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

Samtools 0.1.19 and 0.1.18 - linux-aarch64 and osx-arm64 (0.1.18) support #52557

Merged
merged 9 commits into from
Dec 4, 2024
Merged

Samtools 0.1.19 and 0.1.18 - linux-aarch64 and osx-arm64 (0.1.18) support #52557

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
5540b7c
Bump build number, will this bump a rebuild on linux-aarch64?
dslarm Nov 27, 2024
31ab618
Merge branch 'master' of github.com:dslarm/bioconda-recipes
dslarm Nov 27, 2024
a74023d
Merge branch 'master' of github.com:dslarm/bioconda-recipes
dslarm Nov 28, 2024
fdea842
merge
dslarm Nov 28, 2024
d114b05
Merge branch 'master' of github.com:dslarm/bioconda-recipes
dslarm Nov 29, 2024
87dffb8
Merge branch 'master' of github.com:dslarm/bioconda-recipes
dslarm Dec 2, 2024
b454697
update legacy builds for samtools to support linux-aarch64 and osx-arm64
dslarm Dec 3, 2024
cf7150d
don't build for osx - fails with
dslarm Dec 3, 2024
dd29671
Merge branch 'master' into samtools-0119-arm
dslarm Dec 4, 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/samtools/0.1.18/build.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,6 @@
# does not affect the linux build
# this is has been fixed in newer versions: https://github.com/samtools/samtools/issues/22
sed -i.bak -E 's/(inline void __ks_insertsort_)/static \1/g' ksort.h
make INCLUDES="-I. -I$PREFIX/include -I$PREFIX/include/ncurses" LIBCURSES="-L$PREFIX/lib -lncurses -ltinfo" LIBPATH="-L$PREFIX/lib" CC=$CC CFLAGS="-g -Wall -O2 -I$PREFIX/include -L$PREFIX/lib"
make -j ${CPU_COUNT} INCLUDES="-I. -I$PREFIX/include -I$PREFIX/include/ncurses" LIBCURSES="-L$PREFIX/lib -lncurses -ltinfo" LIBPATH="-L$PREFIX/lib" CC=$CC CFLAGS="-g -Wall -O2 -I$PREFIX/include -L$PREFIX/lib"
mkdir -p $PREFIX/bin
mv samtools $PREFIX/bin
mv samtools $PREFIX/bin
9 changes: 8 additions & 1 deletion recipes/samtools/0.1.18/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
{% set name = "samtools" %}

package:
name: samtools
version: 0.1.18
Expand All @@ -7,7 +9,9 @@ source:
url: https://github.com/samtools/samtools/archive/0.1.18.tar.gz

build:
number: 13
number: 14
run_exports:
- {{ pin_subpackage(name, max_pin="x") }}

requirements:
build:
Expand All @@ -30,5 +34,8 @@ about:
summary: Tools for dealing with SAM and BAM files

extra:
additional-platforms:
- linux-aarch64
- osx-arm64
identifiers:
- biotools:samtools
2 changes: 1 addition & 1 deletion recipes/samtools/0.1.19/build.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
#!/bin/sh
make INCLUDES="-I. -I$PREFIX/include -I$PREFIX/include/ncurses" LIBCURSES="-L$PREFIX/lib -lncurses -ltinfo" LIBPATH="-L$PREFIX/lib" CC=$CC CFLAGS="-g -Wall -O2 -I$PREFIX/include -L$PREFIX/lib"
make -j ${CPU_COUNT} INCLUDES="-I. -I$PREFIX/include -I$PREFIX/include/ncurses" LIBCURSES="-L$PREFIX/lib -lncurses -ltinfo" LIBPATH="-L$PREFIX/lib" CC=$CC CFLAGS="-g -Wall -O2 -I$PREFIX/include -L$PREFIX/lib"
mkdir -p $PREFIX/bin
mv samtools $PREFIX/bin
mv bcftools/bcftools $PREFIX/bin
Expand Down
11 changes: 9 additions & 2 deletions recipes/samtools/0.1.19/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
{% set name = "samtools" %}
package:
name: samtools
version: 0.1.19
Expand All @@ -7,8 +8,11 @@ source:
url: https://github.com/samtools/samtools/archive/refs/tags/0.1.19.tar.gz

build:
number: 11

number: 12
skip: True # [osx]
run_exports:
- {{ pin_subpackage(name, max_pin="x") }}

requirements:
build:
- make
Expand All @@ -30,5 +34,8 @@ about:
summary: Tools for dealing with SAM and BAM files

extra:
additional-platforms:
- linux-aarch64
- osx-arm64
identifiers:
- biotools:samtools
Loading