Re: [galaxy-dev] Galaxy broken after update to 16.01
Mattias, what does your supervisord config look like? Specifically, does it contain an environment variable to direct the Galaxy handler to the correct virtualenv? Peter On 9 February 2016 at 16:03, Matthias De Smetwrote: > Hi all, > > > We were tracking the galaxy master branch on our local server and are > looking to migrate to v16.01. > The galaxy processes are managed bij supervisor as shown here ( > https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling). > After updating all dependencies in our venv we tried to restart the server > but got the following issue: > > Loading paste environment: > config:/home/galaxy/galaxy-dist/config/galaxy.ini > Traceback (most recent call last): > File > "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py", > line 247, in loadapp > return loadobj(APP, uri, name=name, **kw) > File > "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py", > line 271, in loadobj > global_conf=global_conf) > File > "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py", > line 296, in loadcontext > global_conf=global_conf) > File > "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py", > line 320, in _loadconfig > return loader.get_context(object_type, name, global_conf) > File > "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py", > line 458, in get_context > section) > File > "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py", > line 517, in _context_from_explicit > value = import_string(found_expr) > File > "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py", > line 22, in import_string > return pkg_resources.EntryPoint.parse("x=" + s).load(False) > File > "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pkg_resources/__init__.py", > line 2380, in load > return self.resolve() > File > "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pkg_resources/__init__.py", > line 2386, in resolve > module = __import__(self.module_name, fromlist=['__name__'], level=0) > File "lib/galaxy/web/buildapp.py", line 5, in > from galaxy.webapps.galaxy.buildapp import app_factory > File "lib/galaxy/webapps/galaxy/buildapp.py", line 15, in > import galaxy.app > File "lib/galaxy/app.py", line 9, in > import galaxy.queues > File "lib/galaxy/queues.py", line 9, in > from kombu import Exchange, Queue, Connection > File > "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/__init__.py", > line 67, in __getattr__ > module = __import__(object_origins[name], None, None, [name]) > File > "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/entity.py", > line 10, in > from .abstract import MaybeChannelBound, Object > File > "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/abstract.py", > line 12, in > from .connection import maybe_channel > File > "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/connection.py", > line 19, in > from kombu import exceptions > File > "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/exceptions.py", > line 12, in > from amqp import ChannelError, ConnectionError, ResourceError > File > "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/amqp/__init__.py", > line 34, in > from .connection import Connection # noqa > File > "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/amqp/connection.py", > line 40, in > from .transport import create_transport > File > "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/amqp/transport.py", > line 21, in > import ssl > File "/Shared/Software/Cellar/python/2.7.11/lib/python2.7/ssl.py", line > 97, in > import _ssl # if we can't import it, let the error > propagate > ImportError: > /home/galaxy/galaxy-dist/.venv/lib/python2.7/lib-dynload/_ssl.so: undefined > symbol: SSL_CTX_set_alpn_protos > > So far we have tried: > - rebuilding the venv > - reinstalling python > > Funny thing is, when we start the configuration with the “run.sh” script > instead of through supervisor everything seems to work just fine. > > We’re at a loss, please help! > Thanks! > Matthias > > > ___ > 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/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to
Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration
Hi, sorry for the late response ! I tested the modifications proposed in the "Allow to select multiple database" pull request and it works !!! Thanks a lot ! Floreline. P.S : I'm not familiar with all github functionnalities yet, but I will work on it ;) 2016-01-20 16:07 GMT+01:00 Peter Cock: > On Wed, Jan 20, 2016 at 2:43 PM, Gildas Le Corguillé > wrote: > > Hi, > > > > A long time ago, in a far far svn repo, we did this "multiple=true" on > Peter > > wrappers. > > > > I will try to propose it quickly :) > > > > Gildas > > Great - a pull request against https://github.com/peterjc/galaxy_blast > but if your SVN repo is still online, or you can make a patch/diff file, > we could look at that and try to port the changes. My guess is a lot > of macro work was done in the meantime so it may not be trivial to > repeat your changes :( > > Thanks, > > Peter > ___ 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/mailinglists/
[galaxy-dev] Galaxy broken after update to 16.01
Hi all, We were tracking the galaxy master branch on our local server and are looking to migrate to v16.01. The galaxy processes are managed bij supervisor as shown here ( https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling). After updating all dependencies in our venv we tried to restart the server but got the following issue: Loading paste environment: config:/home/galaxy/galaxy-dist/config/galaxy.ini Traceback (most recent call last): File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py", line 247, in loadapp return loadobj(APP, uri, name=name, **kw) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py", line 271, in loadobj global_conf=global_conf) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py", line 296, in loadcontext global_conf=global_conf) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py", line 320, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py", line 458, in get_context section) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py", line 517, in _context_from_explicit value = import_string(found_expr) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py", line 22, in import_string return pkg_resources.EntryPoint.parse("x=" + s).load(False) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2380, in load return self.resolve() File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2386, in resolve module = __import__(self.module_name, fromlist=['__name__'], level=0) File "lib/galaxy/web/buildapp.py", line 5, in from galaxy.webapps.galaxy.buildapp import app_factory File "lib/galaxy/webapps/galaxy/buildapp.py", line 15, in import galaxy.app File "lib/galaxy/app.py", line 9, in import galaxy.queues File "lib/galaxy/queues.py", line 9, in from kombu import Exchange, Queue, Connection File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/__init__.py", line 67, in __getattr__ module = __import__(object_origins[name], None, None, [name]) File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/entity.py", line 10, in from .abstract import MaybeChannelBound, Object File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/abstract.py", line 12, in from .connection import maybe_channel File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/connection.py", line 19, in from kombu import exceptions File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/exceptions.py", line 12, in from amqp import ChannelError, ConnectionError, ResourceError File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/amqp/__init__.py", line 34, in from .connection import Connection # noqa File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/amqp/connection.py", line 40, in from .transport import create_transport File "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/amqp/transport.py", line 21, in import ssl File "/Shared/Software/Cellar/python/2.7.11/lib/python2.7/ssl.py", line 97, in import _ssl # if we can't import it, let the error propagate ImportError: /home/galaxy/galaxy-dist/.venv/lib/python2.7/lib-dynload/_ssl.so: undefined symbol: SSL_CTX_set_alpn_protos So far we have tried: - rebuilding the venv - reinstalling python Funny thing is, when we start the configuration with the “run.sh” script instead of through supervisor everything seems to work just fine. We’re at a loss, please help! Thanks! Matthias ___ 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/mailinglists/
[galaxy-dev] NGS.plot script freeze
Dear All, we are trying to use NGS-plot on our local docker-galaxy-stable instance. The script freezes whenever we click on the tool. Does anybody have an idea what is wrong and how to fix this? There is no error message or anything. Thank you very much. Kind regards, Philipp ___ 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/mailinglists/
Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration
Good to know :) https://github.com/peterjc/galaxy_blast/pull/77 The pull request looks good - sadly distracted by TravisCI failures from Galaxy/planemo/dependency changes. Thanks, Peter On Tue, Feb 9, 2016 at 3:28 PM, Floreline TOUCHARDwrote: > Hi, > > sorry for the late response ! I tested the modifications proposed in the > "Allow to select multiple database" pull request and it works !!! > > Thanks a lot ! > Floreline. > > P.S : I'm not familiar with all github functionnalities yet, but I will work > on it ;) > ___ 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/mailinglists/
Re: [galaxy-dev] A Report Calc tool which provides a scripting language and interpreter for text mining and quality control
Hi folks, I'm back with one more feeler to gauge interest in the approach we are trying out for a Galaxy quality control tool to interject into existing bioinformatics pipelines. With some nudging (thanks Bob) I've implemented basic infix math expressions. As well we're trying out the inclusion of ontology metadata within report data to encourage data import/export/comparison. The goal is to make it easy to see and change quality control metrics (without having to recompile code or modify Galaxy workflow mechanics.) The QC scripting language/interpreter as a Galaxy tool lets us read in text file(s) - some assembly contig data say - and then run a program (a set of rules) like: store( 200 report/contigs/contig_count_QC_threshold ) store( 20 report/contigs/contig_N50_QC_threshold ) store( 2000 report/contigs/contig_N99_QC_threshold ) if( ( genome_size_ratio > genome_size_ratio_QC_threshold ) fail(qc "Failed genome size ratio threshold") ) store( statisticN( contig_lengths 50 ) report/contigs/contig_N50 ) store( statisticN( contig_lengths 99 ) report/contigs/contig_N99 ) if( contig_N50 < contig_N50_QC_threshold fail(qc "Failed minimum N50 contig length threshold") ) if( contig_N99 < contig_N99_QC_threshold fail(qc "Failed minimum N99 contig length threshold") ) if( report/contigs/contigs_count > contig_count_QC_threshold fail(job "Failed minimum contig count threshold" ) ) Which is like a generic, basic function(parameter1 parameter2...) type of language. On a good run this yields a JSON report like: { "title": "RCQC Quality Control Report", "tool_version": "0.0.7", "job": { "status": "ok" }, "quality_control": { "status": "ok" }, "date": "2016-02-09 09:21", "contigs": { "contig_lengths": [ 128, 172, 221, 224, 238, 230, 240, 246, 407, ... , 242, 2284, 1506], "genome_size_ratio_QC_threshold": 0.10001, "contig_N99_QC_threshold": 2000, "assembly_genome_size": 4615592, "genome_size_ratio": 0.04970310891496809, "contig_N50": 427122, "contig_N99": 8542, "contig_count_QC_threshold": 200, "contig_count": 44, "reference_genome_identifier": "serovar Typhimurium LT2", "reference_genome_size": 4857000, "contig_N50_QC_threshold": 20 }, "@context": { "contigs": "http://purl.obolibrary.org/obo/SO_0001462;, "genome_size_ratio_QC_threshold": "http://purl.obolibrary.org/obo/GenEpiO_0001564;, "contig_N99_QC_threshold": "http://purl.obolibrary.org/obo/GenEpiO_0001566;, "assembly_genome_size": "http://purl.obolibrary.org/obo/GenEpiO_0001561;, "genome_size_ratio": "http://purl.obolibrary.org/obo/GenEpiO_0001563;, "contig_N50": "http://purl.obolibrary.org/obo/OBI_0001941;, "contig_N99": "http://purl.obolibrary.org/obo/GenEpiO_0001570;, "contig_count_QC_threshold": "http://purl.obolibrary.org/obo/GenEpiO_0001571;, "contig_count": "http://purl.obolibrary.org/obo/GenEpiO_093;, "reference_genome_identifier": "http://purl.obolibrary.org/obo/GenEpiO_0001562;, "date": "http://purl.obolibrary.org/obo/IAO_416;, "reference_genome_size": "http://purl.obolibrary.org/obo/GenEpiO_0001560;, "contig_N50_QC_threshold": "http://purl.obolibrary.org/obo/GenEpiO_0001565; } } So we'd appreciate any advice on roadblocks or desired features you perceive on this... - Damion > ___ 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/mailinglists/