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Add colabfold #5785

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merged 33 commits into from
Mar 24, 2024
Merged

Add colabfold #5785

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84ed956
add colabfold
Feb 20, 2024
060543d
missed shed in git add
Feb 20, 2024
a2a3b29
tar file
Feb 20, 2024
1b2a6ab
Update tools/colabfold/.shed.yml
astrovsky01 Feb 21, 2024
75bc21a
update with most of the suggestion
Feb 21, 2024
a7ed2f2
add tests for msa, change minor params
Mar 11, 2024
f6c0b30
fix shed file to make suite
Mar 11, 2024
a7a50d2
fix file name problem, add pre-set param for naming files to prevent …
Mar 11, 2024
e722272
add num_outputs test to alphafold tool
Mar 12, 2024
9852142
fix test because inputs removed conditionals
Mar 12, 2024
f645e67
fix missing text modifier
Mar 12, 2024
75ba87b
Add hardcoded file names to prevent file headers from breaking datase…
Mar 15, 2024
522a5e1
fix typo from creating an advanced section
Mar 19, 2024
d513720
fix msa filenames
Mar 19, 2024
fdfee66
update archive member paths, assert expect_error
Mar 19, 2024
ae36f0f
test update
Mar 19, 2024
c30fc11
print dir content test
Mar 19, 2024
eb62b2f
try as just tar
Mar 20, 2024
0a84144
add back ls
Mar 20, 2024
e305800
wrong place for &&
Mar 20, 2024
7a025df
quotes and another archive test
Mar 20, 2024
c5531fc
make tests match now that one passed
Mar 20, 2024
031b711
switch back to colab.tar
Mar 20, 2024
7d612ba
test fail state of alphafold tool
Mar 20, 2024
b181a94
Failed properly, tool ready
Mar 20, 2024
a75d4bb
Try expect code
Mar 21, 2024
783c58d
Expect both failure and exit code
Mar 21, 2024
e94b467
Expect fail, exit code, and num outputs
Mar 21, 2024
5f9df6d
remove num_outputs to fix lint
Mar 21, 2024
dfebe1e
matthias final pass
Mar 22, 2024
eb670e9
better descrption for alphafold
Mar 22, 2024
0295aae
small changes
bgruening Mar 24, 2024
bedeb9f
another round
bgruening Mar 24, 2024
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2 changes: 1 addition & 1 deletion tools/colabfold/colabfold_alphafold.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -122,7 +122,7 @@
<data name="a3m_out" format="a3m" from_work_dir="output/output.a3m" label="${tool.name} on ${on_string}: a3m file"/>
</outputs>
<tests>
<test expect_failure="true">
<test expect_exit_code="1">
<param name="input" value="input.tar"/>
<section name="advanced">
<param name="num_recycles" value="4"/>
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