Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Staramr add DM and update tool with database information #6609

Open
wants to merge 45 commits into
base: main
Choose a base branch
from
Open

Staramr add DM and update tool with database information #6609

wants to merge 45 commits into from

Conversation

hugolefeuvre
Copy link
Contributor

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 15 commits December 2, 2024 16:47
@hugolefeuvre
remove git submodule
9b5d189
@hugolefeuvre
Squashed 'tools/staramr/test-data/resfinder_d1e607b_pointfinder_69491…
8690cda 
…9f_plasmidfinder_3e77502/update/plasmidfinder/' content from commit 4add28296

git-subtree-dir: tools/staramr/test-data/resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502/update/plasmidfinder
git-subtree-split: 4add282963c788762cdc3c6e91eb46c3d109f19b
@hugolefeuvre
Merge commit '8690cda403a59c74e281a3cf3d7b825754585208' as 'tools/sta…
4cb3a6b 
…ramr/test-data/resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502/update/plasmidfinder'
@hugolefeuvre
Squashed 'tools/staramr/test-data/resfinder_d1e607b_pointfinder_69491…
7121809 
…9f_plasmidfinder_3e77502/update/resfinder/' content from commit e0525f203

git-subtree-dir: tools/staramr/test-data/resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502/update/resfinder
git-subtree-split: e0525f203e43bcd6dc91348e561a2cb09fd4014b
@hugolefeuvre
Merge commit '7121809013ad7872a50bc27bd72260b0bdcf21a8' as 'tools/sta…
17cf6a0 
…ramr/test-data/resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502/update/resfinder'
@hugolefeuvre
Squashed 'tools/staramr/test-data/resfinder_d1e607b_pointfinder_69491…
789121f 
…9f_plasmidfinder_3e77502/update/pointfinder/' content from commit 694919f59

git-subtree-dir: tools/staramr/test-data/resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502/update/pointfinder
git-subtree-split: 694919f59a38980204009e7ade76bf319cb7df0b
@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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@hugolefeuvre @clsiguret