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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
Dan Fornika
@dfornika
Could I request that this be merged? galaxyproject/tools-iuc#2831
Slugger70
@Slugger70
Done
Dan Fornika
@dfornika
Could this be merged too? It updates iqtree to handle custom models correctly: galaxyproject/tools-iuc#2835
Wolfgang Maier
@wm75
Done, too
Dan Fornika
@dfornika
Thanks!
Björn Grüning
@bgruening
:heart:
JayanthiGangiredla
@JayanthiGangiredla
Hi, Can you please update data managers for busco. Looks like Busco team has moved their databases to new location from the one before. The new location URL is http://busco-archive.ezlab.org/datasets/ for all the databases. Please help!
Marius van den Beek
@mvdbeek
Screenshot 2020-01-30 at 12.39.23.png
starting to look really good
M Bernt
@bernt-matthias
hooray. what is left?
Marius van den Beek
@mvdbeek
let me upload the failed stuff
Nicola Soranzo
@nsoranzo
qiime and maker?
Marius van den Beek
@mvdbeek
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?
Marius van den Beek
@mvdbeek
(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!
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?