this was apparently changed here: galaxyproject/tools-iuc#884 ... before the input had a validator for a genome build which seemingly never has been used.
so if you want to stick to this tool version I guess you need to set the build. But for this tool any value should be OK.
if datasets are in a collection we don't unhide each individual member anymore, that's new, yes
another one: apparently nowadays 3 columns should be available in a tool data table: value, path, and name. For older tools (e.g. mothur again) this seems sometimes not to be the case. For mothur I have now 3 columns id, path, type (last one just added). What would be the best strategy to update the tool?
- do I need to add tool_data_table_conf.xml.oldlocstyle?
- is it possible to test this?
Furthermore, what would be the best strategy to add a column (for mothur aligndb I just added the 3rd column)?
@nsoranzo : thanks for the answer: I was just reading at https://galaxyproject.org/admin/tools/data-tables/ that "value, path, and name should all be included". Also: Why do I need to create a new data table? Can't I just add a column?
Also wondering why this https://github.com/galaxyproject/tools-iuc/blob/60e2302cfac90d0c909ef61815aaaafaaad5816a/tools/mothur/align.seqs.xml#L17 works. I would have expected something like reference.fields.... in the case of cached reference data.
There seem to be a few remaining issues with the
snippy tool that prevent asnippy -> snippy-core pipeline from working. I've filed an issue here: galaxyproject/tools-iuc#2451
...and I'm working on a fix here: galaxyproject/tools-iuc#2452
gentle ping for IUC & annotatemyids tool. Know most are very busy with GCC prep. but any help/feedback, even if just some type of acknowledgement (a tool update ticket?), would be nice. https://help.galaxyproject.org/t/annotating-gene-ids-local-deseq2-rats-annotatemyids/1327/9
@bgruening you replied to that ^^ originally and updated EU server to test out addition of the rat id lookup. am sure you are personally swamped. though maybe someone else could help out...
If you want me to make a ticket, lmk, can do that and give it back to the user. But I wouldn't know how to help them update outside of the MTS... would need someone else to help with that part (assume is possible :)
@nsoranzo the default isn't loading in the box. I restarted both the tool screen and galaxy, and it remains empty
<param name="name" type="text" optional="true" default="galaxy_seurat" label="Optional name of the experiment for Seurat" help="Default name is galaxy_seurat"/>
http://images.galaxyproject.org/planemo/latest.ova I published what I think will become the GCC image for the tool dev workshop. I don't know how realistic VMs are in an hour and half long training though
I'll make sure these land up on USB sticks
@pvanheus Could you take a look at my proposed fix for galaxyproject/tools-iuc#2451 when you have a chance? Pull request is here: galaxyproject/tools-iuc#2452
I've also pushed to the test toolshed: https://testtoolshed.g2.bx.psu.edu/view/dfornika/snippy/04f229b754cd
I think I may have misunderstood the error when I started working on my fix, so I've probably changed a bit more than strictly necessary. If you look at the command-line generated for
snippy-corethat I've included in the issue, the arguments for snippy-core aren't quoted (except for the --ref file).
mkdir 'snippy on data 2, data 1, and data 8 dir for snippy core' &&
tar -xf '/export/galaxy-central/database/files/000/dataset_587.dat' -C 'snippy on data 2, data 1, and data 8 dir for snippy core' --strip-components=1 &&
mkdir 'snippy on data 5, data 3, and data 8 dir for snippy core' &&
tar -xf '/export/galaxy-central/database/files/000/dataset_590.dat' -C 'snippy on data 5, data 3, and data 8 dir for snippy core' --strip-components=1 &&
mkdir 'snippy on data 4, data 6, and data 8 dir for snippy core' &&
tar -xf '/export/galaxy-central/database/files/000/dataset_593.dat' -C 'snippy on data 4, data 6, and data 8 dir for snippy core' --strip-components=1 &&
snippy-core --ref '/export/galaxy-central/database/files/000/dataset_563.dat' snippy on data 2, data 1, and data 8 dir for snippy core snippy on data 5, data 3, and data 8 dir for snippy core snippy on data 4, data 6, and data 8 dir for snippy core
...so I think that was the cause of the error, because the error message is:
Fatal error: Exit code 2 ()
This is snippy-core 4.3.6
Obtained from http://github.com/tseemann/snippy
Enabling bundled tools.
Found any2fasta - /export/tool_deps/_conda/envs/__snippy@4.3.6/binaries/noarch/any2fasta
Found samtools - /export/tool_deps/_conda/envs/__snippy@4.3.6/bin/samtools
Found minimap2 - /export/tool_deps/_conda/envs/__snippy@4.3.6/bin/minimap2
Found bedtools - /export/tool_deps/_conda/envs/__snippy@4.3.6/bin/bedtools
Found snp-sites - /export/tool_deps/_conda/envs/__snippy@4.3.6/bin/snp-sites
Saving reference FASTA: core.ref.fa
This is any2fasta 0.4.2
Opening '/export/galaxy-central/database/files/000/dataset_563.dat'
Detected FASTA format
Read 20520 lines from '/export/galaxy-central/database/files/000/dataset_563.dat'
Wrote 1 sequences from FASTA file.
Processed 1 files.
Done.
Loaded 1 sequences totalling 1641481 bp.
Will mask 0 regions totalling 0 bp ~ 0.00%
ERROR: Sample 'snippy' is not a folder, seems to be a file?
But it seems a bit strange to be creating those directories called
'snippy on data 2, data 1, and data 8 dir for snippy core' etc. I noticed that the snippy tool already creates a .tar.gz file that contains a snippy results directory that is named with the sample name. So it seems to me that we just need to extract those into the working directory and pass them to snippy-core. It seems unnecessary to create new directories in the snippy-core tool to extract into.
I think the issue with the
snippy-core input directories not being quoted is still unresolved in PR: https://github.com/galaxyproject/tools-iuc/pull/2452/files#r296449599
Does anyone know why the
Salmon option is commented out in the MultiQC tool? I'm assuming something doesn't work, but curious if anyone knows more as I'd like to get this working. https://github.com/galaxyproject/tools-iuc/blob/master/tools/multiqc/multiqc.xml#L540
@pvanheus The
.tar.gz files that I was referring to are created by the snippy tool wrapper here: https://github.com/galaxyproject/tools-iuc/blob/6afb87d2f226ac2fb61255b89dd9c36940b482c9/tools/snippy/snippy.xml#L66
