phnmnl/galaxy

Data intensive science for everyone.

The latest information about Galaxy is available via https://galaxyproject.org/

Galaxy Quickstart

Galaxy requires Python 2.7 To check your python version, run:

$ python -V
Python 2.7.3

Start Galaxy:

$ sh run.sh

Once Galaxy completes startup, you should be able to view Galaxy in your browser at:

http://localhost:8080

Configuration & Tools

You may wish to make changes from the default configuration. This can be done in the config/galaxy.ini file.

Tools can be either installed from the Tool Shed or added manually.

For details please see the tutorial.

Note that not all dependencies for the tools provided in the tool_conf.xml.sample are included. To install them please visit "Manage dependencies" in the admin interface.

Issues and Galaxy Development

Please see CONTRIBUTING.md .

Roadmap

Interested in the next steps for Galaxy? Take a look at the roadmap.

galaxy's Issues

ISA-Tab logging is not working properly

I've updated isa.py to use the logging package, the same way do other data types:

logger = logging.getLogger(__name__)

And I've added at least one information message in each method. But I'm only seeing the ones in the constructor:

galaxy.datatypes.isa INFO 2017-10-02 09:39:36,565 Isa::__init__ 01
galaxy.datatypes.isa INFO 2017-10-02 09:39:36,565 Isa::__init__ 02
galaxy.datatypes.isa INFO 2017-10-02 09:39:36,565 Isa::__init__ 01
galaxy.datatypes.isa INFO 2017-10-02 09:39:36,565 Isa::__init__ 02
galaxy.datatypes.isa INFO 2017-10-02 09:39:36,645 Isa::__init__ 01
galaxy.datatypes.isa INFO 2017-10-02 09:39:36,645 Isa::__init__ 02
galaxy.datatypes.isa INFO 2017-10-02 09:39:36,645 Isa::__init__ 01
galaxy.datatypes.isa INFO 2017-10-02 09:39:36,645 Isa::__init__ 02

When uploading a Metabolights study zip file with "Upload File" tool (specifying isa-tab type explicitly), no other messages are printed. Why?

Update nmrml2isa to new ISA datatype

See https://github.com/phnmnl/container-nmrml2isa

ISA-Tab no primary file displayed

Once a study has been imported in Galaxy, if I click on the "View data" icon, nothing is displayed. Instead, the browser download the investigation file with an encoded name (e.g.: Bq1h32eJ) without extension.
Tested under Safari and Firefox.

Integrate isatools Python2 version in requirements

Add py2_isatools-lite version of isatools library inside the requirements file of Galaxy, and make sure it installs correctly automatically.

Failed to upload MTBLS520

Using branch release_18.01_plus_isa_runnerRestartJobs, I've tried to upload study MTBLS520.zip (metadata only).
The ISA dataset creation failed, displaying the message Unable to finish job.
The error in the Galaxy log was:

galaxy.model.metadata DEBUG 2018-07-12 10:03:30,674 [p:1897,w:1,m:0] [LocalRunner.work_thread-0] setting metadata externally failed for HistoryDatasetAssociation 1: 'NoneType' object has no attribute 'datatype'
galaxy.jobs.runners.local ERROR 2018-07-12 10:03:30,679 [p:1897,w:1,m:0] [LocalRunner.work_thread-0] Job wrapper finish method failed
Traceback (most recent call last):
  File "lib/galaxy/jobs/runners/local.py", line 152, in queue_job
    self._finish_or_resubmit_job(job_state, stdout, stderr, exit_code)
  File "lib/galaxy/jobs/runners/__init__.py", line 432, in _finish_or_resubmit_job
    job_state.job_wrapper.finish(stdout, stderr, exit_code, check_output_detected_state=check_output_detected_state)
  File "lib/galaxy/jobs/__init__.py", line 1288, in finish
    dataset.datatype.set_meta(dataset, overwrite=False)
  File "lib/galaxy/datatypes/isa.py", line 419, in set_meta
    self._set_dataset_name(dataset)
  File "lib/galaxy/datatypes/isa.py", line 426, in _set_dataset_name
    investigation = self._get_investigation(dataset)
  File "lib/galaxy/datatypes/isa.py", line 160, in _get_investigation
    investigation = self._make_investigation_instance(main_file)
  File "lib/galaxy/datatypes/isa.py", line 519, in _make_investigation_instance
    parser.parse(fp)
  File "/Users/pierrick/dev/galaxy/.venv/lib/python2.7/site-packages/isatools/isatab_meta.py", line 88, in parse
    self._parse(filepath_or_buffer)
  File "/Users/pierrick/dev/galaxy/.venv/lib/python2.7/site-packages/isatools/isatab_meta.py", line 783, in _parse
    self._parse_publications_section(section_label, section)
  File "/Users/pierrick/dev/galaxy/.venv/lib/python2.7/site-packages/isatools/isatab_meta.py", line 676, in _parse_publications_section
    status_accession, status_term_source, fillvalue=''):
TypeError: izip_longest argument #5 must support iteration
galaxy.tools.error_reports DEBUG 2018-07-12 10:03:31,413 [p:1897,w:1,m:0] [LocalRunner.work_thread-0] Bug report plugin <galaxy.tools.error_reports.plugins.sentry.SentryPlugin object at 0x124cb51d0> generated response None
galaxy.model.metadata DEBUG 2018-07-12 10:03:31,421 [p:1897,w:1,m:0] [LocalRunner.work_thread-0] Cleaning up external metadata files
galaxy.model.metadata DEBUG 2018-07-12 10:03:31,453 [p:1897,w:1,m:0] [LocalRunner.work_thread-0] Failed to cleanup MetadataTempFile temp files from /Users/pierrick/dev/galaxy/database/jobs_directory/000/1/metadata_out_HistoryDatasetAssociation_1__sJSY9: No JSON object could be decoded

Can we rename the ISA composite dataset

Try to change the default of the uploaded ISA composite dataset ("Uploaded Composite Dataset (isa)") to the name of the uploaded zip file or the title or identifier of the investigation, or the identifier of the study.

Split ISA type into ISA-Tab and ISA-JSON

Split Isa class into two classes IsaTab and IsaJson that inherits from Isa, as it was done initially by @kikkomep .

Update mzml2isa to new ISA datatype

See https://github.com/phnmnl/container-mzml2isa

NmrML datatype is missing

NmrML datatype is missing in release_18.01_plus_isa_runnerRJ_clean branch.

See phnmnl/container-galaxy-k8s-runtime#289

Use ISA data type as output of mtbls-dwnld

The uploader is for the moment the only tool that output an ISA type. However it requires a ZIP file to upload.
The metabolights downloader (mtbls-dwnld) needs also to output an ISA type instead of W4M format.

Generation of primary file in ISA datatype

The generated primary file contains only basic information, and only list the filename of the archive file (ZIP file).
Could the archive file be extracted earlier in the process? It is currently extracted inside the groom_dataset_content() method, but I wonder if this is the right place.

Remove the sniff method of the ISA data type

The ISA data type being a composite data type, the sniff() method seems useless. Automatic detection is only used inside the uploader tool for normal data types, not the composite data types.

No ISA composite type displayed in uploader

Under macOS, the ISA type is not displayed in the list of composite types. Only ISA-Tab and ISA-Json are displayed. Under Linux/Ubuntu all three types are displayed (ISA, ISA-Tab and ISA-Json).

ISA-Tab/ISA-Json code merging

The distinction between IsaTab and IsaJson, does not seem pertinent from the point of view of the user.
How the user could know how to choose between IsaTab and IsaJson from inside the "Upload File" Galaxy tool, since he blindly uploads a zip file? We should try to have only one ISA class and handle Tab/Json file types inside.

Use ISA type in tool input

Use first new tool made with isatab2w4m.py script from mtbls-dwnld for testing.
See https://github.com/workflow4metabolomics/mtbls-dwnld/tree/feature/galaxy-isa-datatype.

After success, a tool that can handle ISA-Json too will be needed.

ISA-Tab type

Hi @kikkomep , could you explain a bit how your new type works?
I've assumed I have to upload a zipped MTBLS study through the uploader, and that the containt will be detected as ISA-Tab. Am I right?

Galaxy should report job as failed if Kubernetes cannot pull the image

Currently, if Kubernetes cannot pull an image for a job:

huelen:mzml2isa pmoreno$ kubectl get pods
NAME               READY     STATUS             RESTARTS   AGE
galaxy-10-01l6r    0/1       ImagePullBackOff   0          1m
galaxy-k8s-dk9vj   1/1       Running            0          4m

galaxy shows a waiting status for the job (clock in grey background). This should be fixed.