galaxy-dev January 2017

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36 participants
37 discussions

January 2017 News of the Galaxy: Register now for GAMe 2017!
by Dave Clements 04 Jan '17

04 Jan '17

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wrapper for tool with multiple outputs
by Jochen Bick 04 Jan '17

04 Jan '17

Hi, I have a tool that produces multiple output files a log file, two bam files. (https://github.com/nugentechnologies/nudup) The tool it self provides an option called --out to specify a path to a directory with a prefix that will be added to the output files: --out /tmp/out this will produce 3 files: /tmp/out_dup_log.txt /tmp/out.sorted.dedup.bam /tmp/out.sorted.markdup.bam so my question is if this out prefix will give me problems overwriting next output files coming from this tool? Cheers Jochen

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installation error on venv dependencies.xml
by Bakker, Linda 04 Jan '17

04 Jan '17

Hi All, I posted my question before the holidays but i got not reply. Can someone please point me in the right direction? I am having some problems with my tool dependencies to setup a python venv. Dependencies.xml looks like this: [X] [X][cid:7b48a44d-07dd-4838-8f90-5024d9d22593] When i install my tool from the toolshed, it fails to install the venv dependency with this error message: [X][cid:0f2c174a-5011-423f-9eaf-ef2ed88c353d] I am not sure what the problem exactly seems to be. os.py should be a default python package right or do i need to specify it in the dependencies file? Together with our system administrator, we have been trying to solve the issue, but no luck so far. Is my dependencies.xml file ok? Thanks & a happy new year! with regards , Linda Bakker -- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 email: linda.bakker(a)wur.nl<mailto:linda.bakker@wur.nl>

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GalaxyAdmins Online Meetup 15 December
by Dave Clements 04 Jan '17

04 Jan '17

Hello all, The next GalaxyAdmins online meetup <https://new.galaxyproject.org/Community/GalaxyAdmins/Meetups/2016_12_15/> is this Thursday, 15 December at [see your local time <http://bit.ly/2h2QOsT>]. The meetup will feature two presentations: - Galaxy Training Materials: Community creation, curation, and use, by Björn Grüning and Bérénice Batut, University of Freiburg - The new Galaxy Hub: Community creation, curation, and use, by Dannon Baker, Johns Hopkins University. The call will last around an hour, and will include discussion. Hope to see you there, Dave C & HAns-Rudolf -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Dump SQlite to mySQL
by evan clark 03 Jan '17

03 Jan '17

Is there a script someone has designed to properly dump the galaxy sqlite database to a mySQL database?

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psycopg2 module and SSL connection to postgresql
by Floreline TOUCHARD 03 Jan '17

03 Jan '17

Hi Galaxy Community, I have the same problem than Nikolay few years ago ( http://dev.list.galaxyproject.org/connecting-to-a-DB-on-a-different-host-td…) : I would like to connect my Galaxy instance to my postgresql database using SSL encryption and Auth method md5. I have no problems connecting to the DB via the command line with SSL encryption. When setting the galaxy.ini file with postgresql database connection to "postgresql://<USERNAME>:<PWD>@<HOST>:5432/<DB_NAME>?sslmode=require", I get the following message : "OperationalError: (psycopg2.OperationalError) sslmode value "require" invalid when SSL support is not compiled in" Regarding the former post I thought that it might come from the module psycopg2's compilation. I followed the steps of the post but encounter a different error. What I did: 1. Downloaded a tar.gz of psycopg2 2.5.1 (I saw the needed version in the file eggs.ini) to <install dir>/galaxy/ and unpacked it there 2. cd into psycopg2, modified the setup.py according to the instructions (added the line containing scramble_lib) 3. export the path to pg_config (export PATH=<path/to/postgresql>/bin:$PATH) 4. added the file ez_setup.py (downloaded from https://bootstrap.pypa.io/ez_setup.py) to <install dir>/galaxy/scripts/scramble/lib/, the same dir where scramble_lib.py is located 5. ran PYTHONPATH=<install dir>/galaxy/scripts/scramble/lib python setup.py egg_info --tag-build=_9.4.4_static bdist_egg And get the following error : " Traceback (most recent call last): File "setup.py", line 57, in <module> from scramble_lib import * File "<install dir>/galaxy/scripts/scramble/lib/scramble_lib.py", line 150, in <module> use_setuptools( download_delay=8, to_dir=os.path.dirname( __file__ ) ) File "<install dir>/galaxy/scripts/scramble/lib/ez_setup.py", line 160, in use_setuptools version = _resolve_version(version) File "<install dir>/galaxy/scripts/scramble/lib/ez_setup.py", line 368, in _resolve_version resp = urlopen(meta_url) File "/usr/lib64/python2.6/urllib2.py", line 126, in urlopen return _opener.open(url, data, timeout) File "/usr/lib64/python2.6/urllib2.py", line 391, in open response = self._open(req, data) File "/usr/lib64/python2.6/urllib2.py", line 409, in _open '_open', req) File "/usr/lib64/python2.6/urllib2.py", line 369, in _call_chain result = func(*args) File "/usr/lib64/python2.6/urllib2.py", line 1198, in https_open return self.do_open(httplib.HTTPSConnection, req) File "/usr/lib64/python2.6/urllib2.py", line 1165, in do_open raise URLError(err) urllib2.URLError: <urlopen error [Errno -2] Name or service not known> " Could it be because I have no internet access ? What module should I install to enable SSL encryption ? Additional information : - Postgresql version 9.4.4 - Galaxy version 15.10 - I use virtualenv for python environment Thanks in advance, Floreline

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GIE security implications
by Tamir,Ido 03 Jan '17

03 Jan '17

Hi, what are the security implications of GIE? I saw the overview on the GIE page, but its not clear to me how dangerous they are. "They have complex interactions with numerous services, you’ll need to be a fairly competent SysAdmin to debug all of the possible problems that can occur during deployment” Is it possible to describe what the docker container has access to and what could possibly go wrong? thank you very much, ido

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galaxy-dev January 2017