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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
Marius van den Beek
@mvdbeek
yeah
not in the list
qiime is 33 failing tests
Nicola Soranzo
@nsoranzo
OK, still pretty awesome! Thanks for the hard work on this!
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I tried bumping the outdated dependencies, but the perl script just doesn’t run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
Marius van den Beek
@mvdbeek
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:
Marius van den Beek
@mvdbeek
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
Marius van den Beek
@mvdbeek
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
Marius van den Beek
@mvdbeek
Marius van den Beek
@mvdbeek
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
Marius van den Beek
@mvdbeek
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
Marius van den Beek
@mvdbeek
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:
Marius van den Beek
@mvdbeek
what? now it passes for me too
wasn’t this the premise of containerisation ? argrgrgrgr :laughing:
Marius van den Beek
@mvdbeek
Nicola Soranzo
@nsoranzo
I can reproduce locally with planemo test --galaxy_python_version 3.7 --biocontainers on master
Marius van den Beek
@mvdbeek
Trimming: base 1 to 27
Input: 2 reads.
Output: 2 reads.
the stderr of the failing test … so maybe the redirection isn’t working ?
Nicola Soranzo
@nsoranzo
On master there is no redirection, it uses -o
Marius van den Beek
@mvdbeek
ah, right
Nicola Soranzo
@nsoranzo
But the error is the same
Only difference is that the message you pasted is printed on stdout instead of stderr
Marius van den Beek
@mvdbeek
that makes (some) sense, I suppose that’s the -o switch, we wouldn’t want to get that message into stdout
when not using -o
Nicola Soranzo
@nsoranzo
$ ldd ~/miniconda3/envs/__fastx_toolkit@0.0.14/bin/fastx_trimmer 
    linux-vdso.so.1 (0x00007ffde777a000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f2e03e6d000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f2e0425e000)