From 7c65bfc208f7b7eb7406458ae499b267682193b3 Mon Sep 17 00:00:00 2001 From: Rohit Goswami Date: Fri, 2 Oct 2026 11:12:52 +0200 Subject: [PATCH 1/2] {2026.06}[GCC/15.2.0,GCCcore/15.2.0] BEDTools 2.31.1, SAMtools 1.23.1, GATK 4.6.2.0 --- .../2026.06/eessi-2026.06-eb-5.4.0-2026.1.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easystacks/software.eessi.io/2026.06/eessi-2026.06-eb-5.4.0-2026.1.yml b/easystacks/software.eessi.io/2026.06/eessi-2026.06-eb-5.4.0-2026.1.yml index 00ec3d4060..ceafb8d428 100644 --- a/easystacks/software.eessi.io/2026.06/eessi-2026.06-eb-5.4.0-2026.1.yml +++ b/easystacks/software.eessi.io/2026.06/eessi-2026.06-eb-5.4.0-2026.1.yml @@ -102,3 +102,9 @@ easyconfigs: options: # see https://github.com/easybuilders/easybuild-easyconfigs/pull/26789 from-commit: 01d6674a4eda858d5a2fdc3e52535bd772901d27 + - BEDTools-2.31.1-GCC-15.2.0.eb: + options: + # see https://github.com/easybuilders/easybuild-easyconfigs/pull/26634 + from-commit: 097f4708abcfd5b29a607013475f71de708efc8e + - SAMtools-1.23.1-GCC-15.2.0.eb + - GATK-4.6.2.0-GCCcore-15.2.0-Java-25.eb From cdf203aafa2aee90d348148ab50a14690ebc81fd Mon Sep 17 00:00:00 2001 From: Rohit Goswami Date: Wed, 21 Oct 2026 21:51:56 +0000 Subject: [PATCH 2/2] move BEDTools, SAMtools and GATK to EB 5.4.1 easystack EasyBuild 5.4.1 ships BEDTools 2.31.1, SAMtools 1.23.1 and GATK 4.6.2.0, so the from-commit pin is no longer needed. --- .../2026.06/eessi-2026.06-eb-5.4.0-2026.1.yml | 6 ------ .../2026.06/eessi-2026.06-eb-5.4.1-2026.1.yml | 4 ++++ 2 files changed, 4 insertions(+), 6 deletions(-) create mode 100644 easystacks/software.eessi.io/2026.06/eessi-2026.06-eb-5.4.1-2026.1.yml diff --git a/easystacks/software.eessi.io/2026.06/eessi-2026.06-eb-5.4.0-2026.1.yml b/easystacks/software.eessi.io/2026.06/eessi-2026.06-eb-5.4.0-2026.1.yml index 4ebc9234b5..a67dd2eb70 100644 --- a/easystacks/software.eessi.io/2026.06/eessi-2026.06-eb-5.4.0-2026.1.yml +++ b/easystacks/software.eessi.io/2026.06/eessi-2026.06-eb-5.4.0-2026.1.yml @@ -151,9 +151,3 @@ easyconfigs: - PnetCDF-1.14.1-gompi-2026.1.eb - h5py-3.16.0-foss-2026.1.eb - netcdf4-python-1.7.4-foss-2026.1.eb - - BEDTools-2.31.1-GCC-15.2.0.eb: - options: - # see https://github.com/easybuilders/easybuild-easyconfigs/pull/26634 - from-commit: 097f4708abcfd5b29a607013475f71de708efc8e - - SAMtools-1.23.1-GCC-15.2.0.eb - - GATK-4.6.2.0-GCCcore-15.2.0-Java-25.eb diff --git a/easystacks/software.eessi.io/2026.06/eessi-2026.06-eb-5.4.1-2026.1.yml b/easystacks/software.eessi.io/2026.06/eessi-2026.06-eb-5.4.1-2026.1.yml new file mode 100644 index 0000000000..b5dd0efaa5 --- /dev/null +++ b/easystacks/software.eessi.io/2026.06/eessi-2026.06-eb-5.4.1-2026.1.yml @@ -0,0 +1,4 @@ +easyconfigs: + - BEDTools-2.31.1-GCC-15.2.0.eb + - SAMtools-1.23.1-GCC-15.2.0.eb + - GATK-4.6.2.0-GCCcore-15.2.0-Java-25.eb