that looks about right, here’s the documentation: https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-inputs-param-options-column
so in fact each term of the first line, each term separated y a tab
from a tabular file
in fact I want the list of columns "names" (name = header)
Thank you VERY much Marius !!
@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
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
``
@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..
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
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 ?
I have a select
name="oformat" .. and the values correspond to the name of the outputs that should be written if selected.
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?
I restarted the job
I used to get one from travis
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?
and push manually if needed, sorry @bwlang ... github had problems and then the TS on its own