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

Circster save just hangs
by Anthonius deBoer 13 Feb '13

13 Feb '13

Hi, I had created a trackster vizualization that had not finished indexing yet, and I decided to change it into a circster visualization. I then added a few more BAM files and tried to save the visualization and now it just hangs there... no errors in the logs so far, but no saving of the visualization either... Thon

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Problems linking Data inside Galaxy
by Gaueko Erge 13 Feb '13

13 Feb '13

Hi, I have followed, carefully, the instructions posted in: http://wiki.galaxyproject.org/Admin/Data%20Integration Yet, despite my best efforts when I get, say all exons from hg19 build and try to their fetch sequences, galaxy tells me that the sequences for hg19 are not there I find this surprising because I have downloaded: rsync://datacache.g2.bx.psu.edu/indexes/ rsync://hgdownload.cse.ucsc.edu/gbdb/ rsync://hgdownload.cse.ucsc.edu/goldenPath/vicPac1/bigZips databases and added the correct paths to the 'alignseq.loc' file Any ideas will be appreciated Thanks --G

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Uploading a Directory of Files - IOError: [Errno 28] No space left on device
by greg 13 Feb '13

13 Feb '13

Hi guys, When I try to upload a directory of files from a server directory I'm seeing the error below. It appears to be trying to write to a temp directory somewhere that I'm guessing doesn't have enough space? Is there a way I can direct where it writes to for temporary files like this? Am I understanding right, that these upload jobs are running on our cluster? I think it would be a problem if its trying to use the default temp directory on each cluster node since they aren't provisioned with much space. Please advise. Thanks, Greg Miscellaneous information:Traceback (most recent call last): File "/misc/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 384, in __main__() File "/misc/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 373, in __main__ add_file( dataset, Job Standard Error Traceback (most recent call last): File "/misc/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 384, in __main__() File "/misc/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 373, in __main__ add_file( dataset, registry, json_file, output_path ) File "/misc/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 270, in add_file line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place ) File "/misc/local/galaxy/galaxy-dist/lib/galaxy/datatypes/sniff.py", line 99, in convert_newlines fp.write( "%s\n" % line.rstrip( "\r\n" ) ) IOError: [Errno 28] No space left on device

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Problem to upload files to Galaxy
by Blum, Roy 13 Feb '13

13 Feb '13

Dear Galaxy support, In the last 24 hours we are unable to load files to the Galaxy server. We tried doing so as "guest" and by login as users but failed. We try to load a small file (about 1M) but so far no success. Has the Galaxy server been experienced problems recently? Thanks a lot, Roy _______________________________ Roy Blum, Ph.D. New York University School of Medicine, Cancer Institute, Smilow Research Building, 11th Floor, Room 1106 552 First Ave. New York, NY, 10016 Mob: +1 (646) 716-2875<tel:%2B1%20%28646%29%20716-2875> Lab: +1 (212) 263-6169<tel:%2B1%20%28212%29%20263-6169> http://blumroy.googlepages.com<http://blumroy.googlepages.com/>

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Still seeing this CRITICAL message in the logs when its trying to delete the working directories
by Anthonius deBoer 13 Feb '13

13 Feb '13

Hi, I continue to see this error in the logs, every time a jobs finishes: galaxy.objectstore CRITICAL 2013-01-30 11:42:14,161 /mnt/ngs/analysis/svcgalaxy/DATA/job_working_directory/000/327 delete error [Errno 39] Directory not empty: '/mnt/ngs/analysis/svcgalaxy/DATA/job_working_directory/000/327' When I check the directory, it is of course empty: $ls -la /mnt/ngs/analysis/svcgalaxy/DATA/job_working_directory/000/327 total 68 drwxrwsr-x 2 svcgalaxy Domain Linux Users 0 Jan 30 11:42 . drwxrwsr-x 283 svcgalaxy Domain Linux Users 5793 Jan 30 11:45 .. Any ideas why this keeps happening? I end up with thousands of directories in the working directories which I need to clean out manually now... Thanks Thon

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Error executing tophat2
by Sachit Adhikari 13 Feb '13

13 Feb '13

I got this error which executing tophat2 in Galaxy: Error in tophat: [2013-02-13 02:02:43] Beginning TopHat run (v2.0.7) ----------------------------------------------- [2013-02-13 02:02:43] Checking for Bowtie Bowtie version: 2.0.6.0 [2013-02-13 02:02:43] Checking for Samtools Samtools version: 0.1.18.0 [2013-02-13 02:02:43] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (/data/bowtie2-2.0.6/hg19/Homo_sapiens/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/.*.bt2) The tool produced the following additional output: TopHat v2.0.7 tophat2 -p 4 /data/bowtie2-2.0.6/hg19/Homo_sapiens/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/ /opt/galaxyprod/galaxy-dist/database/files/000/dataset_197.dat I have these files under the Index directory: genome.1.bt2 genome.2.bt2 genome.3.bt2 genome.4.bt2 genome.fa genome.rev.1.bt2 genome.rev.2.bt2 tophat_out

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hg clone link on news brief incorrect
by Anthonius deBoer 13 Feb '13

13 Feb '13

I think the hg clone link on the news brief is incorrect: it states: hg clone https://bitbucket.org/galaxy-dist#stable Probably should be hg clone https://bitbucket.org/galaxy/galaxy-dist#stable Thon

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Re: [galaxy-dev] Error when trying to change the permissions in data libraries.
by Christos Kannas 13 Feb '13

13 Feb '13

Hi, The problem has been solved. There was a corruption within a user's email address, there was a character that could not be decoded so it caused errors with permissions and the datasets the user had uploaded. -- Chris On Fri, Feb 8, 2013 at 3:59 PM, <galaxy-dev-request(a)lists.bx.psu.edu> wrote: > From: Christos Kannas <chriskannas(a)gmail.com> > To: galaxy-dev(a)lists.bx.psu.edu > Cc: > Date: Fri, 8 Feb 2013 14:35:25 +0200 > Subject: [galaxy-dev] Error when trying to change the permissions in data > libraries. > Hi, > > In our local Galaxy server an error came up today. > When I try to edit the permissions of data librarles via the Admin panel I > get the following error: > (Also attached is an image of the following error) > > UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 0: > ordinal not in range(128) > > URL: > http://lisis.cs.ucy.ac.cy/library_common/library_permissions?show_deleted=F… > File > '/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', > line 364 in respond > app_iter = self.application(environ, detect_start_response) > File > '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', > line 98 in __call__ > environ, self.app) > File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', > line 539 in intercept_output > app_iter = application(environ, replacement_start_response) > File > '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', > line 80 in __call__ > return self.application(environ, start_response) > File > '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', > line 632 in __call__ > return self.application(environ, start_response) > File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 > in __call__ > body = method( trans, **kwargs ) > File > '/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/library_common.py', > line 262 in library_permissions > status=status ) > File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line > 832 in fill_template > return self.fill_template_mako( filename, **kwargs ) > File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line > 843 in fill_template_mako > return template.render( **data ) > File > '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line > 296 in render > return runtime._render(self, self.callable_, args, data) > File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', > line 660 in _render > **_kwargs_for_callable(callable_, data)) > File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', > line 692 in _render_context > _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) > File '/home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', > line 718 in _exec_template > callable_(context, *args, **kwargs) > File '/home/galaxy/galaxy-dist/database/compiled_templates/base.mako.py', > line 42 in render_body > __M_writer(unicode(next.body())) > File '/home/galaxy/galaxy-dist/database/compiled_templates/library/common/ > library_permissions.mako.py', line 76 in render_body > __M_writer(unicode(render_permission_form( library, library.name, > h.url_for( controller='library_common', action='library_permissions', > cntrller=cntrller, id=trans.security.encode_id( library.id ), > show_deleted=show_deleted ), roles, do_not_render=[], all_roles=all_roles > ))) > File '/home/galaxy/galaxy-dist/database/compiled_templates/dataset/ > security_common.mako.py', line 108 in render_render_permission_form > __M_writer(unicode(render_select( current_actions, k, v, all_roles ))) > File '/home/galaxy/galaxy-dist/database/compiled_templates/dataset/ > security_common.mako.py', line 34 in render_select > return > render_render_select(context,current_actions,action_key,action,roles) > File '/home/galaxy/galaxy-dist/database/compiled_templates/dataset/ > security_common.mako.py', line 190 in render_render_select > __M_writer(unicode(role.name)) > UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 0: > ordinal not in range(128) > > We are using a modified version of Galaxy. > The info from hg (latest galaxy-dist we have pulled): > > changeset: 7828:b5bda7a5c345 > user: Nate Coraor <nate(a)bx.psu.edu> > date: Fri Oct 05 15:49:26 2012 -0400 > summary: Fix the Compute tool to only allow for execution of a limited > set of expressions. > > What we have to do to fix it? > > Thanks, > Christos > > -- > > Christos Kannas > Researcher > Ph.D Student > > e-Health Laboratory <http://www.medinfo.cs.ucy.ac.cy/> > kannas.christos(a)ucy.ac.cy > kannas.christos(a)cs.ucy.ac.cy > chriskannas(a)gmail.com > > ... > > -- Christos Kannas Researcher Ph.D Student e-Health Laboratory <http://www.medinfo.cs.ucy.ac.cy/> kannas.christos(a)ucy.ac.cy kannas.christos(a)cs.ucy.ac.cy chriskannas(a)gmail.com Mob: (+357) 99530608

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Custom Cheetah filters?
by Smithies, Russell 13 Feb '13

13 Feb '13

I want to add a filter to strip whitespace and newlines from a text input box so I can pipe the sanitized string to a command. Documentation is a bit sparse (and my Python a bit basic) so does anyone have an example? Perhaps there's a better way of doing it - regex maybe? Any ideas? Thanx, --Russell -- ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================

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Re: [galaxy-dev] Questions regarding updating the Galaxy on Amazon AWS
by Enis Afgan 13 Feb '13

13 Feb '13

Hi Chun-Yuan, Sorry to see you're running running into so much trouble. The reality of the situation is that the Update Galaxy button in CloudMan is currently broken due to the changes in Galaxy that make the updates a rather manual process. For the past several weeks, the team has been working on sorting this out and we are getting closer to having that resolved. The upcoming upgrade will include an update to Galaxy itself, a number of tools, and the machine image. Also, a change in the architecture of the cloud deployment will be necessary to accomplish this. Specifically, galaxyTools and galaxyData volumes (ie, file systems) will be merged into a single file system. As far as mi-deployment goes - it has been deprecated at this point in favor of CloudBioLinux (cloudbiolinux.org) Over the past 6 months or so, the functionality from mi-deployment has been merged with CBL and is the preferred way of building images and tools. As far as getting a volume attached to a specific instance, the AWS console allows you to attach a volume to an instance at a given device. Then, the device becomes available on the attached instance. Note that the device ID may differ from the one you used to attach the device as - this is noted in the AWS console at the time of attaching a volume so you should look for a device with that ID. As far as support goes - unfortunately, we do not have resources to offer phone support. Instead, you should subscribe and send emails to galaxy-dev mailing list (http://lists.bx.psu.edu/listinfo/galaxy-dev) I have CC'd that list now and posting to that list in the future should give the biggest exposure to the questions you may have. Hope this helps. Let us know if you have any more questions, Enis On Tue, Feb 12, 2013 at 9:04 AM, Chun-Yuan Huang <huangc(a)uwm.edu> wrote: > Dear Dr. Afgan, > > I am in a lab that focuses on NGS analysis for Zebrafish Bis-seq dataset, > and is about to use the Bismark tool (http://www.bioinformatics.** > babraham.ac.uk/projects/**bismark<http://www.bioinformatics.babraham.ac.uk/projects/bismark>) > for that purpose. We were very excited to learn that Bismark works in the > Galaxy project that you are the main author of, and have been trying to > install Bismark into Galaxy for the past few weeks. We have tried and > received the following: > 1. Start up our own instance on Amazon AWS using ami-da58aab3, > galaxy-cloudman-2011-03-22, and following the instructions from Galaxy Wiki > to install Bismark manually, including the necessary modifications on the > files "universe_wsgi.ini", "tool_conf.xml", "tool_data_table_conf.xml". > However, the installed Bismark kept generating error messages that we could > not fully resolve. > 2. We later noticed that Bismark can be installed from Tool Shed in a > rather automatic way. But in order to take advantage of that, we need to > update the galaxy system into more recent version in order to have the > recent/automatical Tool Shed. Oddly the link in the Cloudman Admin page for > "Update Galaxy from a provided repository" doesn't work for us. So we > tried to update the galaxy manually, then the Bismark from Tool Shed. It > worked partially, as some tools are functional but not others, including > the Bismark. We are in the process of configuring individual tools as well > as Bismark. > 3. During the frustration, I kept wondering whether there is a more > systemic and better documented way of upgrading Galaxy and installing its > tools such as Bismark. Although we may be able to figure out all the > problems eventually, the time and work spent on it is rather expensive as > compared to a stand-alone Linux box. > 4. So in looking out for a more systemic and better documented solution, I > just came across your site for the mi-deployment ( > https://bitbucket.org/afgane/**mi-deployment<https://bitbucket.org/afgane/mi-deployment>). > By reading its overview, it seems this is exactly the solution I have been > looking for (sorry for my ignorance on this matter, as I should have tried > it from the beginning). > > I am in the process of trying mi-deployment. But in the meantime, I would > like to ask a couple of questions: > 1. Is "mi-deployment" the right track I should be following, or I am still > in the wrong place for my situation? Are there more detailed instructions > on doing it? Do you have any other suggestions? I consider myself and my > group with fair literacy on bioinformatic tools, NGS tools, and how Linux > system works (but not experts on it). > 2. Per your instruction on mi-deployment, we have established a > "CloudBioLinux" Ubuntu 12.04 instance (version dated to December 2012) and > have set environment variables for both access key and secret access key, > in addition to using pip to install boto and fabric. We've attempted to > create an EBS volume and link it to our EC2 instance, but it does not show > up within the "/dev" directory following a kernel restart. How may we get > it to display such that we can then mount it with "sudo mount /dev/VOLUME > /mnt/galaxyTools"? > 3. Is it possible that I could reach you by phone for more detailed > discussion? > > Thanks for your great work on Galaxy, and I look forward to hearing from > you. > > Chun-Yuan > > -- > XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX**XXXXXXXXXXXXXXXXX > Chun-Yuan Huang, Ph.D. > Research Scientist > Huangc at uwm.edu > chunyuan.huang at gmail.com > Laboratory for Public Health Informatics and Genomics > Lapham 234, Zilber School of Public Health > University of Wisconsin – Milwaukee > XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX**XXXXXXXXXXXXXXXXX > >

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