galaxy-dev May 2017

galaxy-dev@lists.galaxyproject.org

35 participants
34 discussions

Re: [galaxy-dev] Shiny in Galaxy
by Yvan Le Bras 14 Mar '18

14 Mar '18

Dear Mohamed, Karim, galaxy-dev list, A rapid e-mail to inform you that we plan to work on this task in the upcoming weeks with Thimothée and Valentin, copied. We have had some exchanges with Eric (Rasche) and Björn (Grüning) and it seems that using the Galaxy "interactive environment" functionality is a good way to proceed. Don't hesitate to give us more informations to collaborate on it... Wishing you a good week end. Cheers, Yvan -------- Message d'origine -------- De : "Md. Rezaul Karim" <rezaul.karim(a)insight-centre.org> Date : 26/05/2017 15:45 (GMT+01:00) À : Mohamed Kassam <k.mamoud(a)gmail.com> Cc : Galaxy Dev List <galaxy-dev(a)lists.galaxyproject.org> Objet : Re: [galaxy-dev] Shiny in Galaxy +1 On May 26, 2017 2:44 PM, "Mohamed Kassam" <k.mamoud(a)gmail.com> wrote: Dear all, I have a shiny application working in my RStudio, but I would like to integrate it to Galaxy that the users can call my application via Galaxy . Thanks in Advance, Mohamed ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/

3 5

Groovy tool for galaxy
by Anshul Tak 22 Aug '17

22 Aug '17

Hi, I have a question regarding galaxy. Can I execute groovy scipts using galaxy? I installed groovy in galaxy docker image and all the dependencies. However, when I try to execute a tool which require groovy engine it says "/export/galaxy-central/database/job_working_directory/000/2/tool_script.sh: line 9: groovy: command not found" So I understood the error that galaxy is not able to find groovy but ideally it should take the groovy engine as it is installed. Can you give me some pointers to solve this issue? -- With Regards, Anshul Tak

4 4

Uncaught Error When Installing Tools From Toolshed
by William, Van Der Pol 24 Jul '17

24 Jul '17

Hello All, I have recently cloned and installed a clean version of Galaxy. I installed a tool from the toolshed and Galaxy says it is properly installed, however when I try to open the tool in the main page all I see is an "Uncaught Error" message. Does anyone have any ideas on what is causing this or at least how I can get a more telling error message? Thanks -Liam

3 2

DeepTools installation error
by Timo Janßen 05 Jul '17

05 Jul '17

Hi all, trying to install the deeptools_suite from the toolshed I only get the following error: "500 Internal Server Error nginx/1.11.10" This happens as well for the dependencies, e.g. deeptools_bigwig_compare. I am currently using Galaxy 16.10 with nginx proxy. Also the installation of the dependency package_python_2_7_matplotlib_1_4 fails because of a missing dependency: "Error installing tool dependency python version 2.7.10: Unable to locate required tool shed repository named package_python_2_7_10 owned by iuc with revision 80931fb5f433." Has anyone seen these problems before and knows a solution? Best regards, Timo Janßen -- ------------------------------------------------------------------------ Timo Janßen Wissenschaftliche Hilfskraft Arbeitsgruppe "Anwendungs- und Informationssysteme" Tel.: +49(0)551/201-1791 E-Mail: timo.janssen(a)gwdg.de ------------------------------------------------------------------------ Gesellschaft für wissenschaftliche Datenverarbeitung mbH Göttingen (GWDG) Am Faßberg 11, 37077 Göttingen, URL: http://www.gwdg.de Tel.: +49 551 201-1510, Fax: +49 551 201-2150, E-Mail: gwdg(a)gwdg.de Service-Hotline: Tel.: +49 551 201-1523, E-Mail: support(a)gwdg.de Geschäftsführer: Prof. Dr. Ramin Yahyapour Aufsichtsratsvorsitzender: Prof. Dr. Norbert Lassau Sitz der Gesellschaft: Göttingen Registergericht: Göttingen, Handelsregister-Nr. B 598 ------------------------------------------------------------------------ Zertifiziert nach ISO 9001 ------------------------------------------------------------------------

6 9

Singularity Container forks ?
by Nikos Nikoloutsakos 20 Jun '17

20 Jun '17

Hello, Are there any galaxy forks using Singularity images instead of Docker ? Is it trivial enough to replace "docker run" with "singularity exec" ? Thank you, Nikos -- Nikos Nikoloutsakos Greek Research and Technology Network (GRNET) ☎ +30 210 7471127 ✉ nikoloutsa(a)grnet.gr hpc.grnet.gr

3 6

bwa_mem and "-t" option
by David Kovalic 01 Jun '17

01 Jun '17

Hi, Is it possible, and if so how, to run the galaxy devteam (version546ada4a9f43) of bwa_mem with the "-t" option and a value >1? "-t INT number of threads [1]" This would be quite useful, and used, for accelerating single bwa mem jobs. Thanks, David

2 5

Large Number of jobs Failing following error
by Evan 31 May '17

31 May '17

My galaxy instance has suddenly begun having jobs failing. The error below is what is produced by the log. galaxy.objectstore CRITICAL 2017-05-31 01:44:49,932 None delete error [Errno 39] Directory not empty:

1 0

Issue with GATK2 on Galaxy Repository.
by OLABODE OLUWASEUN AJAYI 31 May '17

31 May '17

Hi Dev, I am running a local instance Galaxy for developing a variant calling pipeline. I ran into this issue after configuring and installing GATK2 on my local when running the GATK *Realigner Target Creator on the BAM file generated by Mark duplicates.* *Can some suggest how to resolve this issue or please point to how to debug this issue from the GATK2 wrapper? BTW, I follow the instruction by ensuring that my GATK3 environment was set as stated in the Galaxy GATk2 readme.txt.* Below here was the issue I encountered; ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A USER ERROR has occurred (version 2.0-7-g7323e98): ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed ##### ERROR Please do not post this error to the GATK forum ##### ERROR ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. ##### ERROR Visit our website and forum for extensive documentation and answers to ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk ##### ERROR ##### ERROR MESSAGE: Argument with name 'num_cpu_threads_per_data_thread' isn't defined. ##### ERROR ------------------------------------------------------------------------------------------ On Mon, May 29, 2017 at 6:44 PM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote: > Thanks, pull request submitted: > > https://github.com/galaxyproject/galaxy/pull/4121 > > Peter > > > On Mon, May 29, 2017 at 5:23 PM, Saravanaraj Ayyampalayam <raj76(a)uga.edu> > wrote: > > Peter, > > > > Here is the git diff output that shows the changes I made: > > > > diff --git a/lib/galaxy/jobs/runners/__init__.py > b/lib/galaxy/jobs/runners/__init__.py > > index ebf4859..6ee51c8 100644 > > --- a/lib/galaxy/jobs/runners/__init__.py > > +++ b/lib/galaxy/jobs/runners/__init__.py > > @@ -419,7 +419,7 @@ class JobState( object ): > > job_name += '_%s' % self.job_wrapper.tool.old_id > > if self.job_wrapper.user: > > job_name += '_%s' % self.job_wrapper.user > > - self.job_name = ''.join( map( lambda x: x if x in ( > string.letters + string.digits + '_' ) else '_', job_name ) ) > > + self.job_name = ''.join( map( lambda x: x if x in ( > string.ascii_letters + string.digits + '_' ) else '_', job_name ) ) > > > > @staticmethod > > def default_job_file( files_dir, id_tag ): > > diff --git a/lib/galaxy/jobs/runners/drmaa.py b/lib/galaxy/jobs/runners/ > drmaa.py > > index 7c08984..5c5dc62 100644 > > --- a/lib/galaxy/jobs/runners/drmaa.py > > +++ b/lib/galaxy/jobs/runners/drmaa.py > > @@ -394,7 +394,7 @@ class DRMAAJobRunner( AsynchronousJobRunner ): > > job_name += '_%s' % job_wrapper.tool.old_id > > if external_runjob_script is None: > > job_name += '_%s' % job_wrapper.user > > - job_name = ''.join( x if x in ( string.letters + string.digits > + '_' ) else '_' for x in job_name ) > > + job_name = ''.join( x if x in ( string.ascii_letters + > string.digits + '_' ) else '_' for x in job_name ) > > if self.restrict_job_name_length: > > job_name = job_name[:self.restrict_job_name_length] > > return job_name > > > > -Raj > > > >> On May 29, 2017, at 11:33 AM, Peter Cock <p.j.a.cock(a)googlemail.com> > wrote: > >> > >> Thanks Saravanaraj, > >> > >> You should not need to change the locale, after all many Galaxy servers > and > >> their users will be labelling their files in non-English with > >> "special" characters - > >> but perhaps en_US.UTF-8 would be safer in your case as it seems that few > >> people use Galaxy with en_US.iso885915 otherwise this would have been > >> reported before? > >> > >> Can you tell us both places you changed string.letters to > string.ascii_letters > >> please? I could then submit this as a pull request to get Galaxy itself > updated > >> for future release. > >> > >> Peter > >> > >> On Mon, May 29, 2017 at 4:28 PM, Saravanaraj Ayyampalayam < > raj76(a)uga.edu> wrote: > >>> Peter, > >>> > >>> You are correct. Changing string.letters to string.ascii_letters fixed > it. I had to change it in two places. > >>> > >>> My locale is : > >>> > >>> LANG=en_US.iso885915 > >>> LC_CTYPE="en_US.iso885915" > >>> LC_NUMERIC="en_US.iso885915" > >>> LC_TIME="en_US.iso885915" > >>> LC_COLLATE="en_US.iso885915" > >>> LC_MONETARY="en_US.iso885915" > >>> LC_MESSAGES="en_US.iso885915" > >>> LC_PAPER="en_US.iso885915" > >>> LC_NAME="en_US.iso885915" > >>> LC_ADDRESS="en_US.iso885915" > >>> LC_TELEPHONE="en_US.iso885915" > >>> LC_MEASUREMENT="en_US.iso885915" > >>> LC_IDENTIFICATION="en_US.iso885915" > >>> LC_ALL= > >>> > >>> I will talk to our sysadmin and see if I can change the locale to > en_US.UTF-8. > >>> > >>> Thank you very much. > >>> -Raj > >>> > >>> > >>>> On May 29, 2017, at 10:58 AM, Peter Cock <p.j.a.cock(a)googlemail.com> > wrote: > >>>> > >>>> Curious, my new guess is this is position 52 a temporary string from > >>>> this expression: > >>>> > >>>> string.letters + string.digits + '_' > >>>> > >>>> This would fit with it being something unusual about the locale of > >>>> your Galaxy server, and my suggested hack may work - replace > >>>> string.letters with string.ascii_letters > >>>> > >>>> Separately at the Linux command line of the server running Galaxy, and > >>>> on a cluster node, what does the command "locale" give? e.g. I get: > >>>> > >>>> $ locale > >>>> LANG=en_US.UTF-8 > >>>> LC_CTYPE="en_US.UTF-8" > >>>> LC_NUMERIC="en_US.UTF-8" > >>>> LC_TIME="en_US.UTF-8" > >>>> LC_COLLATE="en_US.UTF-8" > >>>> LC_MONETARY="en_US.UTF-8" > >>>> LC_MESSAGES="en_US.UTF-8" > >>>> LC_PAPER="en_US.UTF-8" > >>>> LC_NAME="en_US.UTF-8" > >>>> LC_ADDRESS="en_US.UTF-8" > >>>> LC_TELEPHONE="en_US.UTF-8" > >>>> LC_MEASUREMENT="en_US.UTF-8" > >>>> LC_IDENTIFICATION="en_US.UTF-8" > >>>> LC_ALL= > >>>> > >>>> > >>>> Peter > >>>> > >>>> On Mon, May 29, 2017 at 3:43 PM, Saravanaraj Ayyampalayam < > raj76(a)uga.edu> wrote: > >>>>> Peter, > >>>>> > >>>>> The job name looks OK. Here is the output of the debug statements: > >>>>> > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,423 Making > job_name, tag was '15132', plan to use u'g15132_fastq_to_fasta_ > python_raj76(a)uga.edu' with underscores replacements > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,423 Making > job_name, character 0 in proposed job_name u'g' is 103 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,423 Making > job_name, character 1 in proposed job_name u'1' is 49 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,423 Making > job_name, character 2 in proposed job_name u'5' is 53 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,424 Making > job_name, character 3 in proposed job_name u'1' is 49 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,424 Making > job_name, character 4 in proposed job_name u'3' is 51 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,424 Making > job_name, character 5 in proposed job_name u'2' is 50 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,424 Making > job_name, character 6 in proposed job_name u'_' is 95 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,424 Making > job_name, character 7 in proposed job_name u'f' is 102 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,425 Making > job_name, character 8 in proposed job_name u'a' is 97 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,425 Making > job_name, character 9 in proposed job_name u's' is 115 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,425 Making > job_name, character 10 in proposed job_name u't' is 116 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,425 Making > job_name, character 11 in proposed job_name u'q' is 113 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,425 Making > job_name, character 12 in proposed job_name u'_' is 95 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,426 Making > job_name, character 13 in proposed job_name u't' is 116 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,426 Making > job_name, character 14 in proposed job_name u'o' is 111 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,426 Making > job_name, character 15 in proposed job_name u'_' is 95 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,426 Making > job_name, character 16 in proposed job_name u'f' is 102 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,426 Making > job_name, character 17 in proposed job_name u'a' is 97 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,426 Making > job_name, character 18 in proposed job_name u's' is 115 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,427 Making > job_name, character 19 in proposed job_name u't' is 116 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,427 Making > job_name, character 20 in proposed job_name u'a' is 97 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,427 Making > job_name, character 21 in proposed job_name u'_' is 95 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,427 Making > job_name, character 22 in proposed job_name u'p' is 112 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,427 Making > job_name, character 23 in proposed job_name u'y' is 121 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,427 Making > job_name, character 24 in proposed job_name u't' is 116 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,428 Making > job_name, character 25 in proposed job_name u'h' is 104 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,428 Making > job_name, character 26 in proposed job_name u'o' is 111 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,428 Making > job_name, character 27 in proposed job_name u'n' is 110 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,428 Making > job_name, character 28 in proposed job_name u'_' is 95 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,428 Making > job_name, character 29 in proposed job_name u'r' is 114 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,429 Making > job_name, character 30 in proposed job_name u'a' is 97 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,429 Making > job_name, character 31 in proposed job_name u'j' is 106 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,429 Making > job_name, character 32 in proposed job_name u'7' is 55 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,429 Making > job_name, character 33 in proposed job_name u'6' is 54 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,429 Making > job_name, character 34 in proposed job_name u'@' is 64 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,430 Making > job_name, character 35 in proposed job_name u'u' is 117 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,430 Making > job_name, character 36 in proposed job_name u'g' is 103 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,430 Making > job_name, character 37 in proposed job_name u'a' is 97 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,430 Making > job_name, character 38 in proposed job_name u'.' is 46 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,430 Making > job_name, character 39 in proposed job_name u'e' is 101 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,431 Making > job_name, character 40 in proposed job_name u'd' is 100 > >>>>> galaxy.jobs.runners.drmaa DEBUG 2017-05-29 10:37:21,431 Making > job_name, character 41 in proposed job_name u'u' is 117 > >>>>> galaxy.jobs.runners ERROR 2017-05-29 10:37:21,431 (15132) Unhandled > exception calling queue_job > >>>>> Traceback (most recent call last): > >>>>> File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy- > dist/lib/galaxy/jobs/runners/__init__.py", line 104, in run_next > >>>>> method(arg) > >>>>> File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy- > dist/lib/galaxy/jobs/runners/drmaa.py", line 132, in queue_job > >>>>> job_name = self._job_name(job_wrapper) > >>>>> File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy- > dist/lib/galaxy/jobs/runners/drmaa.py", line 400, in _job_name > >>>>> job_name = ''.join( x if x in ( string.letters + string.digits + > '_' ) else '_' for x in job_name ) > >>>>> File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy- > dist/lib/galaxy/jobs/runners/drmaa.py", line 400, in <genexpr> > >>>>> job_name = ''.join( x if x in ( string.letters + string.digits + > '_' ) else '_' for x in job_name ) > >>>>> UnicodeDecodeError: 'ascii' codec can't decode byte 0xa6 in position > 52: ordinal not in range(128) > >>>>> > >>>>> > >>>>> There is no sign of the 0xa6 at position 52 (the job name is only 42 > chars long) in the job name. > >>>>> > >>>>> Thanks! > >>>>> -Raj > >>>>> > >>>>> > >>>>>> On May 29, 2017, at 5:50 AM, Peter Cock <p.j.a.cock(a)googlemail.com> > wrote: > >>>>>> > >>>>>> Time for more debugging, try inserting something like this inserted > >>>>>> the line above into > >>>>>> /panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy- > dist/lib/galaxy/jobs/runners/drmaa.py > >>>>>> (having backed up the file): > >>>>>> > >>>>>> log.debug( 'Making job_name, tag was %r, plan to use %r with > >>>>>> underscores replacements' % (galaxy_id_tag, job_name)) > >>>>>> > >>>>>> And if that doesn't help, check all the characters: > >>>>>> > >>>>>> for i, letter in enumerate(job_name): log.debug( 'Making job_name, > >>>>>> character %i in proposed job_name %r is %i' % (i, letter, > >>>>>> ord(letter))) > >>>>>> > >>>>>> My hunch is that the locale of the Galaxy server differs from that > on > >>>>>> the cluster, meaning DRMAA is stricter about allowed characters > >>>>>> because Python's string.letters would be whatever is allowed on the > >>>>>> Galaxy server's locale. > >>>>>> > >>>>>> If I am right, a crude fix would be switching to using > >>>>>> string.ascii_letters, i.e. > >>>>>> > >>>>>> job_name = ''.join( x if x in ( string.ascii_letters + > string.digits + > >>>>>> '_' ) else '_' for x in job_name ) > >>>>>> > >>>>>> Peter > >>>>>> > >>>>>> On Mon, May 29, 2017 at 6:54 AM, Saravanaraj Ayyampalayam < > raj76(a)uga.edu> wrote: > >>>>>>> Hello, > >>>>>>> > >>>>>>> I updated to the latest version (17.05) galaxy code. I was > updating from a very old version. > >>>>>>> I fixed all the issues with except one. I am getting the following > error when I submit a job. > >>>>>>> > >>>>>>> galaxy.jobs.runners ERROR 2017-05-29 01:42:44,008 (15131) > Unhandled exception calling queue_job > >>>>>>> Traceback (most recent call last): > >>>>>>> File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy- > dist/lib/galaxy/jobs/runners/__init__.py", line 104, in run_next > >>>>>>> method(arg) > >>>>>>> File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy- > dist/lib/galaxy/jobs/runners/drmaa.py", line 132, in queue_job > >>>>>>> job_name = self._job_name(job_wrapper) > >>>>>>> File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy- > dist/lib/galaxy/jobs/runners/drmaa.py", line 397, in _job_name > >>>>>>> job_name = ''.join( x if x in ( string.letters + string.digits + > '_' ) else '_' for x in job_name ) > >>>>>>> File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy- > dist/lib/galaxy/jobs/runners/drmaa.py", line 397, in <genexpr> > >>>>>>> job_name = ''.join( x if x in ( string.letters + string.digits + > '_' ) else '_' for x in job_name ) > >>>>>>> UnicodeDecodeError: 'ascii' codec can't decode byte 0xa6 in > position 52: ordinal not in range(128) > >>>>>>> > >>>>>>> I spent a day trying to debug this and didn’t get anywhere. The > job_name looks OK. > >>>>>>> > >>>>>>> I would really appreciate some help from the community. > >>>>>>> > >>>>>>> Thanks! > >>>>>>> -Raj > >>>>>>> > >>>>>>> ___________________________________________________________ > >>>>>>> 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: > >>>>>>> https://lists.galaxyproject.org/ > >>>>>>> > >>>>>>> To search Galaxy mailing lists use the unified search at: > >>>>>>> http://galaxyproject.org/search/ > >>>>> > >>> > > > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ > -- Ajayi Olabode O. University of the western cape South Africa National Bioinformatics Institute(Msc In Progress) Department of Computer Science Computer Science (B.sc & Hons) SAP ERP, MCSE,MCTS,MCP,MCSA Mechanical Engineering E-mail: boraton2010(a)gmail.com Mobile Phone: 0791024568 "You are the future. Believe in yourself, in your greatness... Become all you are capable of and more. Dare to dream. Dare to innovate. Dare to Lead" -- Disclaimer - This e-mail is subject to UWC policies and e-mail disclaimer published on our website at: https://www.uwc.ac.za/Pages/emaildisclaimer.aspx

3 2

jupyter notebook / nginx / ssl
by cristel thomas 30 May '17

30 May '17

Hi Galaxy developers, we are trying to get notebooks to run on our production server, with half success: we can get jupyter to load, and it does access the history, but notebooks uploaded to history do not load, and any modification to the notebook provided can be saved but do not show up when the notebook is re-opened. we're running NGINX and have SSL certs in place. Any idea how to fix this? Thanks Cris

1 0

Issue with job_name, UnicodeDecodeError in drmaa
by Saravanaraj Ayyampalayam 29 May '17

29 May '17

Hello, I updated to the latest version (17.05) galaxy code. I was updating from a very old version. I fixed all the issues with except one. I am getting the following error when I submit a job. galaxy.jobs.runners ERROR 2017-05-29 01:42:44,008 (15131) Unhandled exception calling queue_job Traceback (most recent call last): File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 104, in run_next method(arg) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 132, in queue_job job_name = self._job_name(job_wrapper) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 397, in _job_name job_name = ''.join( x if x in ( string.letters + string.digits + '_' ) else '_' for x in job_name ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 397, in <genexpr> job_name = ''.join( x if x in ( string.letters + string.digits + '_' ) else '_' for x in job_name ) UnicodeDecodeError: 'ascii' codec can't decode byte 0xa6 in position 52: ordinal not in range(128) I spent a day trying to debug this and didn’t get anywhere. The job_name looks OK. I would really appreciate some help from the community. Thanks! -Raj

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galaxy-dev May 2017