Add FragPipe #761
Add FragPipe #761
Conversation
… Correct --accept_license flag.
- Add IonQuant path for headless fragpipe - Populate options for LFQ-MBR workflow - Add data_type option for scan inputs - Make isotope_error a selection option
|
You can now see the planemo error reports at this page: https://github.com/galaxyproteomics/tools-galaxyp/actions/runs/9046215197?pr=761 scroll down. Seems like the mv command has nothing to move. How do you run the tests locally? |
|
Yes - it looks like When I try to add it to the recipe with I'll add |
In those cases its probably the wrong, incompatible zlib version. Try on your commandline But you are correct, fixing the conda recipe is the correct thing to do.
Oh I see, this is wrong :) Just do |
This sort-of how I came to zlib=1.2.13. I built the fragpipe recipe with an unpinned zlib dependency and used the resulting zlib version. Creating a new environment with zlib and fragpipe as separate dependencies also resolved to 1.2.13. I'm wondering if there's a way to find logs of the mulled environment creation?
Okay, thanks for the advice! I'm just getting started with |
|
@bgruening Is there a way to force builds to use a biocontainer with a more recent build of the fragpipe bioconda package? I fixed the zlib issue in the recipe, since I had trouble with it here, but I think it's still using the older version. |
Apologies - I didn't sufficiently fix the dependency. And it is using the most recent biocontainer. |
|
Are you saying the _3 container here: https://quay.io/repository/biocontainers/fragpipe?tab=tags&tag=latest is not working? |
1 similar comment
|
Are you saying the _3 container here: https://quay.io/repository/biocontainers/fragpipe?tab=tags&tag=latest is not working? |
|
Never mind, the dependency fix was fine. |
|
This is ready for review now. There actually was an issue with the biocontainer - it seems like |
reid-wagner
force-pushed
the
add_fragpipe
branch
from
f441870
to
ef0f93e
Compare
reid-wagner
force-pushed
the
add_fragpipe
branch
from
47e4265
to
97718b1
Compare
reid-wagner
force-pushed
the
add_fragpipe
branch
4 times, most recently
from
cf595a1
to
6ebe238
Compare
… FragPipe creates cache relative to the lib location, this allows a local FragPipe cache.
reid-wagner
force-pushed
the
add_fragpipe
branch
from
6ebe238
to
3031e8f
Compare
| <when value="default"/> | ||
| <when value="no"/> | ||
| <when value="yes"> | ||
| <section name="options" expanded="true" title="Isobaric Quantification"> |
There was a problem hiding this comment.
Does having a single section make sense here?
There was a problem hiding this comment.
A little confused on this point. Would it be to remove the "no" and "default" options? The "yes"/"no" distinction allows us to set the param that enables this in FragPipe. The "default" is usually a bit redundant but the argument could be that if a user is re-running a shared job, they might not know the workflow default and could use that option to revert to it.
There was a problem hiding this comment.
default / no / yes is fine for me. was just wondering if a single section inside a conditional is helpful.
but fine with me.
Co-authored-by: M Bernt <[email protected]>
Temporarily reverting because this change doesn't pass tests.
|
@bernt-matthias Thanks for the review! |
…nd use_glycan_composition accessed incorrectly.
|
Awesome! Thanks @reid-wagner and @bernt-matthias |
|
Thank you @bgruening and @bernt-matthias! |
Re-creating #759
This PR adds a wrapper for the FragPipe tool suite.
A handful of default FragPipe workflows are provided for the user, while more may be added in the future. Most FragPipe parameters are duplicated in the Galaxy tool, many of which are optional to allow the workflow defaults to be used.
Some components have not yet been implemented due to license restrictions (DIA-NN & MSBooster). Other parameters need further work and testing before implementation, and will default to the workflow defaults. The workflow, along with the log file and some other FragPipe outputs are optionally selected as Galaxy outputs.
License keys are hard-coded into the tool, and a required select option and text warnings are in place to ensure a user understands the licenses, as has been discussed with the developers.