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Tophat for Illumina Error: Could not find Bowtie 2 index files
by greg 13 Dec '12

13 Dec '12

I'm seeing the error below when I try to run Tophat for Illumina. Has anyone seen this before? Could I have installed bowtie incorrectly or am I simply running with the wrong data/parameters? Thanks, Greg (I'm also really confused why the error is mentioned /tmp/* paths. I never assigned anything to /tmp in the universe_wsgi.ini. Where is it getting that from?) Error in tophat: [2012-12-13 13:55:01] Beginning TopHat run (v2.0.6) ----------------------------------------------- [2012-12-13 13:55:01] Checking for Bowtie Bowtie version: 2.0.2.0 [2012-12-13 13:55:01] Checking for Samtools Samtools version: 0.1.18.0 [2012-12-13 13:55:01] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (/tmp/4036894.1.f04.q/tmp4TrEQQ/dataset_75.*.bt2)

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Re: [galaxy-dev] Impersonate a User
by Edward Hills 13 Dec '12

13 Dec '12

Hi Greg, Try clicking the logout button. That should logout of the user you are impersonating and back into you. Although, this does have a few quirks also and may log you right out. Don't forget that when you are impersonating someone the history may not be automatically loaded and you will have to do that manually. Cheers, Ed

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Local galaxy
by Jennifer Jackson 13 Dec '12

13 Dec '12

Repost to mailing list ___________________________________________________________ For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev Hi I am doing NGS analysis in our local galaxy, I would like to access the output files for further analysis. I do have an account on the server where galaxy is installed, so I would like to access the output files without actually downloading them( aince they are huge). Can you please tell me where I can find my (local galaxy) output files on the server ? Is it stored under databases ? Thanks. Selvi Ramalingam Sent from my iPhone -- Jennifer Jackson http://galaxyproject.org

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Server Error / Edit attribut of a dataset generated by a tool
by Sarah Maman 13 Dec '12

13 Dec '12

Hello, One of my users gets the following message when he wishes to edit the attribute of a dataset which is generated by using a tool (same problem as it is a tool provided by Galaxy or a tool coded by us). Do you have any idea? Thanks in advance, Sarah Maman URL: http://sigenae-workbench.toulouse.inra.fr/galaxy/datasets/b9580783e2098a2b/… File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/usr/local/bioinfo/src/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 '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 111 in __call__ return self.app( environ, start_response ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/controllers/dataset.py', line 600 in edit refresh_frames=refresh_frames ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 722 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 733 in fill_template_mako return template.render( **data ) File '/usr/local/bioinfo/src/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 '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/usr/local/bioinfo/src/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 '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/base.mako.py', line 42 in render_body __M_writer(unicode(next.body())) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/dataset/edit_attributes.mako.py', line 95 in render_body __M_writer(filters.html_escape(unicode(data.info ))) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 31: ordinal not in range(128)

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Re: [galaxy-dev] How to add to add hg16 index into the build-in index / reference gnome list?
by Jennifer Jackson 13 Dec '12

13 Dec '12

Hello Sachit, There are a few problems with the command line. If you want to install hg19, then hg16 should not be used. Also, the <reference_in> to the tool should be an uncompressed fasta file. This is described in the tool documentation. You will also need to use as the '<index_basename>' the same dbkey identifier for the genome as you are using to name the reference fasta file (minus the ".fasta" extension) and for the SAM index. This is also the same dbkey identifier as used in the $GALAXYROOT/tool-data/shared/ucsc/builds.txt file. Using simply "hg19" as the dbkey would be the simplest choice. The original link I sent you explains this, but perhaps you did not find the data integration wiki page linked from the top? It is important to know about, as it also covers the builds.txt file in the first section. It can be found here: http://wiki.galaxyproject.org/Admin/Data%20Integration You may find it helpful to rsync the current hg19 genome and indexes from our server to help you get started. These could be used as a base from where bowtie2 indexes could be added. Please note that some genomes, including hg19, have variants in our data archives and that this particular genome is very large with many indexes and related files (just a warning if space is a concern). The tool forms for the RNA-seq tools describe variant content, but in short, the "full" genome is the same as the original. It is important to follow the symbolic links to note which datasets are associated with which indexes and to follow the same conventions when adding new data. Or take what you need and reorganize is as it makes the most sense for your own use. This is not overly complicated - you will be able to see which are associated by browsing the contained data. The second section on the data integration wiki page above describes how to rsync, if you choose to do this. To use the data, even rsync data, the loc files must still be set up. You only have to set up the ones that you plan to use. The original wiki link and the one above have information about .loc files, as do the sample .loc files themselves. Hopefully this helps, Jen Galaxy team On 12/12/12 9:56 PM, Sachit Adhikari wrote: > I need to install hg19 not hg16. > > On Thu, Dec 13, 2012 at 4:26 AM, Sachit Adhikari > <sachit.technerves(a)gmail.com <mailto:sachit.technerves@gmail.com>> wrote: > > Hello Jen, > > Thanks for your reply. I have installed bowtie2 and tophat2. I am > trying to use this command to build the index: > bowtie2-build [options]* <reference_in> <index_basename> > > My file name is Homo_sapiens_UCSC_hg19.tar.gz. Thus I used > bowtie2-build -f Homo_sapiens_UCSC_hg19.tar.gz hg16 > > But it doesn't work. What am I doing wrong? Thanks > > On Wed, Dec 12, 2012 at 9:23 PM, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > > Hello Sachit, > > Instructions for setting up local indexes are in our wiki here: > http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup > > Bowtie2 is not specifically listed, but the instructions for > Bowtie and Bowtie2 are nearly identical. The same indexes are > used for Bowtie2 and Tophat2. When building the index, you > simply replace "bowtie-build" with "bowtie2-build" in the > command string and create/modify the bowtie2_index.loc file > the same as you would the bowtie_index.loc file. > > The Tophat2 manual has some more details about getting set up > here: > http://tophat.cbcb.umd.edu/manual.html > > Next time, for questions about local installs, using just the > galaxy-dev(a)bx.psu.edu <mailto:galaxy-dev@bx.psu.edu> list is > best (no need to post to multiple lists). If your question has > been misunderstood, please send more details to clarify. > > Best, > > Jen > Galaxy team > > > > On 12/12/12 3:46 AM, Sachit Adhikari wrote: >> How do I add hg16 into the build-in index? >> >> >> ___________________________________________________________ >> 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 > > > -- Jennifer Jackson http://galaxyproject.org

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Doesn't have enable_beta_job_managers options in configuration file
by Sachit Adhikari 13 Dec '12

13 Dec '12

My Galaxy Doesn't have enable_beta_job_managers option in universe_conf.ini file.

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tools imported from toolshed stay in "waiting to run status"
by Philipe Moncuquet 13 Dec '12

13 Dec '12

Hi dev, We are running a local instance of Galaxy, last update was the November release (7148:17d57db9a7c0 I think). We are facing problem when trying to run tools that were imported via the toolshed. The never start and the status stays on "waiting to run". Other tools work fine, and this generic to all tools from toolshed. Any suggestions on where should I look to fix this ? Philippe

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Tool dependency installation fail, any documentation?
by Franco Caramia 13 Dec '12

13 Dec '12

Hi list, I got the following tool_dependencies.xml file failing: <?xml version="1.0"?> <tool_dependency> <package name="bedtools" version="2.17.0"> <install version="1.0"> <actions> <action type="download_by_url" target_filename="bedtools-2.17.0.tar. gz" >http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz</action> <action type="shell_command">make clean</action> <action type="shell_command">make all</action> <action type="move_directory_files"> <source_directory>bin</source_directory> <destination_directory>$INSTALL_DIR/bin</destination_directory> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DI R/bin</environment_variable> </action> </actions> </install> <readme> GCC version 4.1 or greater is recommended. 3.x versions will typically not c ompile BEDTools </readme> </package> </tool_dependency> The error given is: ############################################# make clean STDOUT ############################################# ############################################# make clean STDERR make: *** No rule to make target clean'. Stop. ############################################# I basically just copied the example code from the Galaxy wiki for R: <?xml version="1.0"?> <tool_dependency> <set_environment version="1.0"> <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment> <package name="R" version="2.15.1"> <install version="1.0"> <actions> <action type="download_by_url">http://CRAN.R-project.org/src/base/R-2/R-2.15.1.tar.g z</action> <action type="shell_command">./configure --prefix=$INSTALL_DIR</action> <action type="shell_command">make</action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R. </readme> </package> </tool_dependency> I have found no documentation to what the tag <action type="download_by_url"> does... I have asumed it downloads, unzips and moves into the unzipped directory.. But apparently it doesn¹t.. Any advice on this or at least a link to the pertinent documentation?? Thanks a lot in advance... Franco This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

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"Delete Permanently" problem
by Fenglou Mao 12 Dec '12

12 Dec '12

I installed a local galaxy server, did some calculation. Now I want to clean datasets for some space. I tried "Delete Permanently" on both datasets and histories, none of them worked. The datasets and histories will be marked as "deleted", but it will not be really deleted even I am using "Delete Permanently". They will not be really removed, and space are not released. Sometimes it will give me a message "this feature is not enabled", sometimes it won't. Any one know how to enable "Delete Permanently" feature? Thanks, Fenglou

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Re: [galaxy-dev] help on galaxy on the cloud
by Enis Afgan 12 Dec '12

12 Dec '12

Hi Alfonso, How did you launch your instance? Did you try using http://usegalaxy.org/cloudlaunch If not, give that a shot and see if you get up and going fine. If not, please send another email and we'll figure it out there. (I've CC-d galaxy-dev mailing list, which is the best place to get help on these topics.) Cheers, Enis On Thu, Dec 13, 2012 at 5:12 AM, Alfonso Garrido-Lecca < Alfonso.Garrido-lecca(a)colorado.edu> wrote: > Hello Enis, > I am a post-doc in the Blumenthal lab in Boulder, Colorado, US. > I been trying to set galaxy on the cloud on the lab, but I am experiencing > some > difficulties connecting with the galaxy interface. > When you have a chance could you please let me know who could help me on > this? > please let me know, > thanks, > Alfonso >

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