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Nate Coraor natefoo @galaxyproject State College, PA System Administrator, Programmer, Whatever else

galaxyproject/admin-training 39

Galaxy Admin Training

bgruening/docker-jupyter-notebook 20

:whale: :microscope: :books: Jupyter running in a docker container. This image can be used to integrate Jupyter into Galaxy

galaxyproject/cargo-port 10

cache packages permanently

bxlab/galaxy-hackathon 8

Data intensive science for everyone.

gvlproject/dagobah-training 6

Training ground for aspiring Galaxy skywalkers

jmchilton/galaxy 4

Galaxy Github repository BETA 2. May be destroyed and recreated if additional post-conversion problems are found (but post-conversion commits on this repo will be reapplied to any recreations). Full details:

natefoo/ansible-postgresql-objects 3

A simple Ansible role for managing PostgreSQL objects (users, groups, databases, and privileges).

hexylena/galaxy 1

Data intensive biology for everyone.

martenson/galaxy 0

Data intensive science for everyone.

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Nate Coraor

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Add temporary route for /static/scripts/bundled to /static/dist until bugs are worked out

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Nate Coraor

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Update team list

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Nate Coraor

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Add tool cache/search index dir options

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Templateize some vars on Main

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Update Main to 20.05

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Update Main to 20.05: version file and nginx config changes

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Main mutable configs

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Nate Coraor

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Nate Coraor

commit sha c5969ea8bf5d9313bdbac0ce7f1d6206f24cea27

Move galaxyproject.proftpd to requirements and update to 0.3.0. This includes a fix for the increase of PBKDF2 iterations in Galaxy 20.05. Fixes #299.

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issue closedgalaxyproject/usegalaxy-playbook

Newly created account or reset passwords fail with FTP Upload

Issue: A Galaxy update on April 30, 2020 changed the way new or reset passwords are stored. This will cause FTP Upload authentication to fail.

Example: A message like the following will be reported when using Filezilla (or other FTP methods)

Status:      	Resolving address of usegalaxy.org
Status:      	Connecting to 129.114.60.56:21...
Status:      	Connection established, waiting for welcome message...
Status:      	Initializing TLS...
Status:      	Verifying certificate...
Status:      	TLS connection established.
Command:	USER <account-email-address>
Response: 	331 Password required for <account-email-address>
Command:	PASS ***************
Response: 	530 Login incorrect.
Error:        	Critical error: Could not connect to server

Workaround for End-Users:

Upload data using other methods, including local file browsing or public URLs. Local file browsing is no longer limited to data under 2 GB in size. Data up to 50 GB is possible to load for most data types. The exception is BAM data -- maximum file size is 25-35 GB (with any Upload method, including FTP).

FAQ: Loading Data https://galaxyproject.org/support/loading-data/

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jennaj

created taggalaxyproject/ansible-proftpd

tag0.3.0

Ansible role for installing and configuring ProFTPD for Galaxy

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Nate Coraor

commit sha 51c001680e7129c2e93f7f298f1d6c38995f9931

Use splitting instead of substrings of fixed length when pulling apart Galaxy's password field. Also, pull PBKDF2 params from the DB instead of hardcoding.

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Nate Coraor

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mvdbeek

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Switch to lxml for xml parsing

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mvdbeek

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Fall back to stdlib xml.etree if lxml not available

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Adapt to different error emitted by lxml

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mvdbeek

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Import etree from galaxy.util everywhere And prefer calling things etree (instead of ElementTree, XmlET or ET), so we can exchange this more easily should that be necessary.

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mvdbeek

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Pass remove_comments to lxml parser

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Marius van den Beek

commit sha 3e00a576451cb3bd74058b2f75090ebeafcf8a3b

Also import etree from galaxy.util in doctests Co-authored-by: Nate Coraor <nate@bx.psu.edu>

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Marius van den Beek

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Restore line.strip()

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mvdbeek

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Add missing errno to exception raised by lxml for missing file

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Fallback to creating XML elements from bytestrings This is necessary when calling parse_xml_string on (unicode) strings with an encoding declaration.

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Nate Coraor

commit sha fa828ebd0c96121b2e77e147127d3c7696ee0f00

Merge pull request #9759 from mvdbeek/lxml_for_everything [20.05] Switch to lxml for xml parsing

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Nate Coraor

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Merge remote-tracking branch 'upstream/release_20.05' into dev

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mvdbeek

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Switch to lxml for xml parsing

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mvdbeek

commit sha b6610a2bfa46f463b32b3fd993a74fcb1e58f204

Fall back to stdlib xml.etree if lxml not available

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mvdbeek

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Adapt to different error emitted by lxml

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mvdbeek

commit sha a4271a036af5d77172d992bed4b76d2f0f89c425

Import etree from galaxy.util everywhere And prefer calling things etree (instead of ElementTree, XmlET or ET), so we can exchange this more easily should that be necessary.

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mvdbeek

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Pass remove_comments to lxml parser

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Marius van den Beek

commit sha 3e00a576451cb3bd74058b2f75090ebeafcf8a3b

Also import etree from galaxy.util in doctests Co-authored-by: Nate Coraor <nate@bx.psu.edu>

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Marius van den Beek

commit sha 32a1a9504293cbc4154ab278bc91f2fb10342e01

Restore line.strip()

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mvdbeek

commit sha 0a8634b2f70be23c3fae85b88d067844acc2b998

Add missing errno to exception raised by lxml for missing file

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mvdbeek

commit sha 4dd96a20603d0e13a4f3f5cb97e51700ca5503b9

Fallback to creating XML elements from bytestrings This is necessary when calling parse_xml_string on (unicode) strings with an encoding declaration.

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Nate Coraor

commit sha fa828ebd0c96121b2e77e147127d3c7696ee0f00

Merge pull request #9759 from mvdbeek/lxml_for_everything [20.05] Switch to lxml for xml parsing

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PR merged galaxyproject/galaxy

[20.05] Switch to lxml for xml parsing area/framework kind/bug

In https://github.com/galaxyproject/galaxy/pull/9610 I started parsing tool documents using lxml for better speed. Unfortunately you can't add xml.etree.ElementTree.Elements to documents parsed using lxml, so when we add some dynamic parameters like the JobResourceParameters we get this:

galaxy.tools.toolbox.base ERROR 2020-05-11 12:41:10,107 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/749c918495f7/bowtie2/bowtie2_wrapper.xml
Traceback (most recent call last):
  File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tools/toolbox/base.py", line 657, in _load_tool_tag_set
    tool = self.load_tool(concrete_path, guid=guid, tool_shed_repository=tool_shed_repository, use_cached=False, tool_cache_data_dir=tool_cache_data_dir)
  File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tools/toolbox/base.py", line 851, in load_tool
    tool = self.create_tool(config_file=config_file, tool_shed_repository=tool_shed_repository, guid=guid, tool_cache_data_dir=tool_cache_data_dir, **kwds)
  File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tools/__init__.py", line 298, in create_tool
    tool = self._create_tool_from_source(tool_source, config_file=config_file, **kwds)
  File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tools/__init__.py", line 316, in _create_tool_from_source
    return create_tool_from_source(self.app, tool_source, **kwds)
  File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tools/__init__.py", line 237, in create_tool_from_source
    tool = ToolClass(config_file, tool_source, app, **kwds)
  File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tools/__init__.py", line 508, in __init__
    self.populate_resource_parameters(tool_source)
  File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tools/__init__.py", line 1318, in populate_resource_parameters
    inputs.append(resource_xml)
TypeError: Argument 'element' has incorrect type (expected lxml.etree._Element, got xml.etree.ElementTree.Element)

Here I switched all of our ElementTree usage to lxml (if available) and I also tried unifying the names with which we do the imports. The central place to import etree from should be galaxy.util now, which falls back to stdlib if lxml is not available (as could happen when using galaxy-util, galaxy-tool-util, etc).

+235 -218

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Nate Coraor

commit sha 4b3937f4c3083549c29cdbc6b8c348f92c8fe153

Templateize some vars on Test and add a tmpwatch job to clean up the object store cache

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Pull request review commentgalaxyproject/galaxy

[20.05] Switch to lxml for xml parsing

 def generate_tool_elem(self, tool_shed, repository_name, changeset_revision, own                            tool, tool_section):         """Create and return an ElementTree tool Element."""         if tool_section is not None:-            tool_elem = XmlET.SubElement(tool_section, 'tool')+            tool_elem = etree.SubElement(tool_section, 'tool')         else:-            tool_elem = XmlET.Element('tool')+            tool_elem = etree.Element('tool')

Need to get Element first with Element = getattr(etree, '_Element', etree.Element) as you did elsewhere?

mvdbeek

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Pull request review commentgalaxyproject/galaxy

[20.05] Switch to lxml for xml parsing

 def create_element(tag, attributes=None, sub_elements=None):     key / value pairs in the received attributes and sub_elements.     """     if tag:-        elem = XmlET.Element(tag)+        elem = etree.Element(tag)

Element = getattr(etree, '_Element', etree.Element) ?

mvdbeek

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Pull request review commentgalaxyproject/galaxy

[20.05] Switch to lxml for xml parsing

 def unique_id(KEY_SIZE=128):     return md5(random_bits).hexdigest()  -def parse_xml(fname):+def parse_xml(fname, strip_whitespace=True, remove_comments=True):     """Returns a parsed xml tree"""-    # handle deprecation warning for XMLParsing a file with DOCTYPE-    class DoctypeSafeCallbackTarget(ElementTree.TreeBuilder):-        def doctype(*args):-            pass-    tree = ElementTree.ElementTree()+    parser = None+    if remove_comments and LXML_AVAILABLE:+        # If using stdlib etree comments are always removed,+        # but lxml doesn't do this by default+        parser = etree.XMLParser(remove_comments=remove_comments)     try:-        root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget()))-        for elem in root.iter('*'):-            if elem.text is not None:-                elem.text = elem.text.strip()-            if elem.tail is not None:-                elem.tail = elem.tail.strip()-    except ParseError:+        # Restore ENOENT that would otherwise be an OSError in lxml

Weird filesystem semantics make it so it's usually safer to try open, catch, and raise if opening fails (usually faster than checking for existence first too) - is the OSError's errno attribute set incorrectly in the case of lxml?

Plus IOErrors are OSErrors in Python 3.

mvdbeek

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Pull request review commentgalaxyproject/galaxy

[20.05] Switch to lxml for xml parsing

 def populate_state(request_context, inputs, incoming, state, errors={}, prefix='     """     Populates nested state dict from incoming parameter values.     >>> from collections import OrderedDict-    >>> from xml.etree.ElementTree import XML+    >>> from lxml.etree import XML
    >>> from galaxy.util import XML

?

mvdbeek

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Pull request review commentgalaxyproject/galaxy

[20.05] Switch to lxml for xml parsing

 def generate_repository_info_elem(self, tool_shed, repository_name, changeset_re                                       parent_elem=None, **kwd):         """Create and return an ElementTree repository info Element."""         if parent_elem is None:-            elem = XmlET.Element('tool_shed_repository')+            elem = etree.Element('tool_shed_repository')

Element = getattr(etree, '_Element', etree.Element)?

mvdbeek

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Pull request review commentgalaxyproject/galaxy

[20.05] Switch to lxml for xml parsing

 def parse_status(self, status, job_ids):         rval = {}         for line in status.strip().splitlines():             try:-                tree = et.fromstring(line.strip())+                tree = parse_xml_string(line.strip)

Did you mean to remove the parens here?

mvdbeek

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Pull request review commentgalaxyproject/galaxy

[20.05] Switch to lxml for xml parsing

 def __init__(self, provider, config, backend_config):         :type provider: string         :param provider: is the name of the identity provider (e.g., Google). -        :type config: xml.etree.ElementTree.Element+        :type config: lxml.etree.ElementTree._Element

Just a doc so I'm probably bikeshedding here but does this make sense when the parser might not be lxml?

mvdbeek

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Nate Coraor

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Convert Test object store config to a template

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Nate Coraor

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Add new config dir paths to Test config, and decrease logging verbosity of some chatty modules

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Enable iRODS object store on Test

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Nate Coraor

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Nate Coraor

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Nate Coraor

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Nate Coraor

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Nate Coraor

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Nate Coraor

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Missed some files to commit when restoring Bridges jobs

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Nate Coraor

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issue openedalexdobin/STAR

STAR does not terminate when running under parrot_run

This is a bit obscure, but seems to be similar to the issue reported on #627, except that no version (dynamic, static, or locally compiled) solves the issue. Essentially, running STAR under the cctools Parrot tool causes a similar issue where STAR apparently runs to completion but doesn't terminate.

We have STAR (in this case 2.6.0b, because we haven't yet built indexes for 2.7) installed from Bioconda into CVMFS, and indexes stored in CVMFS as well. cctools' parrot_run is used to "fake" mount CVMFS on HPC systems where we run STAR but don't have root privileges to properly mount CVMFS.

A run with some test data and hg19 indexes looks like:

$ export PARROT_CVMFS_REPO="data.galaxyproject.org:url=http://cvmfs1-psu0.galaxyproject.org/cvmfs/@fqrn@/,pubkey=$HOME/data.galaxyproject.org.pub main.galaxyproject.org:url=http://cvmfs1-psu0.galaxyproject.org/cvmfs/@fqrn@/,pubkey=$HOME/main.galaxyproject.org.pub"
$ export PARROT_ALLOW_SWITCHING_CVMFS_REPOSITORIES=yes
$ export PARROT_CVMFS_ALIEN_CACHE=/tmp/cvmfs
$ $HOME/cctools-7.1.2-x86_64-centos7/bin/parrot_run bash
$ . /cvmfs/main.galaxyproject.org/deps/_conda/bin/activate /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-b0db0252c036e828bd636008a91dcc510a9fc0e3f41eab2161dc707e5ec49628
$ STAR --runThreadN 4 --genomeLoad NoSharedMemory --genomeDir /cvmfs/data.galaxyproject.org/managed/rnastar_index2/hg19/dataset_950899_files --readFilesIn $HOME/forward.fastq $HOME/reverse.fastq --outSAMtype BAM SortedByCoordinate --sjdbOverhang 100 --sjdbGTFfile $HOME/model.gtf

STAR appears to run normally until:

May 01 16:45:57   Finished inserting junction indices
May 01 16:46:01   Finished SAi
May 01 16:46:01 ..... finished inserting junctions into genome
Created thread # 1
Created thread # 2
Created thread # 3
Thread #1 end of input stream, nextChar=-1
Completed: thread #2
Completed: thread #3
Completed: thread #0

Parrot works through the use of ptrace and so I suspect something it's doing is interfering with STAR's use of threads, but was wondering if there's something I could try to debug further.

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Nate Coraor

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Set MariaDB tuning params recommended by SlurmDBD.

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Nicola Soranzo

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Add PAF datatype

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Add GFA 1.0 datatype

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add odgi as well needed for https://github.com/galaxyproject/tools-iuc/pull/2956

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Björn Grüning

commit sha 7adb2a38b34c1a4459c45eb3002f10f522bc44f0

Merge pull request #9592 from nsoranzo/release_19.09_add_paf_gfa_datatypes [19.09] Add PAF, GFA1 and odgi datatypes

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Nicola Soranzo

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Merge branch 'release_19.09' into release_20.01

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Bjoern Gruening

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add xg,vg,protobuf datatypes

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Björn Grüning

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add display_in_upload

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Marius van den Beek

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Merge pull request #9593 from bgruening/new_datatypes [20.01] Add xg, vg and protobuf datatypes

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Dannon Baker

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Change session timeout redirect URL to login entrypoint.

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Enis Afgan

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Merge pull request #9626 from dannon/timeout-redirect-url Change session timeout redirect URL to login entrypoint.

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Nicola Soranzo

commit sha dc5791c585ae89ce9ecbef09c0208ce2c8c11683

Fix `TypeError: OSError object is not subscriptable` under Python 3 Fix the following exception: ``` test/integration/test_cli_runners.py:90: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ lib/galaxy_test/driver/integration_util.py:73: in setUpClass cls._test_driver.setup(config_object=cls) lib/galaxy_test/driver/driver_util.py:942: in setup self._register_and_run_servers(config_object) lib/galaxy_test/driver/driver_util.py:1008: in _register_and_run_servers config_object=config_object, lib/galaxy_test/driver/driver_util.py:827: in launch_server host=host, port=port _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ webapp = <paste.urlmap.URLMap object at 0x7f011b68c110>, port = '8845' host = '127.0.0.1' def serve_webapp(webapp, port=None, host=None): """Serve the webapp on a recommend port or a free one. Return the port the webapp is running on. """ server = None for port in attempt_ports(port): try: server = httpserver.serve(webapp, host=host, port=port, start_loop=False) break except socket.error as e: > if e[0] == 98: E TypeError: 'OSError' object is not subscriptable ``` Also use `e.errno` instead of `e.args[0]` to get the errno of `socket.error`, since the latter may return an error string depending on how the exception was raised. Also: - move standard library imports to the top - fix issues reported by flake8-bugbear

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Dannon

commit sha 2ff26d40fd6324bc9f7fc8ddec664cec67b13a93

Merge pull request #9640 from nsoranzo/release_19.09_OSError_not_subscriptable [19.09] Fix `TypeError: OSError object is not subscriptable` under Python 3

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Nicola Soranzo

commit sha 9397576e4ec85dd0fafcb12591d37c2bef88ab4a

Merge branch 'release_19.09' into release_20.01

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mvdbeek

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Fix workfow parameter connections and default values in workflow editor and run form. The main problem was that `default_source = dict(name="default", label="Default Value", type=parameter_type)`, where `parameter_type` is the top-level parameter that is always `text`. This has changed with the Conditional introduced in 20.01. In addition BooleanToolParameters use `check` instead of `value`. I also added ColorToolParameter. One thing for dev is that I think we should pull the default values out of the optional conditional so we can set defaults for required parameters. Fixes https://github.com/galaxyproject/galaxy/issues/9646

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John Chilton

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Reduce duplication in test_kubernetes_staging

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John Chilton

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Rework conditions for running Kubernetes staging tests.

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John Chilton

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Refactor galaxy instance ID parsing for k8s for reuse.

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John Chilton

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Refactor local job cancel test case for reuse.

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John Chilton

commit sha 1c512af82e08d4b947213a61f09f4dbac905c87a

Set random instance ID in K8S staging tests. Before we were using UUID but Pulsar switching to using stable IDs - so we can use this method to avoid duplicate job names instead.

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John Chilton

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Test case for stopping Pulsar Kubernetes job.

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issue commentgalaxyproject/usegalaxy-tools

Deploy doesn't seem to deploy completely

I don't see any changes to shed_tool_conf.xml in the deploy output of that PR.

davebx

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issue commentgalaxyproject/usegalaxy-playbook

Scatterplot w ggplot2 (Galaxy Version 2.2.1+galaxy1) fails at usegalaxy.org

@bgruening Would you mind getting a conda list of your mulled-v1-3ed3a1ca990ccd31d8603d426d444c25343ad90a8f7378000926d72f8a90a339 env?

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Nate Coraor

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Restore jobs on Bridges

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Nate Coraor

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Nate Coraor

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Nicola Soranzo

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Add PAF datatype

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Nicola Soranzo

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Add GFA 1.0 datatype

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Björn Grüning

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add odgi as well needed for https://github.com/galaxyproject/tools-iuc/pull/2956

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Björn Grüning

commit sha 7adb2a38b34c1a4459c45eb3002f10f522bc44f0

Merge pull request #9592 from nsoranzo/release_19.09_add_paf_gfa_datatypes [19.09] Add PAF, GFA1 and odgi datatypes

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Nicola Soranzo

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Merge branch 'release_19.09' into release_20.01

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Bjoern Gruening

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add xg,vg,protobuf datatypes

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Björn Grüning

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add display_in_upload

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Marius van den Beek

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Merge pull request #9593 from bgruening/new_datatypes [20.01] Add xg, vg and protobuf datatypes

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Dannon Baker

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Change session timeout redirect URL to login entrypoint.

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Enis Afgan

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Merge pull request #9626 from dannon/timeout-redirect-url Change session timeout redirect URL to login entrypoint.

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Nicola Soranzo

commit sha dc5791c585ae89ce9ecbef09c0208ce2c8c11683

Fix `TypeError: OSError object is not subscriptable` under Python 3 Fix the following exception: ``` test/integration/test_cli_runners.py:90: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ lib/galaxy_test/driver/integration_util.py:73: in setUpClass cls._test_driver.setup(config_object=cls) lib/galaxy_test/driver/driver_util.py:942: in setup self._register_and_run_servers(config_object) lib/galaxy_test/driver/driver_util.py:1008: in _register_and_run_servers config_object=config_object, lib/galaxy_test/driver/driver_util.py:827: in launch_server host=host, port=port _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ webapp = <paste.urlmap.URLMap object at 0x7f011b68c110>, port = '8845' host = '127.0.0.1' def serve_webapp(webapp, port=None, host=None): """Serve the webapp on a recommend port or a free one. Return the port the webapp is running on. """ server = None for port in attempt_ports(port): try: server = httpserver.serve(webapp, host=host, port=port, start_loop=False) break except socket.error as e: > if e[0] == 98: E TypeError: 'OSError' object is not subscriptable ``` Also use `e.errno` instead of `e.args[0]` to get the errno of `socket.error`, since the latter may return an error string depending on how the exception was raised. Also: - move standard library imports to the top - fix issues reported by flake8-bugbear

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Dannon

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Merge pull request #9640 from nsoranzo/release_19.09_OSError_not_subscriptable [19.09] Fix `TypeError: OSError object is not subscriptable` under Python 3

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Nicola Soranzo

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Merge branch 'release_19.09' into release_20.01

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mvdbeek

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Fix workfow parameter connections and default values in workflow editor and run form. The main problem was that `default_source = dict(name="default", label="Default Value", type=parameter_type)`, where `parameter_type` is the top-level parameter that is always `text`. This has changed with the Conditional introduced in 20.01. In addition BooleanToolParameters use `check` instead of `value`. I also added ColorToolParameter. One thing for dev is that I think we should pull the default values out of the optional conditional so we can set defaults for required parameters. Fixes https://github.com/galaxyproject/galaxy/issues/9646

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John Chilton

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Reduce duplication in test_kubernetes_staging

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John Chilton

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Rework conditions for running Kubernetes staging tests.

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John Chilton

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Refactor galaxy instance ID parsing for k8s for reuse.

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John Chilton

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Refactor local job cancel test case for reuse.

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John Chilton

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Set random instance ID in K8S staging tests. Before we were using UUID but Pulsar switching to using stable IDs - so we can use this method to avoid duplicate job names instead.

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John Chilton

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Test case for stopping Pulsar Kubernetes job.

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Peter Selten

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Add support for Okta OIDC authentication. This is dependent on https://github.com/python-social-auth/social-core/pull/333.

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Peter Selten

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Update documentation for Okta

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Peter Selten

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Merge branch 'dev' of https://github.com/galaxyproject/galaxy into okta-auth

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Peter Selten

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OIDC configuration, change dependencies

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Peter Selten

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Merge origin/dev with selten/okta-oidc-auth

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Peter Selten

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Updates for Okta IdP and general IdPs

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Peter Selten

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social-auth-core should be pinned... can't be optional right now

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Peter Selten

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Merge branch 'dev' of https://github.com/galaxyproject/galaxy into okta-oidc-auth # Conflicts: # client/galaxy/scripts/components/login/Login.vue # config/oidc_backends_config.xml.sample # lib/galaxy/authnz/managers.py # lib/galaxy/authnz/psa_authnz.py # lib/galaxy/config/__init__.py # lib/galaxy/dependencies/__init__.py

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Peter Selten

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Add Okta to oidc_backends_config.xml.sample

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Peter Selten

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Add documentation on how to get the application set up in Okta.

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Bjoern Gruening

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move ITs to tools/interactive (cherry picked from commit 1c5bc4f55a781e48e4fd6017e4e49a52db8c4657)

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Bjoern Gruening

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move default notebook as well (cherry picked from commit 6d8848e399446fdc3cb1e0c81b1e88c80b03c515)

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Bjoern Gruening

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improve description of Askomics (cherry picked from commit 1d4dc27e509a4084857fec63c20698d69979c8eb)

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Peter Selten

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Update okta backend name

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Peter Selten

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Merge branch 'dev' of https://github.com/galaxyproject/galaxy into okta-oidc-auth

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Helena Rasche

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move to right dir

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Bjoern Gruening

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add wilson

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Bjoern Gruening

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deactivate monitor script

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Bjoern Gruening

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fix tool id

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temporarily disable all input data

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Nate Coraor

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Nate Coraor

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- Fixes for deplying JS stratum 1s - Make JS controllers local proxies since they have so much extra memory - Jetstream updates for newer Ansible versions - General recombination of IU and TACC JS envs

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Nate Coraor

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Nate Coraor

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Nate Coraor

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Nate Coraor

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Add failover stratum 1 servers

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Nate Coraor

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Disable trinity_psc as it will fill up $HOME on Stampede2

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Nate Coraor

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Run Stampede2 jobs under the CVMFS Parrot Connector

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Nate Coraor

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Add old Picard tools to python2 legacy environment

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nickeener

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Dave B

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nickeener

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Dave B

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Update Mutect2 on usegalaxy.org

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Dave B

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Nate Coraor

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Nate Coraor

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Nate Coraor

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Run sam_bw_filter in python2 legacy env, run abyss-pe on Stampede2 (later Bridges), run blast* on Stampede2.

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Annovar -- complete fixup for Py3 on Main

This should now be fixed by the fix referenced in #288.

jennaj

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issue commentgalaxyproject/usegalaxy-playbook

GATK 1.4 tools -- updated all after MTS is updated to run these in a Py2 env

This should now be fixed. There's no tool update, the fix was some clever job running hackery by @mvdbeek in #288.

jennaj

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issue closedgalaxyproject/usegalaxy-playbook

process updating MTS is broken

possibly because the inventory has been switched from radegast to jetstream(?)

https://github.com/galaxyproject/usegalaxy-playbook/commit/ea0e690af12b4ab1a493a11fb21d2a57f7481089#diff-ff26bdaa2061dd18a5ad8817134dc789R29-R35

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martenson

issue commentgalaxyproject/usegalaxy-playbook

process updating MTS is broken

Unbroken in 054faadc767f81a6cfd0fec93baddd66ac41c9e4

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Nate Coraor

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Increase legacy multi cores to 4.

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PR opened galaxyproject/tools-devteam

Fix tab in sam_bitwise_flag_filter, and use print function

Fixes:

  File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/sam_bitwise_flag_filter/0b2424a404d9/sam_bitwise_flag_filter/sam_bitwise_flag_filter.py", line 111
    infile = open ( options.input_sam, 'r')
                                          ^
TabError: inconsistent use of tabs and spaces in indentation

I thought python 2 cared about this as well, so I'm not sure how this tool ever worked. Maybe it didn't?

+3 -2

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Nate Coraor

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Add arkarachai-fungtammasan/str_fm tools to python2 legacy tools

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Nate Coraor

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issue openedgalaxyproject/tools-iuc

gatk2_mutect2 always fails if $_JAVA_OPTIONS is set

This construct always results in a tool failure if $_JAVA_OPTIONS is set, since [[ -z $_JAVA_OPTIONS ]] evaluates false and skips the rest of the &&'d commands.

ln -s /galaxy/files/001/dataset_1.dat input.bam && samtools index input.bam \
    && [[ -z $_JAVA_OPTIONS ]] && export JAVA_OPTS=$_JAVA_OPTIONS \
    && gatk GetSampleName --input="input.bam" --output="samplename.txt" \
    && sample=`cat samplename.txt` && [[ -z $_JAVA_OPTIONS ]] \
    && export JAVA_OPTS=$_JAVA_OPTIONS && \
    gatk Mutect2 --QUIET --tumor-sample $sample --input input.bam --output output.vcf.gz

Also, correct me if I'm wrong, but $sample seems unsafe here. gatk GetSampleName reads the SM field from RG, which in my testing, can contain anything.

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Nate Coraor

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Nate Coraor

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Remove whitespace inside braces in NVC dynamic rule

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Nate Coraor

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Add a multicore environment for python 2 legacy tools, plus template all known multicore tools into the job conf.

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Nate Coraor

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Update mock sbatch output for Slurm 18.08+

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Nate Coraor

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Disable jetstream-tacc-large tests

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Nate Coraor

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Merge pull request #296 from galaxyproject/test-new-sbatch Update mock sbatch output for Slurm 18.08+

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PR merged galaxyproject/usegalaxy-playbook

Update mock sbatch output for Slurm 18.08+

Also disable jetstream-tacc tests since that cluster is being rebuilt

+35 -32

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natefoo

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PR opened galaxyproject/usegalaxy-playbook

Update mock sbatch output for Slurm 18.08+

Also disable jetstream-tacc tests since that cluster is being rebuilt

+35 -32

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Nate Coraor

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Nate Coraor

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Include tools resolving via galaxy_packages

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Nate Coraor

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pull request commentgalaxyproject/usegalaxy-tools

Update Variant Annotator to Python 3 version on Main.

@galaxybot deploy this

NickSto

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issue commentgalaxyproject/usegalaxy-playbook

GALAXY_VIRTUAL_ENV python 2 destination for legacy tools

Can you think of a way to generate a list of these tools?

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Nate Coraor

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Nate Coraor

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Add spaln to multi

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GALAXY_VIRTUAL_ENV python 2 destination for legacy tools

I tried it with StructureFold Iterative Mapping and it worked!

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Variant Annotator: Fix bug in previous update.

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Fix for GDPR safe mode

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Helena Rasche

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Merge pull request #42 from natefoo/gdpr-safe-fix Fix for GDPR safe mode

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Nate Coraor

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Add documentation for query errored-jobs and add --details to changelog

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Nate Coraor

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Update query job-info help for new column and run make

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issue commentgalaxyproject/usegalaxy-playbook

Update Trinity once in MTS to capture a new tool wrapper in the suite

The errors were related to cluster upgrades and the exhaustion of our XSEDE credits for Bridges. I have hidden the old version of Trinity and am running a test of the new version, but don't have super high hopes for it because it's going to run on Stampede2 now instead of Bridges until we get a new allocation or supplement.

jennaj

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Nate Coraor

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Redirect James news to permanent page

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Nate Coraor

commit sha d4957168f4ee98009fd70030a5dee754d6e53db6

Run Bridges jobs on Stampede2 until we get our allocation sorted (Main changes)

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create barnchnatefoo/galaxy-hub

branch : main-compute-updates

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Nate Coraor

commit sha 0356972ab5861f48eb7fd34e94e25b3a05a29f75

Run Bridges jobs on Stampede2 until we get our allocation sorted

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tnabtaf

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Changing masthead to black. God damnit.

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tnabtaf

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Draft news item

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tnabtaf

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Added link to form.

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Dannon Baker

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Add James splash.

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tnabtaf

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Linkifying

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Dannon Baker

commit sha 43143fabcc186347f54d12c2cfa14d2c6f8b96ed

Fix date

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Dannon Baker

commit sha ae29d69691bce7d7148a7cf5bd80cbc549f8d118

rebuild.

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Martin Cech

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minor style change

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tnabtaf

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Added first set of thoughts from the community about James' passing.

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tnabtaf

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Added more response on James's page.

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Martin Cech

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add eulogies from tweets

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Martin Cech

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eulogies

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Martin Cech

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another sad commit

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Martin Cech

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add more

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tnabtaf

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Added excerpts and links to 3 online memoriam pages to James

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tnabtaf

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Added more tributes

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dependabot[bot]

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Bump minimist from 1.2.2 to 1.2.3 Bumps [minimist](https://github.com/substack/minimist) from 1.2.2 to 1.2.3. - [Release notes](https://github.com/substack/minimist/releases) - [Commits](https://github.com/substack/minimist/compare/1.2.2...1.2.3) Signed-off-by: dependabot[bot] <support@github.com>

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tnabtaf

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More tributes for James.

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Dannon

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Merge pull request #589 from galaxyproject/dependabot/npm_and_yarn/minimist-1.2.3 Bump minimist from 1.2.2 to 1.2.3

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tnabtaf

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More posts, and shoes too.

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Nate Coraor

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Make Jetstream scratch clean time period adaptive based on full percentage

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PR opened usegalaxy-eu/gxadmin

Add handler to query job-info
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