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

Use openjdk 11 for hmftools-redux and update hmftools-sage jar #51831

Merged
merged 12 commits into from
Nov 4, 2024
+7 −7
Merged

Use openjdk 11 for hmftools-redux and update hmftools-sage jar #51831

Show file tree
Hide file tree
Changes from 3 commits
Commits
Show all changes
12 commits
Select commit Hold shift + click to select a range
438a857
Use openjdk 11 for hmftools redux, sage, and esvee
luan-n-nguyen Oct 31, 2024
ac9a3a0
Add space between tool name and version
luan-n-nguyen Oct 31, 2024
8e4c1ca
Use exact open jdk version
luan-n-nguyen Oct 31, 2024
2388e6d
Use open jdk version between 8 and 11
luan-n-nguyen Oct 31, 2024
196ea42
Increment build version
luan-n-nguyen Oct 31, 2024
d4e35b2
Increase allowed open jdk version to 17, and restore build increment
luan-n-nguyen Oct 31, 2024
43f8f9f
Increment build to try to trigger rebuild
luan-n-nguyen Nov 1, 2024
4489988
Merge branch 'master' into use_java_11_for_variant_callers
luan-n-nguyen Nov 1, 2024
bd7945d
Restore build increment
luan-n-nguyen Nov 1, 2024
f2e3862
Relax openjdk version for sage and esvee
luan-n-nguyen Nov 3, 2024
a929b54
Update hmftools-sage to 4.0_beta.3
luan-n-nguyen Nov 3, 2024
53f081d
Require openjdk >=9 for hmftools-sage
luan-n-nguyen Nov 3, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions recipes/hmftools-esvee/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,13 +12,13 @@ source:

build:
noarch: generic
number: 3
number: 4
run_exports:
- {{ pin_subpackage("hmftools-esvee", max_pin="x.x") }}

requirements:
run:
- openjdk >=8
- openjdk ==11.0.1
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Those pins are too strict? Why do you need exactly this version? can it be >=11?

Copy link
Contributor Author

@luan-n-nguyen luan-n-nguyen Oct 31, 2024 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I've now allowed openjdk versions 8 to 17.

This version restriction was to prevent a multithreading crash related to later versions of java as mentioned in this github issue.

I'm now going to test to make sure this crash doesn't occur with openjdk 17

- sambamba ==0.6.8

test:
Expand Down
4 changes: 2 additions & 2 deletions recipes/hmftools-redux/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,13 +12,13 @@ source:

build:
noarch: generic
number: 2
number: 3
run_exports:
- {{ pin_subpackage('hmftools-redux', max_pin="x.x") }}

requirements:
run:
- openjdk >=8
- openjdk ==11.0.1
- sambamba >=1.0.1

test:
Expand Down
4 changes: 2 additions & 2 deletions recipes/hmftools-sage/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,14 +12,14 @@ source:

build:
noarch: generic
number: 2
number: 3
run_exports:
- {{ pin_subpackage('hmftools-sage', max_pin="x") }}

requirements:
run:
- zlib
- openjdk >=8
- openjdk ==11.0.1
- bioconductor-variantannotation
- bioconductor-genomicranges
- r-dplyr
Expand Down
Loading