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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

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

2 7

Shiny in Galaxy
by Mohamed Kassam 26 May '17

26 May '17

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

2 1

protein ligand docking
by Matthias Bernt 24 May '17

24 May '17

Dear list, I have recently evaluated the software for protein docking that is available in the toolshed. I could need some help / suggestions. 1. autodock_vina The receptor of my example contains Au atoms which are not understood by autodock_vina. For autodock there is the possibility to add configuration for atoms: http://autodock.scripps.edu/faqs-help/how-to/adding-new-atom-parameters-to-… Does somebody know if this is also possible for autodock_vina in galaxy? In my pdb file there are CONECT lines which cause autodock_vina to abort. If I remove them the program runs (when the Au atoms are also removed). So this is the smaller problem (Maybe this can be solved by extending openbabel). 2. rdock Fails with a memory access failure /gpfs1/data/galaxy_server/galaxy-dev/database/dependencies/_conda/envs/__rDock(a)2013.1/bin/rbcavity: Zeile 7: 104454 Speicherzugriffsfehler (Speicherabzug geschrieben) "$RBT_ROOT/bin/$PROGNAME" "$@" 3. caddsuite_workflows + caddsuite_linux_x86_64 The installation of the workflows works, but I do not see them in galaxy? The installation of the other package fails with: No information is available for the requested repository revision. One or more of the following parameter values is likely invalid: tool_shed_url: https://toolshed.g2.bx.psu.edu/ name: caddsuite_linux_x86_64 owner: marcel changeset_revision: 026f5a483650 err_code: 400008 4. BALL I just tested one tool of the suite: ProteinProtonator. This fails with command not found. Fatal error: Exit code 127 () /gpfs1/data/galaxy_server/galaxy-dev/jobs_dir/000/165/tool_script.sh: Zeile 9: ProteinProtonator: Kommando nicht gefunden. Are there any suggestion on how to solve these problems or other options for docking with galaxy. Cheers, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

1 0

python subprocess OSError when running bwa-mem
by Georgios Nikolis 24 May '17

24 May '17

2 3

Decrease Galaxy polling of slurm?
by Philip Blood 24 May '17

24 May '17

An admin at our center noticed our Galaxy instance is polling slurm every second and asked if the polling frequency can be decreased. Is there an easy way to do this? Phil -- Philip D. Blood, Ph.D. Senior Computational Scientist Voice: (412) 268-9329 Pittsburgh Supercomputing Center Fax: (412) 268-5832 Carnegie Mellon University Email: blood(a)psc.edu

2 2

vcftools - errors running vcf-merge
by Poole, Richard 24 May '17

24 May '17

Hi all, I am trying to run the vcf-merge tool, which depends on the vcftools 0.1.11 package. I have this vcftools package and also the required tabix 0.2.6 both installed via the toolshed (tabix is set in the PATH of the Galaxy startup script). However, I keep getting gunzip error messages such as the following: Log: tool progress gunzip: error writing to output: Broken pipe gunzip: 0.vcf.sorted.gz: uncompress failed Using column name 'mutant' for 0.vcf.sorted.gz:mutant Using column name 'sibling' for 0.vcf.sorted.gz:sibling gunzip: error writing to output: Broken pipe gunzip: 1.vcf.sorted.gz: uncompress failed Using column name '1.vcf.sorted_mutant' for 1.vcf.sorted.gz:mutant Using column name '1.vcf.sorted_sibling' for 1.vcf.sorted.gz:sibling Does anyone have any idea how to solve this? The command that the wrapper is generating is: vcf-sort /Volumes/ngs/database/files/058/dataset_58073.dat > 0.vcf.sorted ; bgzip 0.vcf.sorted ; tabix -p vcf 0.vcf.sorted.gz ; vcf-sort /Volumes/ngs/database/files/058/dataset_58078.dat > 1.vcf.sorted ; bgzip 1.vcf.sorted ; tabix -p vcf 1.vcf.sorted.gz ; vcf-merge 0.vcf.sorted.gz 1.vcf.sorted.gz > /Volumes/ngs/database/files/058/dataset_58489.dat Thanks, Richard

1 0

cluster access
by Matthias Bernt 22 May '17

22 May '17

Dear list, I'm just starting to get jobs submitted to our cluster as real system user. I read in the documentation that the name of the system user is determined by "the Galaxy user's email address (with the @domain stripped off)". But this does not work on our system, rather the username stored in the galaxy_user table is the name of the user (this is correctly generated by the LDAP login). The job runner script seems to get the user id, so I guess I need to dig deeper. So my question is: Where could I change this behavior? Thanks a lot. Cheers, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

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OpenBabel Requirements
by Matthias Bernt 22 May '17

22 May '17

Dear galaxy-dev list, I have problems to install package_openbabel. The problem seems to be that cmake is not found during installation. The documentation also states that: "Compiling OpenBabel requires g++ and CMake 2.4+" My question is: Does this refer to cmake installed on the system or in galaxy (since there is also package_cmake_3_2_3)? Thanks a lot. Cheers, Matthias

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