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

[galaxy-dev] Complete Genomics CGA Tools� in Galaxy
by Birgit Crain 26 Jun '12

26 Jun '12

Dear Community Members Complete Genomics, Inc<http://www.completegenomics.com/>. is happy to announce the release of a CGA Tools™ implementation in Galaxy. CGA Tools™ is an open source project<http://cgatools.sourceforge.net/> to provide tools for downstream analysis of Complete Genomics Whole Genome Sequencing data. This first release includes the most commonly used functions of CGA Tools™ such as listvariants, testvariants, calldiff, snpdiff, junctiondiff, join and varfilter. Ongoing development will add other functions of CGA Tools™, which were not part of this release, and a variety of data analysis workflows. There are two repositories available for download from the Galaxy Tools Shed<http://toolshed.g2.bx.psu.edu/>: a linux version, cg_cgatools_linux, and a Mac OSX version, cg_cgatools_mac_osx. Both repositories are bundled with the latest version of CGA Tools™ (1.5.0.31) for the respective operating system and contain instructions for automated and manual installation of the tools, as well as instructions for the download and installation of reference genome files. Please reply to this post with any comments to this release and suggestions for future development, or contact us at ProfServ(a)completegenomics.com<mailto:ProfServ@completegenomics.com> Best regards Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete Genomics, Inc. ________________________________ The contents of this e-mail and any attachments are confidential and only for use by the intended recipient. Any unauthorized use, distribution or copying of this message is strictly prohibited. If you are not the intended recipient please inform the sender immediately by reply e-mail and delete this message from your system. Thank you for your co-operation.

1 0

Re: [galaxy-dev] Fully Purged Histories and still 30% used
by Jennifer Jackson 26 Jun '12

26 Jun '12

Hello again, These numbers are in-line with the disk quota limits on Main: http://wiki.g2.bx.psu.edu/Main#User_data_and_job_quotas Just as a reminder, datasets must be 'permanently deleted', not just 'deleted', in order to not count in a quota usage amount. Instructions for reviewing deleted histories to see if they are permanently deleted or not is in the wiki link I sent earlier. In short, under the History menu -> Options (gear icon) -> Shared Histories, and clicking on "advanced search", then "view -> all" will display all of your work, with sizes and status. The screencast on the wiki has a walk-through. The other times this has come up, a review of "all" has cleared up any lingering questions about where the data is. Take care, Jen Galaxy team On 6/26/12 11:18 AM, David-Georges Vitrant Phd wrote: > Hi Jennifer, > Thanks for the update. I'm not 100% sure anymore. I've deleted/purged > histories and datasets as far as I know. It's showing 80% usage. This > is on the public instance. Says i'm using 79% and 160gb so that seems > a bit more correct then before. > > > On Tue, Jun 26, 2012 at 2:12 PM, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > > Hello, > > Are you still having this problem? Is this on the public main > instance or your own local instance? > > The display numbers can take up to a few hours to update on the > main server, depending on load. The update time on your local > install will vary depending on your configuration. > > If the counts still do not seem right, double checking for > deleted, but not permanently deleted histories is a good place to > start. Looking for deleted/hidden datasets in existing histories > is also recommended. This wiki can help: > http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Delete_vs_Delete_Perman… > > Best, > > Jen > Galaxy team > > > > On 6/23/12 12:18 PM, David-Georges Vitrant Phd wrote: >> I hadn't found this bug anywhere. I deleted all my histories and >> purged them but my counter still says I have 30% used. Am I >> missing something? >> >> -- >> Thanks, >> >> >> >> ___________________________________________________________ >> 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/ > > -- > Jennifer Jackson > http://galaxyproject.org > > > > > > > -- > Thanks, > David-Georges Vitrant Ph.D. > -- Jennifer Jackson http://galaxyproject.org

1 0

Fully Purged Histories and still 30% used
by David-Georges Vitrant Phd 26 Jun '12

26 Jun '12

I hadn't found this bug anywhere. I deleted all my histories and purged them but my counter still says I have 30% used. Am I missing something? -- Thanks,

2 1

Requests to display_application mistakenly routed to route
by Rob Syme 25 Jun '12

25 Jun '12

Galaxy type: local I'm trying to get IGV to download files served from the galaxy instance through "display_application". When IGV makes a request for the BAM file, it is re-routed to root like so: wget http://example.org/galaxy/display_application/e2132aef71b11dbf/igv_bam/loca… --2012-06-22 13:58:00-- http://example.org /galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default/cc7ba224ab9e7b70/data/galaxy_e2132aef71b11dbf.bam Connecting to example.org:80... connected. HTTP request sent, awaiting response... 302 Found Location: /galaxy/root?app_action=data&user_id=cc7ba224ab9e7b70&app_name=igv_bam&link_name=local_default&action_param=galaxy_e2132aef71b11dbf.bam&dataset_id=e2132aef71b11dbf [following] --2012-06-22 13:58:00-- http://example.org /galaxy/root?app_action=data&user_id=cc7ba224ab9e7b70&app_name=igv_bam&link_name=local_default&action_param=galaxy_e2132aef71b11dbf.bam&dataset_id=e2132aef71b11dbf Reusing existing connection to example.org:80. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/html] Saving to: 'galaxy_e2132aef71b11dbf.bam.1' [ <=> ] 27,581 --.-K/s in 0s 2012-06-22 13:58:00 (146 MB/s) - 'galaxy_e2132aef71b11dbf.bam.1' saved [27581] Giving us a text/html page rather than the BAM file. I see that I'm not the first person to run into this: http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007901.html but I'm still not really sure how to solve the problem. I'm no sysadmin, so my apache config skills are very patchy. My config is up at https://gist.github.com/2970592. Any help would be very much appreciated. Rob Syme PhD Student Curtin University

3 6

Re: [galaxy-dev] unable to start galaxy
by izmiyati razikin 25 Jun '12

25 Jun '12

Re-send From: izmiyati razikin [mailto:izmiyati@novaglobal.com.sg] Sent: Monday, 25 June, 2012 11:01 PM To: 'galaxy-dev(a)lists.bx.psu.edu' Subject: unable to start galaxy Hello, I'm having problem starting up galaxy. I'm using RHEL 5.3 which comes with python 2.4.3. So I compiled python 2.6.5. I've created a symbolic link and set it in PATH. Yet I'm unable to start galaxy. Thanks in advance for help! Fetch successful. Starting subprocess with file monitor Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/home/software/apps/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/scri pt/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/home/software/apps/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/scri pt/command.py", line 123, in invoke exit_code = runner.run(args) File "/home/software/apps/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/scri pt/command.py", line 218, in run result = self.command() File "/home/software/apps/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/scri pt/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/home/software/apps/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/scri pt/serve.py", line 313, in loadapp **kw) File "/home/software/apps/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/depl oy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/home/software/apps/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/depl oy/loadwsgi.py", line 224, in loadobj global_conf=global_conf) File "/home/software/apps/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/depl oy/loadwsgi.py", line 248, in loadcontext global_conf=global_conf) File "/home/software/apps/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/depl oy/loadwsgi.py", line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/home/software/apps/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/depl oy/loadwsgi.py", line 413, in get_context section) File "/home/software/apps/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/depl oy/loadwsgi.py", line 458, in _context_from_explicit value = import_string(found_expr) File "/home/software/apps/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/depl oy/loadwsgi.py", line 18, in import_string return pkg_resources.EntryPoint.parse("x="+s).load(False) File "/home/software/apps/galaxy-dist/lib/pkg_resources.py", line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/home/software/apps/galaxy-dist/lib/galaxy/web/buildapp.py", line 19, in <module> from galaxy import config, jobs, util, tools File "/home/software/apps/galaxy-dist/lib/galaxy/jobs/__init__.py", line 4, in <module> from galaxy import util, model File "/home/software/apps/galaxy-dist/lib/galaxy/model/__init__.py", line 13, in <module> import galaxy.datatypes.registry File "/home/software/apps/galaxy-dist/lib/galaxy/datatypes/registry.py", line 6, in <module> import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo, binary, assembly, ngsindex, wsf File "/home/software/apps/galaxy-dist/lib/galaxy/datatypes/tabular.py", line 15, in <module> from sniff import * File "/home/software/apps/galaxy-dist/lib/galaxy/datatypes/sniff.py", line 8, in <module> from galaxy.datatypes.binary import unsniffable_binary_formats File "/home/software/apps/galaxy-dist/lib/galaxy/datatypes/binary.py", line 12, in <module> from bx.seq.twobit import TWOBIT_MAGIC_NUMBER, TWOBIT_MAGIC_NUMBER_SWAP, TWOBIT_MAGIC_SIZE File "/home/software/apps/galaxy-dist/eggs/bx_python-0.7.0_494c2d1d68b3_rebuild1- py2.6-linux-x86_64-ucs2.egg/bx/seq/__init__.py", line 7, in <module> from bx.seq.core import * File "/home/software/apps/galaxy-dist/eggs/bx_python-0.7.0_494c2d1d68b3_rebuild1- py2.6-linux-x86_64-ucs2.egg/bx/seq/core.py", line 10, in <module> import fasta, nib, qdna File "/home/software/apps/galaxy-dist/eggs/bx_python-0.7.0_494c2d1d68b3_rebuild1- py2.6-linux-x86_64-ucs2.egg/bx/seq/nib.py", line 28, in <module> import _nib ImportError: /home/software/apps/galaxy-dist/eggs/bx_python-0.7.0_494c2d1d68b3_rebuild1-p y2.6-linux-x86_64-ucs2.egg/bx/seq/_nib.so: undefined symbol: Py_InitModule4_64 [240223 refs] [55760 refs] Rgds, Izy

1 0

Link display in gbrowse
by Pierre Cressant 25 Jun '12

25 Jun '12

Hi, I'm new to galaxy and I don't know many about the configurations to set. I'm trying to connect my gbrowse 2 to galaxy. Currently, i'm able to export data from gbrowse to galaxy.I've read that a link "display in gbrowse" in the history panel can be create, but i can't find a way to do it ? I've tried many configurations and none of them work, somebody can help me ? greetings, Pierre CRESSANT

1 0

Exporting histories through API
by Martin Dahlö 25 Jun '12

25 Jun '12

Hello there As the subject hints, I am trying to export histories through the API. Doing it through the web interface is a breeze, but has it been implemented in the API yet? I could not find anything about it in the examples or by searching the web/this list. I am planning to only use Galaxy through the API to import my data and run some workflows on it, and then export the results. Preferably specific files from the history, but a bundled history like the one you get from the web interface 'Export history' would be ok as well. Has anyone done something like this, and can point me in the right direction? :) Mvh Martin Dahlö --- Bioinformatic support martin.dahlo(a)scilifelab.uu.se +46 18 611 59 59 +46 706 70 79 55 http://www.scilifelab.uu.se/ http://www.uppnex.uu.se ---

3 3

Configuring Data Library Usage for Non-Admins
by Ciara Ledero 25 Jun '12

25 Jun '12

Hi all, I was able to configure Galaxy so that admins can use its Data Library functionality. My colleague then asked if I could do the same for non-admin users. I looked at the universe_wsgi.ini file and added a folder for the users. How will I know that all is ready? I logged-in with a non-admin account and I found nothing altered in the interface. Is there something else that I need to do? Thanks in advance for the help! Cheers, CL

3 7

Deleting non-.dat files from Galaxy database
by Ciara Ledero 25 Jun '12

25 Jun '12

Hi all, These are some of the data that I have generated via Galaxy while I was experimenting with it. dataset_186.dat.bam dataset_265_files dataset_222.dat.bam dataset_266_files d dataset_346.dat.stat dataset_194.dat.fai dataset_267_files dataset_346.dat.temp dataset_727.dat.stat dataset_272_files dataset_727.dat.temp dataset_150.dat.bam dataset_273_files Is there another way in Galaxy to delete these without having to directly manipulate the database? Thanks! CL

1 0

Script not working in Galaxy
by Ciara Ledero 25 Jun '12

25 Jun '12

Hi all, I have integrated a script that runs rsem in Galaxy and the following is the .xml that shows it in Galaxy: <tool id="sixthStep" name="RESM"> <description></description> <command interpreter="perl">exec_rrsem.pl $input1 $input2 $input3 $output1 $output2 </command> <inputs> <param name="input1" format="fasta" type="data" label="Transcript from OASES"/> <param name="input2" format="fastq" type="data" label="Left read: " /> <param name="input3" format="fastq" type="data" label="Right read: "/> </inputs> <outputs> <data name="output1" format="text" /> <data name="output2" format="text" /> </outputs> </tool> And here is exec_rrsem.pl, the file that accepts the parameters and sets everything up: $genes = $ARGV[3]; $isoforms = $ARGV[4]; $trans = $ARGV[0]; $left = $ARGV[1]; $right = $ARGV[2]; $directory = "/home/applications/galaxy-dist/tools/VELVET-OASES"; $transcript = "$directory/trans.fa"; $left_read = "$directory/left_read.fastq"; $right_read = "$directory/right_read.fastq"; symlink $trans, $transcript; symlink $left, $left_read; symlink $right, $right_read; @out <#@out> = `perl /home/applications/galaxy-dist/tools/VELVET-OASES/ run_rsem.pl 2>&1`; run_rsem.pl is the actual script that runs the rsem programs. I'm wondering though, why Galaxy isn't executing the command properly. This is the same pattern I've used in other programs that I've integrated with Galaxy, so it came as a surprise to me when this one didn't run. Is there something wrong with my script? By the way, when I run exec_rrsem.pl from the konsole, it works just fine. Any insights on this? Thanks a lot! CL

2 2