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Staramr add DM and update tool with database information #6609

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Staramr add DM and update tool with database information #6609

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hugolefeuvre
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FOR CONTRIBUTOR:

  • I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • License permits unrestricted use (educational + commercial)
  • This PR adds a new tool or tool collection
  • This PR updates an existing tool or tool collection
  • This PR does something else (explain below)

clsiguret and others added 30 commits September 19, 2024 10:57
@clsiguret
add StarAMR wrapper and creator list from phac-nml
0c6c58f
@clsiguret
Merge branch 'galaxyproject:main' into staramr_add
c49866a
@clsiguret
Indentation correction
48f5d5f
@clsiguret
Merge branch 'staramr_add' of github.com:clsiguret/tools-iuc into sta…
ee0f205 
…ramr_add
@clsiguret
Changed macro token
a706e49
@clsiguret
Parameter arguments and values modified
7255928
@clsiguret
Functional test 1
db4da6a
@clsiguret
Functional test 2
2985b2a
@clsiguret
Functional test 3
0942dad
@clsiguret
Functional test 4
9526638
@clsiguret
Functional test 5
4285e38
@clsiguret
Functional test 6
2189a22
@clsiguret
Functional test 7
4d2c1bc
@clsiguret
Functional test 8
dc84ee9
@clsiguret
Functional test 9
63c0e72
@clsiguret
Functional test 10
6b17bcf
@clsiguret
Changed output label
f7530c8
@clsiguret
Init staramr dta manager
fa21b9b
@clsiguret
Modify pointfinder part to use an argument
92f636d
@clsiguret
Change tag for resfinder
18945b0
@hugolefeuvre
start reworking
f0e5a0f
@hugolefeuvre
finish DM
5a06db5
@hugolefeuvre
add DM part into tool part, add param directory, add db into test, th…
a31eee9 
…e only thing missing is the test database
@hugolefeuvre
DB staramr git index files
108a3a9
@hugolefeuvre
delete index files wrong path
0b5edef
@hugolefeuvre
delete index files
316182d
@hugolefeuvre
index files with good path
fdb68f8
@hugolefeuvre
delete repo index files
d63371f
@hugolefeuvre
Revert "delete repo index files"
f40450f 
This reverts commit d63371f.
Back with db repo with index information
@hugolefeuvre
Merge branch 'galaxyproject:main' into staramr_add
fd2393f
hugolefeuvre and others added 10 commits December 2, 2024 17:48
@hugolefeuvre
Merge commit '789121f2306f28cdcfe21fb3c1eea9d953983eff' as 'tools/sta…
bff83af 
…ramr/test-data/resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502/update/pointfinder'
@hugolefeuvre
files modified by commit + hope .git will be present
9a4542a
@hugolefeuvre
delete reference data, add db build with test values into staramr sea…
07f7fba 
…rch, used only for test with hidden parameter
@hugolefeuvre
Merge branch 'galaxyproject:main' into staramr_add
a397cb2
@hugolefeuvre
update version suffix
2d20089
@hugolefeuvre
Merge branch 'staramr_add' of https://github.com/clsiguret/tools-iuc …
e84dae7 
…into staramr_add
@hugolefeuvre
delete other requirements in DM because dont need them here
7ffa4fb
@hugolefeuvre
just delete . because create biocontainer with mull, hope it will pas…
1cab066 
…s tests
@hugolefeuvre
new staramr version, delete numpy requirement, delete db at the end o…
c765ca6 
…f each test
@hugolefeuvre
Delete .gitmodules
39cfeff
bernt-matthias
bernt-matthias reviewed Jan 12, 2025
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@bernt-matthias bernt-matthias left a comment

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My main question is if the pointfinder, resfinder, and plasmidfinder datasets should be handled in three datatables? In the tool they might be linked together into one folder? Depends a bit how how the contents of these datasets looks like.

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hugolefeuvre and others added 15 commits January 13, 2025 10:14
@hugolefeuvre
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My main question is if the pointfinder, resfinder, and plasmidfinder datasets should be handled in three datatables? In the tool they might be linked together into one folder? Depends a bit how how the contents of these datasets looks like.

When DBs are downloaded with staramr db build, the directories of each DB are put in a common directory which will be given as input to staramr search. I'm not sure that this would work with one datatable per DB, because the way of calling the DB in staramr search doesn't seem to me to be compatible with the use of multiple datatables, but maybe I'm wrong.

@bernt-matthias
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My main question is if the pointfinder, resfinder, and plasmidfinder datasets should be handled in three datatables? In the tool they might be linked together into one folder? Depends a bit how how the contents of these datasets looks like.

When DBs are downloaded with staramr db build, the directories of each DB are put in a common directory which will be given as input to staramr search. I'm not sure that this would work with one datatable per DB, because the way of calling the DB in staramr search doesn't seem to me to be compatible with the use of multiple datatables, but maybe I'm wrong.

Lets leave it as it is.

@hugolefeuvre
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Lets leave it as it is.

Ok, sorry for the re-review request, I didn't mean to do it.

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@hugolefeuvre @bernt-matthias @clsiguret