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  • Jan 31 2019 17:58
    jorgemachucav starred galaxyproject/tools-iuc
  • Jan 31 2019 17:45
    bebatut opened #2270
  • Jan 31 2019 16:18
    cpreviti synchronize #2267
  • Jan 31 2019 14:15
    cpreviti synchronize #2267
  • Jan 31 2019 12:42
    bernt-matthias review_requested #2269
  • Jan 31 2019 12:42
    bernt-matthias edited #2269
  • Jan 31 2019 12:41
    bernt-matthias edited #2269
  • Jan 31 2019 12:40
    bernt-matthias synchronize #2269
  • Jan 31 2019 12:13
    cpreviti commented #2267
  • Jan 31 2019 12:07
    nsoranzo commented #2267
  • Jan 31 2019 12:01
    cpreviti synchronize #2267
  • Jan 31 2019 11:21
    cpreviti synchronize #2267
  • Jan 31 2019 09:47
    cpreviti synchronize #2267
  • Jan 31 2019 09:27
    cpreviti synchronize #2267
  • Jan 30 2019 20:38
    bernt-matthias commented #2131
  • Jan 30 2019 20:19
    hepcat72 commented #2239
  • Jan 30 2019 19:50
    lparsons commented #2239
  • Jan 30 2019 18:36
    bgruening commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2267
Ghost
@ghost~5772e7e2c2f0db084a206e1b
I’ve excluded both, qiime is unable to create proper biom files
I have no idea what’s going on there
make takes forever to test
and fills up my hard disk locally
there is a chance we can get qiime to work though, since it passed travis tests prior to containerizing
we just need to figure out what the container is missing
Nicola Soranzo
@nsoranzo
So they are not included in the 18?
Ghost
@ghost~5772e7e2c2f0db084a206e1b
(and that’s with the extended base already)
yeah
not in the list
qiime is 33 failing tests
Nicola Soranzo
@nsoranzo
OK, still pretty awesome! Thanks for the hard work on this!
Ghost
@ghost~5772e7e2c2f0db084a206e1b
https://mvdbeek.github.io/iuc-tool-test-results/
the raceid tests just need a higher delta (it’s 15 currently ...)
scpipe seems to have trouble contacting biomart
the ebi tools use an API that seems to have changed
CoverageReport2 I would deprecate, it’s a custom tool by @Takadonet et al
I tried bumping the outdated dependencies, but the perl script just doesn’t run
and for coverage we can use multiqc
valet I tried looking into, the test aleays comes out different and with NA NA NA instead of an actual value
no idea what to do there
and finally fastx_trimmer I also spend quite some time figuring out what’s wrong, it’s just the fastq.gz test that fails
Ghost
@ghost~5772e7e2c2f0db084a206e1b
also of note — this is with galaxyproject/galaxy, release_20.01 branch and planemo 0.70.0, so nothing from my fork/branch
I did include my open IUC PRs though
Nicola Soranzo
@nsoranzo
Speaking of Planemo, should we start dropping Py2 ? Maybe John won't notice :laughing:
Ghost
@ghost~5772e7e2c2f0db084a206e1b
Also :tada: for Galaxy, it ran 2750 tests and no Galaxy issue as far as I can tell
if you include the upload jobs I’d guess that comes out to ~ 7500 jobs assuming about 2 input datasets per test
Nicola Soranzo
@nsoranzo
Neat
cshl_fastx_trimmer tests pass for me using Conda deps
So it's something related to the container
Ghost
@ghost~5772e7e2c2f0db084a206e1b
Given it’s the fastq.gz test I’d assume zlib or sth. like that ?
we did bump it recently, let me find the PR
Nicola Soranzo
@nsoranzo
Or gunzip options
Ghost
@ghost~5772e7e2c2f0db084a206e1b
bioconda/bioconda-recipes#19385
the IUC PR is here: https://github.com/galaxyproject/tools-iuc/pull/2791/files
Ghost
@ghost~5772e7e2c2f0db084a206e1b
the weirdest thing about the fastx_trimmer test is that I can mount in the test datsest and run the command manually and all works fine
Nicola Soranzo
@nsoranzo
The tests pass locally for me with planemo test --biocontainers (for fastx_trimmer)
Wolfgang Maier
@wm75
maybe a problem with Galaxy's decompress="true" in some version?
Nicola Soranzo
@nsoranzo
I should specify, with the version on master
Ghost
@ghost~5772e7e2c2f0db084a206e1b
possible, this is also on python 3.7
Nicola Soranzo
@nsoranzo
I'm on Python 3.6.9 for Planemo and 2.7 for Galaxy 20.01
Ghost
@ghost~5772e7e2c2f0db084a206e1b
this is with --galaxy_python_version 3.7
Nicola Soranzo
@nsoranzo
Let me try
John Chilton
@jmchilton
I’ll notice eventually 😂
Nicola Soranzo
@nsoranzo
Damn :wink:
Ghost
@ghost~5772e7e2c2f0db084a206e1b
what? now it passes for me too
wasn’t this the premise of containerisation ? argrgrgrgr :laughing:
Ghost
@ghost~5772e7e2c2f0db084a206e1b
still failing on travis after triggering a new build: https://travis-ci.org/galaxyproject/tools-iuc/jobs/638930688?utm_medium=notification&utm_source=github_status
Nicola Soranzo
@nsoranzo
I can reproduce locally with planemo test --galaxy_python_version 3.7 --biocontainers on master
Ghost
@ghost~5772e7e2c2f0db084a206e1b
Trimming: base 1 to 27
Input: 2 reads.
Output: 2 reads.