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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
@bernt-matthias did you see the new New fromJSON() method in expressions in https://github.blog/changelog/2020-04-15-github-actions-new-workflow-features/ ?
I am thinking about how we could use this, but one way could be to run one job per repository
Nicola Soranzo
@nsoranzo
@mvdbeek The outputs are a cool addition, we can use it for the Galaxy sha instead of using an artifact, I think
M Bernt
@bernt-matthias
@mvdbeek sounds feasible, but: "A job matrix can generate a maximum of 256 jobs per workflow run. This limit also applies to self-hosted runners."
Marius van den Beek
@mvdbeek
yeah, probably not the right thing for the iuc
Brad Langhorst
@bwlang

i just noticed a long delay for the Cache .planemo step, i see underneath that there is a bad archive file… seems to work ok anyway. Any suggesions about what to do?
```
Cache .planemo
25m 35s
[warning]Tar failed with error: The process '/bin/tar' failed with exit code 2
Run actions/cache@v1
Cache Size: ~81 MB (84557824 B)
/bin/tar -xz -f /home/runner/work/_temp/94954d1a-4f23-49a7-9ce0-1954ab78cab1/cache.tgz -C /home/runner/.planemo

gzip: stdin: unexpected end of file
/bin/tar: Unexpected EOF in archive
/bin/tar: Unexpected EOF in archive
/bin/tar: Error is not recoverable: exiting now
[warning]Tar failed with error: The process '/bin/tar' failed with exit code 2
``

Philip Mabon
@Takadonet
Is there a tool to find and replace with collection identified? User is requested to put sample name in their fasta file
Björn Grüning
@bgruening
@Takadonet can you explain again the use-case?
Philip Mabon
@Takadonet
@bgruening Use cases mostly around when they want to collapse a collection of non tabular files (normally fasta file) into a single file to do an alignment but individual fasta file all start with same ID . Example >contig1 , >contig2. They would like to add >SAMPLE_NAME-contig1 , >SAMPLE_NAME2-contig1 etc..
Ajit Singh
@AjitPS
Hi everyone, the hisat2 https://ccb.jhu.edu/software/hisat2/manual.shtml manual shows advanced read group options for --rg <text> and --rg-id <text> but I cannot find them in the latest galaxy hisat2 wrapper 2.1.0+galaxy5 on GalaxyEU. Is there any reason why? We have several biologists who use hisat2 here at RRes, and quite a few have recently asked me if/why this option is not in Galaxy, thanks
Marius van den Beek
@mvdbeek
No reason beyond noone having implemented it. There’s a bunch of macros and tokens in https://github.com/galaxyproject/tools-iuc/blob/master/macros/read_group_macros.xml if you want to take a look at this. I guess most people don’t do much more than counting with their hisat output, so there’s no big need for it ?
Ajit Singh
@AjitPS
ah, ok thanks @mvdbeek I'll have a look
Dave B.
@davebx
@AjitPS I was involved in some stage of that wrapper, so let me know if you'd like me to dust off my memories for anything
M Bernt
@bernt-matthias
Just doing planemo test --galaxy_root ... against dev .. suddenly database migrations starting from 0 are executed. What am I doing wrong?
Slugger70
@Slugger70
Hi all, does anyone know the status of the new GATK 4 wrappers that were started a while ago?
Björn Grüning
@bgruening
ping @davebx
Wolfgang Maier
@wm75
Is there a way for a tool wrapper that works with a built-in genome to mention that genomes id or label in its output label? Sth like ${on_string} for reference data?
M Bernt
@bernt-matthias
Can one compute in cheetah a variable name from the value of another valiable?
I have a select name="oformat" .. and the values correspond to the name of the outputs that should be written if selected.
M Bernt
@bernt-matthias
to answer my own question getVar($oformat)
Nicola Soranzo
@nsoranzo
I think this is affecting tests on GitHub Actions: https://status.quay.io/incidents/kw2627bsdwd9
Brad Langhorst
@bwlang
A colleague of mine recently added a tool to the iuc (https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch), but it’s not yet appearing in the toolshed. I just tweaked the shed.yml file to see if a missing attribute was the problem. How long should I wait before investigating further?
Björn Grüning
@bgruening
It crashed on mater, probably because quay.io was down.
I restarted the job
Jennifer Hillman-Jackson
@jennaj
Hello -- Are there any plans to modify the Trinity tool form to accept BAM inputs directly for genome guided mode? Would that be better asked in a Github ticket?
re: https://help.galaxyproject.org/t/genome-guided-trinity-without-fastq/3734
Björn Grüning
@bgruening
Hi Jen. Yes a ticket would be wonderful.
M Bernt
@bernt-matthias
Is someone getting a notification if the deploy step fails? Otherwise it would be nice to have this, or?
Björn Grüning
@bgruening
I didn't get one
I used to get one from travis
M Bernt
@bernt-matthias
For the test failures usually the one who opens the PR gets an email. Intuitively I would expect, the same for the deploy step .. or the one who hits merge. Can we verify this somehow?
Philip Mabon
@Takadonet
Looks like deployment hung here as well : https://github.com/galaxyproject/tools-iuc/runs/692679197
Brad Langhorst
@bwlang
looks like there is still some problem with iuc-> toolshed for tasmanian-mismatch https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch. Any hints about how to resolve this?
Björn Grüning
@bgruening
I will look at this locally
and push manually if needed, sorry @bwlang ... github had problems and then the TS on its own
Björn Grüning
@bgruening
tests passed locally
Björn Grüning
@bgruening
@bwlang pushed
Brad Langhorst
@bwlang
seems that toolshed is having a rough time these days… ;) thanks for your help - it’s working now!
M Bernt
@bernt-matthias
is <trackster_conf> someting that works in tool xml?
That is: has it any effect?
M Bernt
@bernt-matthias
And maybe off topic: what are the rules for merging devteam tools: galaxyproject/tools-devteam#553
Björn Grüning
@bgruening
same as for IUC :)
but, we actually try to move tools over to IUC
if we really want to maintain them
Dave B.
@davebx
is it possible to use an expression in a workflow input? I want to essentially have an input parameter be #set $sequences_to_keep = min([$input_file.dataset.metadata.sequences for input_file in $input_fastqs])
Marius van den Beek
@mvdbeek
You’d have to write an expression tool, I suppose
Dave B.
@davebx
ok, I anticipated needing to adapt an existing tool to do what we want (subsample fastq files with seqtk sample -s to the lowest common number of sequences)
Marius van den Beek
@mvdbeek
for that you don’t need to write a tool
Dave B.
@davebx
yeah, I was thinking just add a flag to the existing seqtk_sample wrapper, or whatever it's named
Marius van den Beek
@mvdbeek
just output the number of sequences for each dataset in question get the minimum with a regular tool