- galaxy-dev - lists.galaxyproject.org

bwa indexing not automatic?
by Jennifer Jackson 01 Oct '13

01 Oct '13

Hi Joshua, Just to double check, you are running the latest stable distribution? There are a few different BWA wrappers in the tool shed, maybe you are using a different one than previously? Using a custom reference genome from the history with bwa is possible with the wrapper with the owner "devteam" (assuming Galaxy is installed where there are suitable resources - same as command line bwa). If you want to try again and report back any ongoing issues, please use the galaxy-dev(a)bx.psu.edu mailing list to reach the development community (drop galaxy-user(a)bx.psu.edu from the to or cc). Thanks, Jen Galaxy team On 9/27/13 7:37 PM, Joshua Orvis wrote: > I installed a new copy of galaxy today and then added the bwa_wrappers > tool. After I upload my reference genome and left/right reads I get > output like this each time I try to run bwa for illumina: > > The alignment failed. > Error aligning sequence. [bwa_aln] 17bp reads: max_diff = 2 > [bwa_aln] 38bp reads: max_diff = 3 > [bwa_aln] 64bp reads: max_diff = 4 > [bwa_aln] 93bp reads: max_diff = 5 > [bwa_aln] 124bp reads: max_diff = 6 > [bwa_aln] 157bp reads: max_diff = 7 > [bwa_aln] 190bp reads: max_diff = 8 > [bwa_aln] 225bp reads: max_diff = 9 > [bwt_restore_bwt] fail to open file '/seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_4.dat.bwt'. Abort! > /bin/sh: line 1: 11607 Aborted bwa aln -t 4 -I /seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_4.dat /seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_2.dat > /tmp/tmpMuj4l2/tmpUIdxXT > If I manually do the 'bwa index' command on dataset_4.dat it works but in the past this seemed to happen automatically. Any clue what's going on here? > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. 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 > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org

2 1

How can I get a txt output file from R
by Ramon Tiburski 30 Sep '13

30 Sep '13

Code:________________________________________________________________<tool id="predictionModelTool" name="Modelo de Deteccao de Risco">...<command interpreter="bash">r_wrapper.sh $script_file</command><inputs>... </inputs> <configfiles> <configfile name="script_file"> ... file=file("output.txt","w") source("/home/ramao/Galaxy-ES/tools/my_tools/modeloCancroEuropeu.R") close(file) ... </configfile> </configfiles> <outputs><data format="txt" name="output.txt"/></outputs> ... </tool>________________________________________________________________ I'm having the output "empty" and I need that the result be generated in a text file. What can I do? Thank you

3 7

Re: [galaxy-dev] Test Toolshed Biopython package dependency Atlas fails to install (Was: Re: UnboundLocalError: local variable 'prior_installation_required' referenced before assignment)
by Carlos Borroto 30 Sep '13

30 Sep '13

Forgot to copy the list on this email. On Mon, Sep 23, 2013 at 9:32 AM, Carlos Borroto <carlos.borroto(a)gmail.com> wrote: > On Fri, Sep 20, 2013 at 6:12 PM, Björn Grüning > <bjoern.gruening(a)pharmazie.uni-freiburg.de> wrote: >> Hi Carlos, >> >> Can you try again? >> Also the new unstable version if you can. Thanks for the help! ATLAS is >> a beast :( >> > > Sorry for the delayed response. Busy weekend. > > Trying to install package_atlas_3_10 on Ubuntu 13.04: > > STDERR > It appears you have cpu throttling enabled, which makes timings > unreliable and an ATLAS install nonsensical. Aborting. > See ATLAS/INSTALL.txt for further information > ############################################# > > > I think this is the other relevant part in the log: > > # try to disable cpu throttling > if hash cpufreq-selector 2>/dev/null; then > cpufreq-selector -g performance > elif hash cpupower 2>/dev/null; then > cpupower frequency-set -g performance > else > echo 'Please deactivate CPU throttling by your > own, or install cpufreq-selector' > exit > fi > > STDERR > Error calling SetGovernor: Caller is not authorized > > I had to install 'cpufreq-selector' to get here, not installed by > default. I can confirm I get the same error when trying to run this > command directly: > $ cpufreq-selector -g performance > Error calling SetGovernor: Caller is not authorized > > package_atlas_3_11 fails in exactly the same way in this box. > >>> Somehow this is also a silent failing and numpy, biopython and >>> ngs-tools(my tool package depending on biopython) get >>> "Installed"(Green) >> >> Yes that is correct. I designed it (in theory) in that way, that if >> ATLAS crashes (due to CPU throttling enabled) every other package can be >> installed without problem. Every other behaviour is a bug. >> >>> while lapack, atlas and split_by_barcode(my actual >>> tool wrapper depending on ngs-tools package) get "Installed, missing >>> tool dependencies"(Grey). This means if I try to use my wrapper in >>> this state I get this error: >>> /bin/sh: 1: ngs-tools: not found >> >> On Ubuntu it gets installed without errors. Everything is green :) >> >>> However, if I do a "Repair repository" on split_by_barcode it goes >>> into "Installed"(Green) and everything seems to work from then on. >> >> Mh, thats seems to be a bug. I will try to reproduce on a computer where >> ATLAS is crashing. >> > > Thanks for testing this. I also believe this might be a bug. > --Carlos

7 18

October Galaxy Update Newsletter is out
by Dave Clements 30 Sep '13

30 Sep '13

Hello all, The October 2013 Galaxy Update is out<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10> : *Highlights:* - A record *six new public servers<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#New_Public_Servers> * - 44 new papers<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#New_Papers> - Open Positions<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#Who.27s_Hiring> at nine different organizations - Upcoming Events<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#Events>, lots of them in Australia<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#Australia.21> plus 3 other continents<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#All_Those_Other_Contine…>. - Online materials from past events<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#Online_Materials_from_P…>, including all GCC2013 videos on Vimeo <http://bit.ly/gcc2013vimeo> and course materials for the 2013 UC Davis Bioinformatics Short Course<http://bit.ly/16rAUkf>. The UC Davis course featured 5 great days of lecture and hands-on exercises. - More Tool Shed contributions<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#Tool_Shed_Contributions> than you can shake a stick at. If you have anything you would like to see in the next *Galaxy Update<http://wiki.galaxyproject.org/GalaxyUpdates> *, please let us know. Dave Clements and the Galaxy Team <http://wiki.galaxyproject.org/GalaxyTeam> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

1 0

Re: [galaxy-dev] pbkdf2 encryption - disabling does not work
by Jan Hapala 30 Sep '13

30 Sep '13

Ahoj Martine, thanks for your response. That was a pretty stupid mistake, hard to notice even though I program in Python. However, this has not solved my problem, I get the same error. (I have also made sure that it is in the right section.) Jan 2013/9/25 Martin Čech <emulatorer(a)gmail.com> > Ahoj Honzo, > > Python is case-sensitive. Use 'use_pbkdf2 = False' and make sure you put > it under the '[app:main]' section in the config file. > > Enjoy Galaxy! > > best > > Martin Cech > > > > > > On Wed, Sep 25, 2013 at 9:15 AM, Jan Hapala <jan(a)hapala.cz> wrote: > >> Hi, >> >> I need to run Galaxy with ProFTPd, therefore I need to disable the PBKDF2 >> encryption of the passwords (as stated here >> http://dev.list.galaxyproject.org/disable-PBKDF2-revert-to-SHA1-td4661274.h… >> ). >> >> However, when I do add this line: >> use_pbkdf2 = false >> to the universe_wsgi.ini, restart Galaxy, submit the form for the >> password change (or register as a new user) I get an error "_hashlib.HASH >> object has no attribute __getitem__". >> >> I got the same result with a version as of Jul 2 and the most recent tag >> (10411:c42567f43aa7, Aug 19). >> >> I would be much grateful for your suggestions! >> >> Regards, >> Jan >> >> >> URL: >> http://127.0.0.1:8080/user/edit_info?cntrller=user&user_id=f2db41e1fa331b3e >> File >> '.../eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', >> line 364 in respond >> app_iter = self.application(environ, detect_start_response) >> File '.../eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in >> __call__ >> return self.application(environ, start_response) >> File '.../eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 >> in __call__ >> return self.application(environ, start_response) >> File '.../lib/galaxy/web/framework/base.py', line 132 in __call__ >> return self.handle_request( environ, start_response ) >> File '.../lib/galaxy/web/framework/base.py', line 190 in handle_request >> body = method( trans, **kwargs ) >> File '.../lib/galaxy/webapps/galaxy/controllers/user.py', line 842 in >> edit_info >> trans.sa_session.flush() >> File >> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py', >> line 114 in do >> File >> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py', >> line 1718 in flush >> File >> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py', >> line 1789 in _flush >> File >> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py', >> line 331 in execute >> File >> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py', >> line 475 in execute >> File >> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py', >> line 59 in save_obj >> File >> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py', >> line 485 in _emit_update_statements >> File >> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py', >> line 1449 in execute >> File >> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py', >> line 1584 in _execute_clauseelement >> File >> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py', >> line 1651 in _execute_context >> File >> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py', >> line 1647 in _execute_context >> File >> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py', >> line 475 in _init_compiled >> File >> '.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/types.py', >> line 626 in process >> File '.../lib/galaxy/model/custom_types.py', line 125 in >> process_bind_param >> value = value[0:self.impl.length] >> StatementError: '_hashlib.HASH' object has no attribute '__getitem__' >> (original cause: TypeError: '_hashlib.HASH' object has no attribute >> '__getitem__') 'UPDATE galaxy_user SET update_time=%(update_time)s, >> password=%(password)s WHERE galaxy_user.id = %(galaxy_user_id)s' >> [{u'galaxy_user_id': 1, 'password': <sha1 HASH object @ 0x7338bc0>}] >> >> ___________________________________________________________ >> 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/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > >

2 3

problems with toolshed package update process
by Lukasse, Pieter 30 Sep '13

30 Sep '13

Hi Greg, We have been trying out the update process as follows: 1- Make changes to one of the files in the repository 2- Commit and push changes to hg After these two steps we expected to be able to update the tool in Galaxy. However this was not possible. We noticed that every time we pushed a new revision to the toolshed hg we had to use the option "Reset all repository metadata", i.e. the new revision would be seen as an update only after doing this reset. Is this the normal behaviour? I can imagine that in some cases the admin would like to review a new committed changeset before enabling it as an update...could it be this is a configuration we forgot to change somewhere? Best regards, Pieter. [cid:image001.png@01CEB077.957B0FB0] Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

2 2

Messed up a tool installation from a local toolshed
by Joachim Jacob 30 Sep '13

30 Sep '13

Hi all, I have developed a tool in our local Galaxy, and imported it in a local toolshed. I next removed the 'dev' version of the tool in Galaxy, and installed it now via het Tool Shed Manager. I got an error that the dependencies could not be installed. If figured it out that it (needed to add an extra shell_command in the tool_dependencies) (and the mount point on my system needs to have exec permissions of course). So I updated the tool in the toolshed. BUT, then I uninstalled the tool from Galaxy, and reinstalled it from the Tool Shed ... instead of just updating. Anyway, it has happened. Now I have the tool listed in my 'Install Tool Shed Repositories', and when I click on it, it says 'this tool is not installed'. The only action I can apply on this installed tool shed repository is 'Install' (...). But clicking on that 'install' button, leads me to an error page (http error 500). ****************************** URL: http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://lo… Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view >> return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ view >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request view >> body = method( trans, **kwargs ) Module galaxy.web.framework:221 in decorator view >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:825 in prepare_for_install view >> raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url ) Module tool_shed.util.common_util:110 in tool_shed_get view >> response = urlopener.open( uri ) Module urllib2:397 in open view >> response = meth(req, response) Module urllib2:510 in http_response view >> 'http', request, response, code, msg, hdrs) Module urllib2:435 in error view >> return self._call_chain(*args) Module urllib2:369 in _call_chain view >> result = func(*args) Module urllib2:518 in http_error_default view >> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error ************************************ The same happens when I go to the Tool Shed, and try to install the tool from there: Galaxy detects that the tool has been installed before, and points me to that 500 error page. Any help is heartily appreciated, Thanks, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team -- @joachimjacob

4 6

puzzle: tool result always "set dataset state to ERROR"
by ruiwang.sz 30 Sep '13

30 Sep '13

Hi Guys, I'm doing a very simple test about deseq2...there is a weird situation always happening: It looks like the deseq2 tool executed just fine, without any error, and the result files were created, but after the set_metadata, galaxy always 'set dataset state to ERROR'. The xml file for this test is: <tool id="deseq2 test" name="DESeq2" version="2"> <description>Determines differentially expressed transcripts from read alignments</description> <command> t.sh $input1 $test $out $log </command> <inputs> <param format="txt" name="input1" type="data" label="Quant"/> <param format="txt" name="input2" type="data" label="Conditions"/> <param name="test" type="select" label="please choose control condition"> <options from_dataset="input2"> <column name="value" index="0"/> </options> </param> </inputs> <outputs> <data format="txt" name="out" label="DESeq result"/> <data format="txt" name="log" label="DESeq log file"/> </outputs> </tool> Basically, we have an input file from Partek flow(input1), input2 is one column from input1, which has all the conditions, in our test, it has 3 conditions, CTC, LM, PT. input name "test" is the dropdown list that contain all 3 conditions, and we choose one as control condition, in our case it is CTC. t.sh is very simple, it basically calls R script: Rscript /home/bioinfo/app/galaxy-dist/tools/Deseq/workflow.R $1 $2 $3 $4 now, in the workflow.R, the related output part is: for (i in 2:3) { res <- results(dds, contrasts[i]) ## sort the result table by FDR res <- res[order(res$padj),] ## Output the results write.table(as.data.frame(res), file=paste0(args[i+1]), sep = "\t") } So, it looks like the result files were generated as expected, with the correct information. However, it always was set to state ERROR. Am I missing something? Or did anyone see this before? Any inputs will be greatly appreciated! Thanks, Rui

2 4

2 RNAseq jobs in queue to map with Tophat > 48 hours in Galaxy Main
by Theresa Stueve 28 Sep '13

28 Sep '13

Greetings my name is Theresa Stueve; I am a researcher at USC (galaxy mailing list subscription at theresas(a)usc.edu or tstueve(a)gmail.com) I have had 2 RNAseq jobs in queue to map with Tophat to 'hg19 ful' in Galaxy Main for > 48 hours (queued Sept 27). Can you advise? My history is linked below help is much appreciated https://main.g2.bx.psu.edu/u/trstueve/h/rnaseqjegcsc3wkrun130924 -- Theresa Ryan Stueve 510-225-8894 (text better than voicemail for quick response)

1 0

Free Training (Boston): Analyzing NGS Data with Galaxy
by Anushka Brownley 27 Sep '13

27 Sep '13

Galaxy Community, Based on popular demand, we are pleased to announce another Galaxy training event for this year. BioTeam and the Galaxy Team are offering a training session that will focus on analyzing NGS Data using Galaxy. In addition to learning about the NGS related Galaxy features, you will also learn about what it takes to host your own Galaxy instance. This event is kindly hosted by Dana-Farber Cancer Institute. For more information about this training please visit the event website at http://bioteam.net/slipstream/galaxy-edition/galaxy-training/. Date: Tuesday October 22nd, 2013 Time: 9:00am – 12:00pm Location: Dana Farber Cancer Institute, Boston, MA, USA Cost: Free Space is limited so please register for this free event soon. REGISTER NOW: http://bioteam.net/slipstream/galaxy-edition/galaxy-training/galaxy-trainin… Anushka Brownley Senior Scientific Consultant www.bioteam.net SlipStream Appliance Galaxy Edition http://bioteam.net/slipstream/galaxy-edition/ SlipStream Appliance White Paper http://bioteam.net/wp-content/uploads/2013/03/SlipStream_Galaxy-White_Paper…

1 0