November 2016 - galaxy-dev - lists.galaxyproject.org

Error after loading up bebatut MetaPhlAn2 to our local Galaxy instance
by Dooley, Damion 23 Nov '16

23 Nov '16

After loading up MetaPhlAn2 (8991e05c44e4) from toolshed and attaching db_v20, I tried running a few fasta files on it, including the tool's test-data/input_sequences.fasta file, but after about a minute of churning I keep getting this error: Fatal error: Exit code 1 () … Traceback (most recent call last): File "/usr/local/galaxy/shared/tool_dependency/metaphlan2/2.5.0/bebatut/package_ metaphlan2_2_5_0/43a80f92815f/metaphlan2.py", line 1172, in <module> tree = TaxTree( mpa_pkl, ignore_markers ) File "/usr/local/galaxy/shared/tool_dependency/metaphlan2/2.5.0/bebatut/package_ metaphlan2_2_5_0/43a80f92815f/metaphlan2.py", line 857, in __init__ clades_txt = ((l.strip().split("|"),n) for l,n in mpa_pkl['taxonomy'].items()) AttributeError: 'list' object has no attribute 'items' I believe the database is connected properly, but would the tool run for a while even if it wasn't? It seems like the mpa_pkl file data is loaded via the --mpa_pkl attribute as in tool command line: which bowtie2 || exit 200) && metaphlan2.py /galaxy_data/production1/files/013/dataset_13546.dat -o /galaxy_data/production1/files/013/dataset_13547.dat --input_type fasta --bowtie2_exe `which bowtie2` --bowtie2db /usr/local/packages/metaphlan2/db_v20/mpa_v20_m200 --mpa_pkl /usr/local/packages/metaphlan2/db_v20/mpa_v20_m200".pkl" --no_map -t rel_ab --tax_lev a --min_cu_len 2000 --min_alignment_len 0 --stat_q 0.1 -s /galaxy_data/production1/files/013/dataset_13548.dat Tool's xml file does a touch of funny business with the mpa_v20_m200".pkl" file name parameter, but I guess that works if no one else has a problem with it. Thx for any info, Damion

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Code File Execution
by Katherine Beaulieu 21 Nov '16

21 Nov '16

Hi Everyone, Does anyone know how execution of code files happens? Is there a function somewhere that fills the parameters in? Cheers, Katherine

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Running script prior to initial login
by Evan Clark 19 Nov '16

19 Nov '16

Our production instance has been connected to apache for external authentication. What we would like to know if there is a method to run a script after a users initial login to generate a folder with their email in the file upload location. ---Regards, Evan Clark

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More problems installing Galaxy
by Hernán Piqueras 18 Nov '16

18 Nov '16

I have a Linux with both Python 2.6 and Python 2.7. Apparently Python is so bad designed that you cannot simply upgrade from 2.6 to 2.7 without breaking your system. As latest Galaxy works with Python 2.7, I put an alias in my .bashrc to /usr/local/bin/python2.7 and the same with virtualenv. I also enabled bash debugging and enabled expanded alias into .sh scripts. Then I ran : $ sh galaxy/run.sh ... lots of output --- Requirement already satisfied: pysam==0.8.4+gx1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) Requirement already satisfied: PasteScript in ./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.7.0.dev5->-r requirements.txt (line 51)) ++ PYTHONPATH=lib ++ /usr/local/bin/python2.7 -c 'import galaxy.dependencies; print '\''\n'\''.join(galaxy.dependencies.optional('\''config/galaxy.ini'\''))' Traceback (most recent call last): File "<string>", line 1, in <module> File "/home/galaxy/galaxy/lib/galaxy/dependencies/__init__.py", line 9, in <module> from galaxy.util import asbool File "/home/galaxy/galaxy/lib/galaxy/util/__init__.py", line 31, in <module> from six import binary_type, iteritems, PY3, string_types, text_type ImportError: No module named six + GALAXY_CONDITIONAL_DEPENDENCIES= + exit 1 If I check with root user, six package is installed. My guess was I am missing an alias to pip2.7, then I added such alias in my .bashrc and again: $ sh galaxy/run.sh ... lots of output --- ++ '[' -n /bin/bash -o -n '' ']' ++ hash -r + unset PYTHONPATH + '[' -z /home/galaxy/galaxy/.venv ']' + : https://wheels.galaxyproject.org/simple + '[' 1 -eq 1 ']' + /usr/local/bin/pip2.7 install 'pip>=8.1' Traceback (most recent call last): File "/usr/local/bin/pip2.7", line 5, in <module> from pkg_resources import load_entry_point File "/usr/local/lib/python2.7/site-packages/distribute-0.6.44-py2.7.egg/pkg_resources.py", line 2850, in <module> working_set.require(__requires__) File "/usr/local/lib/python2.7/site-packages/distribute-0.6.44-py2.7.egg/pkg_resources.py", line 696, in require needed = self.resolve(parse_requirements(requirements)) File "/usr/local/lib/python2.7/site-packages/distribute-0.6.44-py2.7.egg/pkg_resources.py", line 594, in resolve raise DistributionNotFound(req) pkg_resources.DistributionNotFound: pip==9.0.1 # pip --version pip 9.0.1 from /usr/local/lib/python2.7/site-packages/pip-9.0.1-py2.7.egg (python 2.7) I have installed Python 2.7 and its tools (virtualenv, pip, etc) following official guidelines. How can install the missing dependecies?

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Using pbs-python with glibc version 2.12
by David Lee 18 Nov '16

18 Nov '16

Hi, I'm trying to install Galaxy version 16.07 on a cluster with the PBS job scheduler that is using glibc version 2.12. The following error message suggests that pbs-python needs at least glibc version 2.14 - assert pbs is not None, PBS_IMPORT_MESSAGE AssertionError: The Python pbs-python package is required to use this feature, please install it or correct the following error: ImportError /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/lib/python2.7/site-packages/pbs/_pbs.so) I'm told by an administrator of the cluster that updating to glibc version 2.14 or higher would require a major overhaul of all the software on the cluster. Does anybody have a workaround for this problem? Could a newer version of glibc be used next to version 2.12 just for installation purposes? Thanks for your help, David

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Galaxy on the Cloud with Openstack
by Katherine Beaulieu 17 Nov '16

17 Nov '16

Hi Galaxy Community, Does anyone have a really great guide as to how I could get Galaxy on the Cloud up and running with our private openstack cloud orchestrated by fuel 7.0? Cheers, Katherine

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Restart Galaxy without interruption
by Gildas Le Corguillé 16 Nov '16

16 Nov '16

Hi, Since Galaxy need to be restarted sometime (load datatype, add ressources in .loc, apply changes in the galaxy.ini), is anybody of you have solutions to restart it without interrupt the service? We are now using nginx, uwsgi and supervisord. My hope is to split the Galaxy process in two group (1 uwsgi and 2 job handlers per group). That way, we will be able to restart the group1 and then the group2. I was planning to set the 2 uwsgi servers and delegate the load balancing to ngnix (https://www.nginx.com/resources/admin-guide/load-balancer/ <https://www.nginx.com/resources/admin-guide/load-balancer/>) But maybe, some of you already implemented that and can provide me some advices or warnings. The job handler part seems easier to deal with --server-name=handler1_%(process_num)s --server-name=handler2_%(process_num)s Thanks by advance Gildas ----------------------------------------------------------------- Gildas Le Corguillé - Bioinformatician/Bioanalyste Plateform ABiMS (Analyses and Bioinformatics for Marine Science) http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/> Member of the Workflow4Metabolomics project http://workflow4metabolomics.org <http://workflow4metabolomics.org/> Station Biologique de Roscoff - UPMC/CNRS - FR2424 Place Georges Teissier 29680 Roscoff FRANCE tel: +33 2 98 29 23 81 ------------------------------------------------------------------

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planemo with --docker and --conda_dependency_resolution
by Steve Cassidy 15 Nov '16

15 Nov '16

Hi, I’m trying to test a few tools, one of which uses a docker container, the others use dependencies that can be found in conda. I can test each one by using either —docker or —conda_dependency_resolution with planemo, but when I try to give both of these, it seems to want to only use docker and fails because it can’t find a usable container. I’ve hunted around the planemo sources but i can’t see what magic is creating this problem. Am I just asking too much? Any pointers appreciated. Thanks, Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy

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Elastic Bean Stalk
by Ryan G 15 Nov '16

15 Nov '16

Hi all - I was wondering, if we deploy Galaxy in AWS, can we take advantage of Elastic BeanStalk to scale our instances based on demand instead of trying to configure Galaxy to perform well for our users? Ryan

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Reporting issues for the wiki? e.g. universe_wgsi.ini still widely used
by Peter Cock 15 Nov '16

15 Nov '16

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