Netherlands > Phone: +0317-481122. > E-mail: jose.muino(a)wur.nl > http://www.pri.wur.nl > _______________________________________________ > galaxy-bugs mailing list > galaxy-bugs(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-bugs Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

1 0

Error importing BAM file into Library
by Peter Cock 23 Mar '11

23 Mar '11

Hi all, I think I have fallen over the same problem Glen Beane reported in Nov 2010, http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003943.html I recall from reading the mailing list, that when you import a BAM file into Galaxy, it gets sorted and indexed. That makes sense since most tools need that to be done, and resorting an already sorted file should be quick. However, I'm trying to import some presorted and indexed BAM files into a library in Galaxy via the Admin settings, linking to the file not copying it. I'm getting this: <quote> File size: 4.4 Gb Data type: auto Build: ? Miscellaneous information: uploaded bam fileTraceback (most recent call last): File "/opt/galaxy-dist/tools/data_source/upload.py", line 447, in __main__() File "/opt/galaxy-dist/tools/data_source/upload.py", line 439, in __main__ add_file( dataset, registry, j Job Standard Output [bam_sort_core] merging from 28 files... Job Standard Error Traceback (most recent call last): File "/opt/galaxy-dist/tools/data_source/upload.py", line 447, in __main__() File "/opt/galaxy-dist/tools/data_source/upload.py", line 439, in __main__ add_file( dataset, registry, json_file, output_path ) File "/opt/galaxy-dist/tools/data_source/upload.py", line 381, in add_file datatype.groom_dataset_content( output_path ) File "/opt/galaxy-dist/lib/galaxy/datatypes/binary.py", line 98, in groom_dataset_content shutil.move( samtools_created_sorted_file_name, file_name ) File "/usr/local/lib/python2.6/shutil.py", line 260, in move copy2(src, real_dst) File "/usr/local/lib/python2.6/shutil.py", line 95, in copy2 copyfile(src, dst) File "/usr/local/lib/python2.6/shutil.py", line 51, in copyfile with open(dst, 'wb') as fdst: IOError: [Errno 13] Permission denied: '/data/XXX-bwa-out.sorted.bam' error Database/Build: ? Number of data lines: None Disk file: /data/XXX-bwa-out.sorted.bam </quote> Clearly from the error message, Galaxy is trying to edit the source file (and the Unix account it is running in only has read permission for this file and its containing folder). From the stdout message "[bam_sort_core] merging from 28 files..." it looks like Galaxy is trying to (re)sort my file, and may well attempt to reindex it. Is that likely to be the case? If the "copy" option had been used, then sorting and indexing should work - but I want Galaxy to link to the file as it it. If however "copy" was not selected, then I don't want Galaxy trying to alter the file like this. Could the sort+index be disabled in this mode? I think it is reasonable to expect administrators trying to import BAM files from the local file system to take care of this. Alternatively, you could actually check if the BAM file is pre-sorted or not. Peter

3 6

Login problem.
by Luobin Yang 22 Mar '11

22 Mar '11

Dear Galaxy development team, I've got a problem using the login function of Galaxy. So I downloaded a copy of Galaxy distribution and installed it on a local machine, then I installed PostgreSQL on this machine and made the necessary changes to the universe_wsgi.ini file and Galaxy is able to the use the PostgreSQL database to store information. I was able to register a user account and then I could login to the system for the first time, but after I logout and login again, the system always says that I am logged out. I checked the log file of Postgresql and the log file of Galaxy system, there is no error message indicating what happened at all. I restarted Postgresql database and Galaxy system and then I was able to login, but after I logged out, I can not login again! Have you guys met this kind of problem before? Any suggestions on what could be the cause of this problem? Thanks so much! Luobin

4 6

galaxy python crash with segfault in csamtools.so when using tracks
by Jim Johnson 22 Mar '11

22 Mar '11

We're getting a segfault from csamtool.so when the tracks controller is invoked: Mar 21 17:12:14 bat4 kernel: [4080861.873724] python[14319]: segfault at 45cfb1e8 ip 00007f1559865444 sp 00007f155192d1b0 error 4 in csamtools.so[7f1559837000+55000] Anyone have advice on where to start investigating? Thanks, JJ

2 1