- galaxy-dev - lists.galaxyproject.org

Release of Galaxy 17.05
by Jennifer Hillman-Jackson 12 Jun '17

12 Jun '17

Dear Galaxy Fans, We are pleased to announce the *release of Galaxy 17.05*. Thanks to the #usegalaxy committers and you, our community! Full release notes: https://docs.galaxyproject.org/en/master/releases/17.05_announce.html Highlights: *Tag your data with propagating hashtags* Large Galaxy histories used to be messy. Hashtags make it easy to track dataset (and collection) relationships. These two movies (both under a minute) explain how to use this with datasets <https://vimeo.com/216884518> and with collections <https://vimeo.com/216895965>. Learn more about Galaxy histories in our updated tutorial <https://galaxyproject.org/tutorials/histories/> *Drag & Drop datasets into tool inputs*Interface now allows dragging datasets from history panel into the content selectors of the tool form. Implemented in Pull Request 3871 <https://github.com/galaxyproject/galaxy/pull/3871>.*Upload directly to a collection* You can now bypass the history manipulation and upload your data straight into a collection for convenience. Learn more about collections and how to use them in a new tutorial <https://galaxyproject.org/tutorials/collections/>. We extend special thanks to the 64 New Contributors <https://docs.galaxyproject.org/en/master/releases/17.05_announce.html#new-c…> to Galaxy in the past year. *Thanks for using Galaxy!* *http://galaxyproject.org <http://galaxyproject.org>*

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AD Intergration
by John Chen 08 Jun '17

08 Jun '17

Hi, I am trying to integrate AD with Galaxy. My auth_config.xml look like the below, but galaxy won't start with those setting. If anyone has any other sample of a configuration that they don't mind sharing, it be great. The Python LDAP has been installed, RHEL7 alone with ldap-dev <auth> <authenticator> <type>activedirectory</type> <options> <allow-register>False</allow-register> <auto-register>True</auto-register> <server><a class="moz-txt-link-freetext" href="ldap://dc1.example.com">ldap://dc1.example.com</server> <login-use-username>True</login-use-username> <search-fields>sAMAccountName,mail</search-fields> <search-base>dc=dc1,dc=example,dc=com</search-base> <search-filter>(&(objectClass=user)(sAMAccountName={username}))</search-filter> <search-user>jsmith</search-user> <search-password>mysecret</search-password> <bind-user>{sAMAccountName}</bind-user> <bind-password>{password}</bind-password> <auto-register-username>{sAMAccountName}</auto-register-username> <auto-register-email>{mail}</auto-register-email> </options> </authenticator> </auth> Any suggestion ?? Thanks

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GCC2017: Talk schedule posted; Register by 16 June
by Dave Clements 08 Jun '17

08 Jun '17

Hello all, A few GCC2017 <https://gcc2017.sciencesconf.org/> things: 1) The presentation schedule <https://gcc2017.sched.com/> has been posted. 2) The poster and demo schedule will likely be posted later today 3) Lightning talk <https://gcc2017.sciencesconf.org/page/submit> and birds-of-a-feather <https://docs.google.com/forms/d/e/1FAIpQLSdRCs97OWt47qmMxWZAtSV3TTLJ24IhW0m…> submission are still open 4) There is still limited space available for late poster and computer demo submissions <https://gcc2017.sciencesconf.org/page/submit> 5) Register by 16 June <https://gcc2017.sciencesconf.org/page/registration> >From this point on most/all emails about GCC2017 will go only to those that have registered for it. The final announcement going out to non-Galaxy mailing lists is below. Please forward to anyone who you think might be interested. And, we do hope to see you in Montpellier! Dave C on behalf of the GCC2017 Organizing Committee -- 2017 Galaxy Community Conference (GCC2017) 26-30 June 2017 Montpellier, France https://gcc2017.sciencesconf.org/ https://gcc2017.sched.com/ -- The Galaxy Community Conference (GCC) <https://gcc2017.sciencesconf.org/> brings together researchers working in and supporting data intensive life science research. There is no better place to share your work and learn from others that are addressing diverse questions and facing common challenges in data intensive biology. GCC participants work across the tree of life, around the world, and represent universities, research organizations, industry, medical schools and research hospitals. GCC2017 will be in Montpellier, France, 26-30 June and features two days of presentations, discussions, poster sessions, lightning talks, computer demos, keynotes, and birds-of-a-feather meetups <https://gcc2017.sched.com/overview/type/Conference>, all about data-intensive biology and the tools that support it. GCC2017 also features data and coding hackathons <https://gcc2017.sciencesconf.org/page/hackathon>, and two days of training <https://gcc2017.sched.com/overview/type/Training> covering 16 different topics. GCC2017 will be held at Le Corum Conference Centre <http://www.montpellier-events.com/en/The-Corum/Presentation> in the heart of Montpellier <https://gcc2017.sciencesconf.org/resource/page/id/2>, just 10km from the Mediterranean. Registration closes 16 June <https://gcc2017.sciencesconf.org/page/registration>. Costs start at 75€ per day for postdocs and students. If you work in data intensive life science research then GCC2017 is an ideal opportunity to present your work. Lightning talk <https://gcc2017.sciencesconf.org/page/submit> and birds-of-a-feather <https://docs.google.com/forms/d/e/1FAIpQLSdRCs97OWt47qmMxWZAtSV3TTLJ24IhW0m…> submission are still open, and there is limited space available for late poster and computer demo submissions <https://gcc2017.sciencesconf.org/page/submit>. About Galaxy Galaxy <https://galaxyproject.org/> is an open, web-based platform for data-intensive biomedical analysis used by tens of thousands of researchers around the world. It supports ad hoc exploration and analysis through scalable and repeatable data analysis pipelines for large research studies. Galaxy is available in over 90 free and publicly accessible web servers, on public and national cloud infrastructures, and is locally installed at hundreds, if not thousands, of research organisations around the world. We hope to see you in Montpellier! Au revoir, The GCC2017 Organising Committee -- https://galaxyproject.org/ https://getgalaxy.org/ https://usegalaxy.org/ https://gcc2017.sciencesconf.org/

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Paste/Fetch data, indicate filename before download data (default = Pasted Entry)
by SAPET, Frederic 08 Jun '17

08 Jun '17

hello just like Floreline : http://dev.list.galaxyproject.org/Paste-Fetch-data-indicate-filename-before… some of my colleagues ask me if it could be possible to rename the uploaded ( from pasted data) file before the download. I would like to know if it could be added as an enhancement for a future release ? thank you Fred --- Frederic Sapet Bioinformatics Research Engineer BIOGEMMA - Upstream Genomics Group Centre de Recherche de Chappes CS 90126 63720 CHAPPES FRANCE Tel : +33 (0)4 73 67 88 54 Fax : +33 (0)4 73 67 88 99 E-mail : frederic.sapet(a)biogemma.com<mailto:frederic.sapet@biogemma.com>

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composite datatypes: uploading and optional files
by Peter van Heusden 06 Jun '17

06 Jun '17

Hi there We've got a composite datatype (neostore) for Neo4j databases. Currently the upload is disabled because to upload you need to select each individual file of the database directory (which is tedious). Is there a more efficient way to upload composite datatypes? E.g. as a tar.gz or zip file? If not, has anyone looked into supporting this? (I see @jmchilton was noted as working on a composite uploading for 17.05) Secondly, we're moving to support Neo4j 3.2.0. In this version there is a minor (1 file) change in the files used to store the database. Can composite datatypes have "optional files"? Thanks, Peter

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June 2017 News of the Galaxy
by Dave Clements 06 Jun '17

06 Jun '17

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galaxy & DFARS
by Eric Rasche 02 Jun '17

02 Jun '17

Has anyone dealt with DFARS requirements and data in Galaxy? Similar themes across other requirement sets might be: encryption of data at rest, DoD 32-pass secure deletion of data, providing access logs for datasets/histories/intermediate steps, providing logs of changes to access control policies for histories/datasets. Just wondering before we come under these regs and need to be doing all of this. Cheers, Eric

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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

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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:

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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

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