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

update bedgraphtobigwig with additional platform #46516

Merged
merged 4 commits into from
Mar 20, 2024
Merged

update bedgraphtobigwig with additional platform #46516

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
c681b2f
add additional platform
pablo-aledo Mar 18, 2024
5c56e9f
increase build number
pablo-aledo Mar 18, 2024
1095666
add patch
pablo-aledo Mar 18, 2024
3606edc
fix typo
pabloaledo Mar 20, 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
7 changes: 6 additions & 1 deletion recipes/ucsc-bedgraphtobigwig/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,10 @@ source:
sha256: "{{ sha256 }}"
patches:
- "include.patch"
- "patch1.patch"

build:
number: 0
number: 1
run_exports:
- {{ pin_subpackage(package, max_pin=None) }}

Expand All @@ -40,6 +41,10 @@ test:
# just check for existence, because the individual packages have no unified behavior
- which {{ program }}

extra:
additional-platforms:
- linux-aarch64

about:
home: "http://hgdownload.cse.ucsc.edu/admin/exe/"
license: "varies; see http://genome.ucsc.edu/license"
Expand Down
19 changes: 19 additions & 0 deletions recipes/ucsc-bedgraphtobigwig/patch1.patch
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
--- userApps/kent/src/lib/htmshell.c.old 2022-10-28 08:32:08.344445121 +0000
+++ userApps/kent/src/lib/htmshell.c 2022-10-28 08:32:31.708262420 +0000
@@ -711,11 +711,11 @@
puts("Status: 400\r");
puts("Content-Type: text/plain; charset=UTF-8\r");
puts("\r");
-if (format != NULL && args != NULL)
- {
- vfprintf(stdout, format, args);
- fprintf(stdout, "\n");
- }
+if (format != NULL)
Copy link
Contributor

@martin-g martin-g Mar 19, 2024 •
edited
Loading

Choose a reason for hiding this comment

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

This has been fixed upstream several months ago - ucscGenomeBrowser/kent@8b04462
This fix is in tag v463_preview

Copy link
Contributor Author

Choose a reason for hiding this comment

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

yes, but the recipe takes the source from https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/ (which is at a first glance very different than the linked gihub repository). Doesn't it make sense to apply the patch?. Should we modify the recipe instead so it downloads the source from the mentioned (probably more updated) repository?.

Copy link
Contributor

Choose a reason for hiding this comment

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

Changing the sources would be a big change indeed! Let's continue with the patch for now!
Please apply the suggestion - #46516 (comment)

+ {
+ vfprintf(stdout, format, args);
+ fprintf(stdout, "\n");
+ }
exit(-1);
}